diff --git "a/PyPiBugs.csv" "b/PyPiBugs.csv" new file mode 100644--- /dev/null +++ "b/PyPiBugs.csv" @@ -0,0 +1,57781 @@ +,repo,hash,diff,old_path,rewrite,initial_state,final_state +0,https://:@github.com/emedvedev/attention-ocr.git,291042e7cb623c8a908e9badd132c1fa2360288c,"@@ -465,7 +465,7 @@ class Model(object): + mh = 32 + mw = math.floor(1. * w / h * mh) + img = img.resize( +- (mw, h), ++ (mw, mh), + Image.ANTIALIAS) + img_data = np.asarray(img, dtype=np.uint8) + for idx in xrange(len(output)): +",aocr/model/model.py,"ReplaceText(target='mh' @(468,25)->(468,26))","class Model(object): + mh = 32 + mw = math.floor(1. * w / h * mh) + img = img.resize( + (mw, h), + Image.ANTIALIAS) + img_data = np.asarray(img, dtype=np.uint8) + for idx in xrange(len(output)):","class Model(object): + mh = 32 + mw = math.floor(1. * w / h * mh) + img = img.resize( + (mw, mh), + Image.ANTIALIAS) + img_data = np.asarray(img, dtype=np.uint8) + for idx in xrange(len(output)):" +1,https://:@github.com/emedvedev/attention-ocr.git,6e6593c27fe0e63118adadf11562b1c4699b14e3,"@@ -477,7 +477,7 @@ class Model(object): + attention_orig[i] = attention[int(i/4)-1] + attention_orig = np.convolve(attention_orig, [0.199547, 0.200226, 0.200454, 0.200226, 0.199547], mode='same') + attention_orig = np.maximum(attention_orig, 0.3) +- attention_out = np.zeros((h, mw)) ++ attention_out = np.zeros((mh, mw)) + for i in xrange(mw): + attention_out[:, i] = attention_orig[i] + if len(img_data.shape) == 3: +",aocr/model/model.py,"ReplaceText(target='mh' @(480,42)->(480,43))","class Model(object): + attention_orig[i] = attention[int(i/4)-1] + attention_orig = np.convolve(attention_orig, [0.199547, 0.200226, 0.200454, 0.200226, 0.199547], mode='same') + attention_orig = np.maximum(attention_orig, 0.3) + attention_out = np.zeros((h, mw)) + for i in xrange(mw): + attention_out[:, i] = attention_orig[i] + if len(img_data.shape) == 3:","class Model(object): + attention_orig[i] = attention[int(i/4)-1] + attention_orig = np.convolve(attention_orig, [0.199547, 0.200226, 0.200454, 0.200226, 0.199547], mode='same') + attention_orig = np.maximum(attention_orig, 0.3) + attention_out = np.zeros((mh, mw)) + for i in xrange(mw): + attention_out[:, i] = attention_orig[i] + if len(img_data.shape) == 3:" +2,https://:@github.com/emedvedev/attention-ocr.git,e741baf7170e72a974754908d323cacc0bd55247,"@@ -133,7 +133,7 @@ class Model(object): + self.target_weights = [] + for i in xrange(self.decoder_size + 1): + self.decoder_inputs.append( +- tf.tile([0], [num_images]) ++ tf.tile([1], [num_images]) + ) + if i < self.decoder_size: + self.target_weights.append(tf.tile([1.], [num_images])) +",aocr/model/model.py,"ReplaceText(target='1' @(136,29)->(136,30))","class Model(object): + self.target_weights = [] + for i in xrange(self.decoder_size + 1): + self.decoder_inputs.append( + tf.tile([0], [num_images]) + ) + if i < self.decoder_size: + self.target_weights.append(tf.tile([1.], [num_images]))","class Model(object): + self.target_weights = [] + for i in xrange(self.decoder_size + 1): + self.decoder_inputs.append( + tf.tile([1], [num_images]) + ) + if i < self.decoder_size: + self.target_weights.append(tf.tile([1.], [num_images]))" +3,https://:@github.com/matthewdowney/TogglPy.git,d5b630aec58d29b85ccffa527d24766eef6f61f9,"@@ -197,7 +197,7 @@ class Toggl(): + day = datetime.now().day if not day else day + hour = datetime.now().hour if not hour else hour + +- timestruct = datetime(year, month, day, hour - hourdiff).isoformat() + '.000Z' ++ timestruct = datetime(year, month, day, hour + hourdiff).isoformat() + '.000Z' + data['time_entry']['start'] = timestruct + data['time_entry']['duration'] = hourduration * 3600 + data['time_entry']['pid'] = projectid +",toggl/TogglPy.py,"ReplaceText(target='+' @(200,53)->(200,54))","class Toggl(): + day = datetime.now().day if not day else day + hour = datetime.now().hour if not hour else hour + + timestruct = datetime(year, month, day, hour - hourdiff).isoformat() + '.000Z' + data['time_entry']['start'] = timestruct + data['time_entry']['duration'] = hourduration * 3600 + data['time_entry']['pid'] = projectid","class Toggl(): + day = datetime.now().day if not day else day + hour = datetime.now().hour if not hour else hour + + timestruct = datetime(year, month, day, hour + hourdiff).isoformat() + '.000Z' + data['time_entry']['start'] = timestruct + data['time_entry']['duration'] = hourduration * 3600 + data['time_entry']['pid'] = projectid" +4,https://:@github.com/eEcoLiDAR/eEcoLiDAR.git,f0b2a0b7a5fdd41887ba40b7687c8161c0faba1e,"@@ -28,6 +28,6 @@ class Test3FeatureExtractor(AbstractFeatureExtractor): + return ['test3_a'] + + def extract(self, sourcepc, neighborhood, targetpc, targetindex, volume): +- t2a, t2c = utils.get_features(targetpc, targetindex, self.requires()) ++ t2a, t2c = utils.get_features(targetpc, self.requires(), targetindex) + x, y, z = utils.get_point(targetpc, targetindex) + return t2c - t2a - z # z +",laserchicken/test_feature_extractor/feature_test23.py,"ArgSwap(idxs=1<->2 @(31,19)->(31,37))","class Test3FeatureExtractor(AbstractFeatureExtractor): + return ['test3_a'] + + def extract(self, sourcepc, neighborhood, targetpc, targetindex, volume): + t2a, t2c = utils.get_features(targetpc, targetindex, self.requires()) + x, y, z = utils.get_point(targetpc, targetindex) + return t2c - t2a - z # z","class Test3FeatureExtractor(AbstractFeatureExtractor): + return ['test3_a'] + + def extract(self, sourcepc, neighborhood, targetpc, targetindex, volume): + t2a, t2c = utils.get_features(targetpc, self.requires(), targetindex) + x, y, z = utils.get_point(targetpc, targetindex) + return t2c - t2a - z # z" +5,https://:@github.com/eEcoLiDAR/eEcoLiDAR.git,f0b2a0b7a5fdd41887ba40b7687c8161c0faba1e,"@@ -31,7 +31,7 @@ class TestUtils(unittest.TestCase): + pc[keys.point][""color""] = {""type"": ""double"", ""data"": cols} + pc[keys.point][""flavor""] = {""type"": ""double"", ""data"": flavs} + x, y, z = utils.get_point(pc, 2) +- c, f = utils.get_features(pc, 2, (""color"", ""flavor"")) ++ c, f = utils.get_features(pc, (""color"", ""flavor""), 2) + self.assertEqual(c, 0.5 * (x + y)) + self.assertEqual(f, 0.5 * (x - y)) + +",laserchicken/test_utils.py,"ArgSwap(idxs=1<->2 @(34,15)->(34,33))","class TestUtils(unittest.TestCase): + pc[keys.point][""color""] = {""type"": ""double"", ""data"": cols} + pc[keys.point][""flavor""] = {""type"": ""double"", ""data"": flavs} + x, y, z = utils.get_point(pc, 2) + c, f = utils.get_features(pc, 2, (""color"", ""flavor"")) + self.assertEqual(c, 0.5 * (x + y)) + self.assertEqual(f, 0.5 * (x - y)) + ","class TestUtils(unittest.TestCase): + pc[keys.point][""color""] = {""type"": ""double"", ""data"": cols} + pc[keys.point][""flavor""] = {""type"": ""double"", ""data"": flavs} + x, y, z = utils.get_point(pc, 2) + c, f = utils.get_features(pc, (""color"", ""flavor""), 2) + self.assertEqual(c, 0.5 * (x + y)) + self.assertEqual(f, 0.5 * (x - y)) + " +6,https://:@github.com/eEcoLiDAR/eEcoLiDAR.git,502a365efda1393b130281803702d01f7e2d1dcd,"@@ -29,7 +29,7 @@ class TestExtractEigenValues(unittest.TestCase): + [""eigenv_1"", ""eigenv_2"", ""eigenv_3""], InfiniteCylinder(5)) + + self.assertEqual(""laserchicken.feature_extractor.eigenvals_feature_extractor"", +- target_point_cloud[keys.provenance][0][""module""]) ++ target_point_cloud[keys.provenance][1][""module""]) + + @staticmethod + def test_eigenvalues_of_too_few_points_results_in_0(): +",laserchicken/feature_extractor/test_eigenvals_feature_extractor.py,"ReplaceText(target='1' @(32,61)->(32,62))","class TestExtractEigenValues(unittest.TestCase): + [""eigenv_1"", ""eigenv_2"", ""eigenv_3""], InfiniteCylinder(5)) + + self.assertEqual(""laserchicken.feature_extractor.eigenvals_feature_extractor"", + target_point_cloud[keys.provenance][0][""module""]) + + @staticmethod + def test_eigenvalues_of_too_few_points_results_in_0():","class TestExtractEigenValues(unittest.TestCase): + [""eigenv_1"", ""eigenv_2"", ""eigenv_3""], InfiniteCylinder(5)) + + self.assertEqual(""laserchicken.feature_extractor.eigenvals_feature_extractor"", + target_point_cloud[keys.provenance][1][""module""]) + + @staticmethod + def test_eigenvalues_of_too_few_points_results_in_0():" +7,https://:@github.com/eEcoLiDAR/eEcoLiDAR.git,eb7b021147a60b57e5dec536bd6f118c213f0952,"@@ -29,7 +29,7 @@ class TestExtractEigenValues(unittest.TestCase): + [""eigenv_1"", ""eigenv_2"", ""eigenv_3""], InfiniteCylinder(5)) + + self.assertEqual(""laserchicken.feature_extractor.eigenvals_feature_extractor"", +- target_point_cloud[keys.provenance][1][""module""]) ++ target_point_cloud[keys.provenance][-1][""module""]) + + @staticmethod + def test_eigenvalues_of_too_few_points_results_in_0(): +",laserchicken/feature_extractor/test_eigenvals_feature_extractor.py,"ReplaceText(target='-1' @(32,61)->(32,62))","class TestExtractEigenValues(unittest.TestCase): + [""eigenv_1"", ""eigenv_2"", ""eigenv_3""], InfiniteCylinder(5)) + + self.assertEqual(""laserchicken.feature_extractor.eigenvals_feature_extractor"", + target_point_cloud[keys.provenance][1][""module""]) + + @staticmethod + def test_eigenvalues_of_too_few_points_results_in_0():","class TestExtractEigenValues(unittest.TestCase): + [""eigenv_1"", ""eigenv_2"", ""eigenv_3""], InfiniteCylinder(5)) + + self.assertEqual(""laserchicken.feature_extractor.eigenvals_feature_extractor"", + target_point_cloud[keys.provenance][-1][""module""]) + + @staticmethod + def test_eigenvalues_of_too_few_points_results_in_0():" +8,https://:@github.com/VinF/deer.git,66ea41db02c3361f18874dea7fd97720b1b06590,"@@ -441,7 +441,7 @@ class CircularBuffer(object): + + if end == sys.maxsize: + return self._data[self._lb+start:self._ub] +- elif self._lb + end >= self._ub: ++ elif self._lb + end > self._ub: + raise IndexError() + else: + return self._data[self._lb+start:self._lb+end] +",General_Deep_Q_RL/agent.py,"ReplaceText(target='>' @(444,28)->(444,30))","class CircularBuffer(object): + + if end == sys.maxsize: + return self._data[self._lb+start:self._ub] + elif self._lb + end >= self._ub: + raise IndexError() + else: + return self._data[self._lb+start:self._lb+end]","class CircularBuffer(object): + + if end == sys.maxsize: + return self._data[self._lb+start:self._ub] + elif self._lb + end > self._ub: + raise IndexError() + else: + return self._data[self._lb+start:self._lb+end]" +9,https://:@github.com/VinF/deer.git,fd939e272d5441d48fd7d30bf24312c0f6bc8aaa,"@@ -176,7 +176,7 @@ class MyEnv(Environment): + # Lack of energy + if (self._lastPonctualObservation[0]*self.battery_size>Energy_needed_from_battery): + # If enough energy in the battery, use it +- self._lastPonctualObservation[0]=self._lastPonctualObservation[0]-Energy_needed_from_battery/self.battery_size*self.battery_eta ++ self._lastPonctualObservation[0]=self._lastPonctualObservation[0]-Energy_needed_from_battery/self.battery_size/self.battery_eta + else: + # Otherwise: use what is left and then penalty + reward-=(Energy_needed_from_battery-self._lastPonctualObservation[0]*self.battery_size)*2 #2euro/kWh +",General_Deep_Q_RL/environments/MG_two_storages_env.py,"ReplaceText(target='/' @(179,126)->(179,127))","class MyEnv(Environment): + # Lack of energy + if (self._lastPonctualObservation[0]*self.battery_size>Energy_needed_from_battery): + # If enough energy in the battery, use it + self._lastPonctualObservation[0]=self._lastPonctualObservation[0]-Energy_needed_from_battery/self.battery_size*self.battery_eta + else: + # Otherwise: use what is left and then penalty + reward-=(Energy_needed_from_battery-self._lastPonctualObservation[0]*self.battery_size)*2 #2euro/kWh","class MyEnv(Environment): + # Lack of energy + if (self._lastPonctualObservation[0]*self.battery_size>Energy_needed_from_battery): + # If enough energy in the battery, use it + self._lastPonctualObservation[0]=self._lastPonctualObservation[0]-Energy_needed_from_battery/self.battery_size/self.battery_eta + else: + # Otherwise: use what is left and then penalty + reward-=(Energy_needed_from_battery-self._lastPonctualObservation[0]*self.battery_size)*2 #2euro/kWh" +10,https://:@github.com/piccolbo/altair_recipes.git,4992dd864a317eaad641d0408f003c429ed24af6,"@@ -6,7 +6,7 @@ from vega_datasets import data + + @viz_reg_test + def test_boxplot_melted(): +- return ar.boxplot(data.iris(), ""species"", ""petalLength"") ++ return ar.boxplot(data.iris(), ""petalLength"", ""species"") + + + @viz_reg_test +",tests/test_boxplot.py,"ArgSwap(idxs=1<->2 @(9,11)->(9,21))","from vega_datasets import data + + @viz_reg_test + def test_boxplot_melted(): + return ar.boxplot(data.iris(), ""species"", ""petalLength"") + + + @viz_reg_test","from vega_datasets import data + + @viz_reg_test + def test_boxplot_melted(): + return ar.boxplot(data.iris(), ""petalLength"", ""species"") + + + @viz_reg_test" +11,https://:@github.com/tailhook/zorro.git,dcbc37d47fe2a8de029f5a2f3ae13adf52e7aace,"@@ -121,7 +121,7 @@ class RequestChannel(channel.PipelinedReqChannel): + clen = int(headers.get('Content-Length', '0')) + if clen < 0: + raise EOFError(""Wrong content length"") +- while pos[0] + clen < len(buf): ++ while pos[0] + clen > len(buf): + readmore() + return status, headers, buf[pos[0]:pos[0]+clen] + +",zorro/http.py,"ReplaceText(target='>' @(124,32)->(124,33))","class RequestChannel(channel.PipelinedReqChannel): + clen = int(headers.get('Content-Length', '0')) + if clen < 0: + raise EOFError(""Wrong content length"") + while pos[0] + clen < len(buf): + readmore() + return status, headers, buf[pos[0]:pos[0]+clen] + ","class RequestChannel(channel.PipelinedReqChannel): + clen = int(headers.get('Content-Length', '0')) + if clen < 0: + raise EOFError(""Wrong content length"") + while pos[0] + clen > len(buf): + readmore() + return status, headers, buf[pos[0]:pos[0]+clen] + " +12,https://:@gitlab.com/eavise/brambox.git,f1faeed0b52d6f1c9c9ba6da818c1656f841622c,"@@ -73,7 +73,7 @@ def test_multiclass(parser, df_anno_simple): + parser = parser() + + with pytest.raises(ValueError) as errinfo: +- bb.io.save(parser, df_anno_simple, 'path.txt') ++ bb.io.save(df_anno_simple, parser, 'path.txt') + assert 'single-class problems' in str(errinfo.value) + + +",test/io/parser/test_anno_cvc.py,"ArgSwap(idxs=0<->1 @(76,8)->(76,18))","def test_multiclass(parser, df_anno_simple): + parser = parser() + + with pytest.raises(ValueError) as errinfo: + bb.io.save(parser, df_anno_simple, 'path.txt') + assert 'single-class problems' in str(errinfo.value) + + ","def test_multiclass(parser, df_anno_simple): + parser = parser() + + with pytest.raises(ValueError) as errinfo: + bb.io.save(df_anno_simple, parser, 'path.txt') + assert 'single-class problems' in str(errinfo.value) + + " +13,https://:@github.com/uber/h3-py.git,359924df907144c85ec323ae2804e2c0d173dfc5,"@@ -631,7 +631,7 @@ def hex_ranges(h3_address_list, ring_size): + (1 + math.sqrt(1 + 8 * math.ceil(j / 6.0))) / 2)) - 1 + # hexRanges doesn't return distance array + hex_range_list[ring_index].add( +- h3_to_string(krings[i * num_hexagons + j])) ++ h3_to_string(krings[i * array_len + j])) + return out + + +",h3/h3.py,"ReplaceText(target='array_len' @(634,40)->(634,52))","def hex_ranges(h3_address_list, ring_size): + (1 + math.sqrt(1 + 8 * math.ceil(j / 6.0))) / 2)) - 1 + # hexRanges doesn't return distance array + hex_range_list[ring_index].add( + h3_to_string(krings[i * num_hexagons + j])) + return out + + ","def hex_ranges(h3_address_list, ring_size): + (1 + math.sqrt(1 + 8 * math.ceil(j / 6.0))) / 2)) - 1 + # hexRanges doesn't return distance array + hex_range_list[ring_index].add( + h3_to_string(krings[i * array_len + j])) + return out + + " +14,https://:@github.com/polysquare/polysquare-generic-file-linter.git,e9dbb28ea30955ab59d1339c04f0710b24ba53aa,"@@ -388,7 +388,7 @@ def _maybe_log_technical_terms(global_options, tool_options): + terms = set(terms_file.read().splitlines()) # suppress(PYC70) + terms_file.seek(0) # suppress(PYC70) + terms_file.truncate(0) # suppress(PYC70) +- tech_terms = freduce(lambda x, y: x + y, ++ tech_terms = freduce(lambda x, y: x | y, + _drain(log_technical_terms_to_queue)) + terms_file.write(""\n"".join(list(terms | # suppress(PYC70) + set(tech_terms)))) +",polysquarelinter/linter.py,"ReplaceText(target='|' @(391,48)->(391,49))","def _maybe_log_technical_terms(global_options, tool_options): + terms = set(terms_file.read().splitlines()) # suppress(PYC70) + terms_file.seek(0) # suppress(PYC70) + terms_file.truncate(0) # suppress(PYC70) + tech_terms = freduce(lambda x, y: x + y, + _drain(log_technical_terms_to_queue)) + terms_file.write(""\n"".join(list(terms | # suppress(PYC70) + set(tech_terms))))","def _maybe_log_technical_terms(global_options, tool_options): + terms = set(terms_file.read().splitlines()) # suppress(PYC70) + terms_file.seek(0) # suppress(PYC70) + terms_file.truncate(0) # suppress(PYC70) + tech_terms = freduce(lambda x, y: x | y, + _drain(log_technical_terms_to_queue)) + terms_file.write(""\n"".join(list(terms | # suppress(PYC70) + set(tech_terms))))" +15,https://:@github.com/johntruckenbrodt/spatialist.git,c9d552e64cd47b30156b288e035d17debea48b45,"@@ -300,7 +300,7 @@ def centerdist(obj1, obj2): + + + def intersect(obj1, obj2): +- if not (isinstance(obj1, Vector) or isinstance(obj2, Vector)): ++ if not (isinstance(obj1, Vector) and isinstance(obj2, Vector)): + raise IOError('object must be of type Vector') + obj1.reproject(obj2.srs) + +",pyroSAR/spatial/vector.py,"ReplaceText(target='and' @(303,37)->(303,39))","def centerdist(obj1, obj2): + + + def intersect(obj1, obj2): + if not (isinstance(obj1, Vector) or isinstance(obj2, Vector)): + raise IOError('object must be of type Vector') + obj1.reproject(obj2.srs) + ","def centerdist(obj1, obj2): + + + def intersect(obj1, obj2): + if not (isinstance(obj1, Vector) and isinstance(obj2, Vector)): + raise IOError('object must be of type Vector') + obj1.reproject(obj2.srs) + " +16,https://:@github.com/Toblerity/Shapely.git,9f1b78e6fd5f4286f210b54827bdd26661f0ee7a,"@@ -40,7 +40,7 @@ if __name__ == '__main__': + ] + + if pattern: +- tests = [f for f in docfiles if f.find(pattern) >= 0] ++ tests = [f for f in docfiles if f.find(pattern) == 0] + else: + tests = docfiles + +",tests/runalldoctests.py,"ReplaceText(target='==' @(43,56)->(43,58))","if __name__ == '__main__': + ] + + if pattern: + tests = [f for f in docfiles if f.find(pattern) >= 0] + else: + tests = docfiles + ","if __name__ == '__main__': + ] + + if pattern: + tests = [f for f in docfiles if f.find(pattern) == 0] + else: + tests = docfiles + " +17,https://:@github.com/Toblerity/Shapely.git,d6fc8cc0e0d50b23ba0d7ca6195bc530b2f8d1b9,"@@ -11,7 +11,7 @@ def halton(base): + i = index + while i > 0: + result += f * (i % base) +- i = i/base ++ i = i//base + f = f/base + return result + i = 1 +",shapely/tests/test_unary_union.py,"ReplaceText(target='//' @(14,17)->(14,18))","def halton(base): + i = index + while i > 0: + result += f * (i % base) + i = i/base + f = f/base + return result + i = 1","def halton(base): + i = index + while i > 0: + result += f * (i % base) + i = i//base + f = f/base + return result + i = 1" +18,https://:@github.com/Toblerity/Shapely.git,5f0db7fdc052beeeef36aa1251f19175d0abeedb,"@@ -36,7 +36,7 @@ if version is None: + + # Handle UTF-8 encoding of certain text files. + open_kwds = {} +-if sys.version_info > (3,): ++if sys.version_info >= (3,): + open_kwds['encoding'] = 'utf-8' + + with open('VERSION.txt', 'w', **open_kwds) as fp: +",setup.py,"ReplaceText(target='>=' @(39,20)->(39,21))","if version is None: + + # Handle UTF-8 encoding of certain text files. + open_kwds = {} + if sys.version_info > (3,): + open_kwds['encoding'] = 'utf-8' + + with open('VERSION.txt', 'w', **open_kwds) as fp:","if version is None: + + # Handle UTF-8 encoding of certain text files. + open_kwds = {} + if sys.version_info >= (3,): + open_kwds['encoding'] = 'utf-8' + + with open('VERSION.txt', 'w', **open_kwds) as fp:" +19,https://:@github.com/svetlyak40wt/django-tagging-ng.git,0293b78ee0274d123eb70c1f8c5c01a5b36e2b40,"@@ -163,7 +163,7 @@ class TaggedItemManager(models.Manager): + associated with a given Tag or list of Tags. + """""" + tags = get_tag_list(tags) +- if len(tags) == 0: ++ if len(tags) == 1: + tag = tags[0] # Optimisation for single tag + else: + return self.get_intersection_by_model(Model, tags) +",models.py,"ReplaceText(target='1' @(166,24)->(166,25))","class TaggedItemManager(models.Manager): + associated with a given Tag or list of Tags. + """""" + tags = get_tag_list(tags) + if len(tags) == 0: + tag = tags[0] # Optimisation for single tag + else: + return self.get_intersection_by_model(Model, tags)","class TaggedItemManager(models.Manager): + associated with a given Tag or list of Tags. + """""" + tags = get_tag_list(tags) + if len(tags) == 1: + tag = tags[0] # Optimisation for single tag + else: + return self.get_intersection_by_model(Model, tags)" +20,https://:@github.com/svetlyak40wt/django-tagging-ng.git,3285d40e4c1de628886a7fa45a6d4cf6ed4cd7e7,"@@ -163,7 +163,7 @@ class TaggedItemManager(models.Manager): + associated with a given Tag or list of Tags. + """""" + tags = get_tag_list(tags) +- if len(tags) == 0: ++ if len(tags) == 1: + tag = tags[0] # Optimisation for single tag + else: + return self.get_intersection_by_model(Model, tags) +",models.py,"ReplaceText(target='1' @(166,24)->(166,25))","class TaggedItemManager(models.Manager): + associated with a given Tag or list of Tags. + """""" + tags = get_tag_list(tags) + if len(tags) == 0: + tag = tags[0] # Optimisation for single tag + else: + return self.get_intersection_by_model(Model, tags)","class TaggedItemManager(models.Manager): + associated with a given Tag or list of Tags. + """""" + tags = get_tag_list(tags) + if len(tags) == 1: + tag = tags[0] # Optimisation for single tag + else: + return self.get_intersection_by_model(Model, tags)" +21,https://:@github.com/zzzsochi/yadm.git,03efd06fe95c7d84264455c4fac5c8cbb17eb4dd,"@@ -316,7 +316,7 @@ class QuerySet(BaseQuerySet): + + if data is None: + if exc is not None: +- raise exc(criteria) ++ raise exc(qs) + else: + return None + +",yadm/queryset.py,"ReplaceText(target='qs' @(319,26)->(319,34))","class QuerySet(BaseQuerySet): + + if data is None: + if exc is not None: + raise exc(criteria) + else: + return None + ","class QuerySet(BaseQuerySet): + + if data is None: + if exc is not None: + raise exc(qs) + else: + return None + " +22,https://:@github.com/instacart/lore.git,1c1e0efdac6b27dc111eaa93bb99317c59aaffaf,"@@ -196,7 +196,7 @@ class Base(object): + def upload(self): + self.fitting = 0 + self.save() +- lore.io.upload(self.remote_model_path(), self.model_path()) ++ lore.io.upload(self.model_path(), self.remote_model_path()) + + @classmethod + def download(cls, fitting=0): +",lore/models/base.py,"ArgSwap(idxs=0<->1 @(199,8)->(199,22))","class Base(object): + def upload(self): + self.fitting = 0 + self.save() + lore.io.upload(self.remote_model_path(), self.model_path()) + + @classmethod + def download(cls, fitting=0):","class Base(object): + def upload(self): + self.fitting = 0 + self.save() + lore.io.upload(self.model_path(), self.remote_model_path()) + + @classmethod + def download(cls, fitting=0):" +23,https://:@github.com/instacart/lore.git,1c1e0efdac6b27dc111eaa93bb99317c59aaffaf,"@@ -78,7 +78,7 @@ class Base(lore.models.base.Base): + + def upload(self): + super(Base, self).upload() +- lore.io.upload(self.remote_weights_path(), self.weights_path()) ++ lore.io.upload(self.weights_path(), self.remote_weights_path()) + + @classmethod + def download(cls, fitting=0): +",lore/models/keras.py,"ArgSwap(idxs=0<->1 @(81,8)->(81,22))","class Base(lore.models.base.Base): + + def upload(self): + super(Base, self).upload() + lore.io.upload(self.remote_weights_path(), self.weights_path()) + + @classmethod + def download(cls, fitting=0):","class Base(lore.models.base.Base): + + def upload(self): + super(Base, self).upload() + lore.io.upload(self.weights_path(), self.remote_weights_path()) + + @classmethod + def download(cls, fitting=0):" +24,https://:@github.com/instacart/lore.git,f4ded2b3199d1c33ba6c9c79cd66b25d43c83c81,"@@ -464,7 +464,7 @@ class Base(BaseEstimator): + result = self.keras.predict(dataframe, batch_size=self.batch_size) + + if self.towers > 1: +- result = numpy.mean(result, axis=0).squeeze(axis=0) ++ result = numpy.mean(result, axis=0).squeeze(axis=1) + + return result + +",lore/estimators/keras.py,"ReplaceText(target='1' @(467,61)->(467,62))","class Base(BaseEstimator): + result = self.keras.predict(dataframe, batch_size=self.batch_size) + + if self.towers > 1: + result = numpy.mean(result, axis=0).squeeze(axis=0) + + return result + ","class Base(BaseEstimator): + result = self.keras.predict(dataframe, batch_size=self.batch_size) + + if self.towers > 1: + result = numpy.mean(result, axis=0).squeeze(axis=1) + + return result + " +25,https://:@github.com/baliga-lab/cmonkey2.git,3201a0e97688724450196da8fef96d283c855b3f,"@@ -273,7 +273,7 @@ class ClusterMembership: + #logging.warn(""cluster %s already associated with %s"", + # str(cluster), str(column)) + pass +- if columns not in columns: ++ if column not in columns: + columns.append(column) + + def remove_cluster_from_column(self, column, cluster): +",cmonkey/membership.py,"ReplaceText(target='column' @(276,11)->(276,18))","class ClusterMembership: + #logging.warn(""cluster %s already associated with %s"", + # str(cluster), str(column)) + pass + if columns not in columns: + columns.append(column) + + def remove_cluster_from_column(self, column, cluster):","class ClusterMembership: + #logging.warn(""cluster %s already associated with %s"", + # str(cluster), str(column)) + pass + if column not in columns: + columns.append(column) + + def remove_cluster_from_column(self, column, cluster):" +26,https://:@github.com/baliga-lab/cmonkey2.git,48d14ac785b1013354a55a37239c66433fbf19eb,"@@ -460,7 +460,7 @@ class ClusterMembership: + max_score = sys.float_info.min + for row in range(sm.num_rows()): + if sm_values[row][0] > max_score: +- max_score = sm[row][0] ++ max_score = sm_values[row][0] + max_row = row + return sm.row_names[max_row] + +",cmonkey/membership.py,"ReplaceText(target='sm_values' @(463,32)->(463,34))","class ClusterMembership: + max_score = sys.float_info.min + for row in range(sm.num_rows()): + if sm_values[row][0] > max_score: + max_score = sm[row][0] + max_row = row + return sm.row_names[max_row] + ","class ClusterMembership: + max_score = sys.float_info.min + for row in range(sm.num_rows()): + if sm_values[row][0] > max_score: + max_score = sm_values[row][0] + max_row = row + return sm.row_names[max_row] + " +27,https://:@github.com/baliga-lab/cmonkey2.git,311548905a9def1cbdf63d2e0fd8a17346564742,"@@ -17,7 +17,7 @@ class MicrobesOnlineTest(unittest.TestCase): # pylint: disable-msg=R0904 + """"""test fixture"""""" + if not os.path.exists('testcache'): + os.mkdir('testcache') +- self.service = mo.MicrobesOnline(mo.MICROBES_ONLINE_BASE_URL, 'testcache') ++ self.service = mo.MicrobesOnline('testcache', mo.MICROBES_ONLINE_BASE_URL) + + def tearDown(self): # pylint: disable-msg=C0103 + """"""test cleanup"""""" +",test/microbes_online_test.py,"ArgSwap(idxs=0<->1 @(20,23)->(20,40))","class MicrobesOnlineTest(unittest.TestCase): # pylint: disable-msg=R0904 + """"""test fixture"""""" + if not os.path.exists('testcache'): + os.mkdir('testcache') + self.service = mo.MicrobesOnline(mo.MICROBES_ONLINE_BASE_URL, 'testcache') + + def tearDown(self): # pylint: disable-msg=C0103 + """"""test cleanup""""""","class MicrobesOnlineTest(unittest.TestCase): # pylint: disable-msg=R0904 + """"""test fixture"""""" + if not os.path.exists('testcache'): + os.mkdir('testcache') + self.service = mo.MicrobesOnline('testcache', mo.MICROBES_ONLINE_BASE_URL) + + def tearDown(self): # pylint: disable-msg=C0103 + """"""test cleanup""""""" +28,https://:@github.com/muammar/ml4chem.git,dbb7de0379cb8881538d211899e4bec8794f16e3,"@@ -344,7 +344,7 @@ def train(inputs, targets, model=None, data=None, optimizer=None, lr=None, + logger.info('Training finished in {} hours {} minutes {:.2f} seconds.' + .format(h, m, s)) + logger.info('outputs') +- logger.info(outputs) ++ logger.info(outputs_) + logger.info('targets') + logger.info(targets) + +",mlchem/models/neuralnetwork.py,"ReplaceText(target='outputs_' @(347,16)->(347,23))","def train(inputs, targets, model=None, data=None, optimizer=None, lr=None, + logger.info('Training finished in {} hours {} minutes {:.2f} seconds.' + .format(h, m, s)) + logger.info('outputs') + logger.info(outputs) + logger.info('targets') + logger.info(targets) + ","def train(inputs, targets, model=None, data=None, optimizer=None, lr=None, + logger.info('Training finished in {} hours {} minutes {:.2f} seconds.' + .format(h, m, s)) + logger.info('outputs') + logger.info(outputs_) + logger.info('targets') + logger.info(targets) + " +29,https://:@github.com/chris7/pyquant.git,3730fbdb9789a59a65d38f5a2ae21c645086096f,"@@ -624,7 +624,7 @@ def findAllPeaks(xdata, ydata_original, min_dist=0, method=None, local_filter_si + best_fit = np.array(best_fit) + peak_func = bigauss_ndim if bigauss_fit else gauss_ndim + # Get rid of peaks with low r^2 +- if micro and r2_cutoff is not None: ++ if not micro and r2_cutoff is not None: + final_fit = np.array([]) + for peak_index in xrange(0, len(best_fit), step_size): + +",pyquant/peaks.py,"ReplaceText(target='not ' @(627,7)->(627,7))","def findAllPeaks(xdata, ydata_original, min_dist=0, method=None, local_filter_si + best_fit = np.array(best_fit) + peak_func = bigauss_ndim if bigauss_fit else gauss_ndim + # Get rid of peaks with low r^2 + if micro and r2_cutoff is not None: + final_fit = np.array([]) + for peak_index in xrange(0, len(best_fit), step_size): + ","def findAllPeaks(xdata, ydata_original, min_dist=0, method=None, local_filter_si + best_fit = np.array(best_fit) + peak_func = bigauss_ndim if bigauss_fit else gauss_ndim + # Get rid of peaks with low r^2 + if not micro and r2_cutoff is not None: + final_fit = np.array([]) + for peak_index in xrange(0, len(best_fit), step_size): + " +30,https://:@github.com/chris7/pyquant.git,4a0755563e0a36fecf1f4393554cfaf4c1615c2c,"@@ -615,7 +615,7 @@ def find_peaks_derivative(xdata, ydata, ydata_peaks=None, min_slope=None, rel_pe + # By default, cross points returns the left side + for i in xrange(len(cross_points)): + index = cross_points[i] +- if index < len(cross_points): ++ if index < len(ydata): + if ydata[index] < ydata[index+1]: + cross_points[i] = index+1 + +",pyquant/utils.py,"ReplaceText(target='ydata' @(618,23)->(618,35))","def find_peaks_derivative(xdata, ydata, ydata_peaks=None, min_slope=None, rel_pe + # By default, cross points returns the left side + for i in xrange(len(cross_points)): + index = cross_points[i] + if index < len(cross_points): + if ydata[index] < ydata[index+1]: + cross_points[i] = index+1 + ","def find_peaks_derivative(xdata, ydata, ydata_peaks=None, min_slope=None, rel_pe + # By default, cross points returns the left side + for i in xrange(len(cross_points)): + index = cross_points[i] + if index < len(ydata): + if ydata[index] < ydata[index+1]: + cross_points[i] = index+1 + " +31,https://:@github.com/chris7/pyquant.git,cd61286935d8ca64eb539851e39a98a0655ff400,"@@ -611,7 +611,7 @@ def find_peaks_derivative(xdata, ydata, ydata_peaks=None, min_slope=None, rel_pe + ydata = np.abs(ydata_peaks) + + if min_peak_width is None: +- max_peak_width = int(len(ydata) / 2) ++ min_peak_width = int(len(ydata) / 2) + if min_peak_width > 5: + min_peak_width = 5 + +",pyquant/utils.py,"ReplaceText(target='min_peak_width' @(614,8)->(614,22))","def find_peaks_derivative(xdata, ydata, ydata_peaks=None, min_slope=None, rel_pe + ydata = np.abs(ydata_peaks) + + if min_peak_width is None: + max_peak_width = int(len(ydata) / 2) + if min_peak_width > 5: + min_peak_width = 5 + ","def find_peaks_derivative(xdata, ydata, ydata_peaks=None, min_slope=None, rel_pe + ydata = np.abs(ydata_peaks) + + if min_peak_width is None: + min_peak_width = int(len(ydata) / 2) + if min_peak_width > 5: + min_peak_width = 5 + " +32,https://:@github.com/ssec/sift.git,24ce052cd497c42c917de06f0c89a7c5be13ab50,"@@ -599,7 +599,7 @@ class ProbeGraphDisplay (object) : + x_point = self.workspace.get_content_point(x_uuid, point_xy) + format_str, unit_str, x_point = self.document.convert_units(x_uuid, x_point) + y_point = self.workspace.get_content_point(y_uuid, point_xy) +- format_str, unit_str, y_point = self.document.convert_units(x_uuid, y_point) ++ format_str, unit_str, y_point = self.document.convert_units(y_uuid, y_point) + else: + x_point = None + y_point = None +",py/cspov/view/ProbeGraphs.py,"ReplaceText(target='y_uuid' @(602,76)->(602,82))","class ProbeGraphDisplay (object) : + x_point = self.workspace.get_content_point(x_uuid, point_xy) + format_str, unit_str, x_point = self.document.convert_units(x_uuid, x_point) + y_point = self.workspace.get_content_point(y_uuid, point_xy) + format_str, unit_str, y_point = self.document.convert_units(x_uuid, y_point) + else: + x_point = None + y_point = None","class ProbeGraphDisplay (object) : + x_point = self.workspace.get_content_point(x_uuid, point_xy) + format_str, unit_str, x_point = self.document.convert_units(x_uuid, x_point) + y_point = self.workspace.get_content_point(y_uuid, point_xy) + format_str, unit_str, y_point = self.document.convert_units(y_uuid, y_point) + else: + x_point = None + y_point = None" +33,https://:@github.com/threatwatch/twigs.git,7ee5d95178a459a8c2e8ff7855e3156e620c395c,"@@ -85,7 +85,7 @@ def parse_inventory(email,data,params): + asset_map = {} + asset_map['owner'] = email + asset_map['host'] = host +- asset_map['id'] = host ++ asset_map['id'] = vmuuid + asset_map['name'] = host + asset_map['tags'] = [ ] + asset_map['patch_tracker'] = { } # To help remove duplicate patches +",twigs/azure.py,"ReplaceText(target='vmuuid' @(88,30)->(88,34))","def parse_inventory(email,data,params): + asset_map = {} + asset_map['owner'] = email + asset_map['host'] = host + asset_map['id'] = host + asset_map['name'] = host + asset_map['tags'] = [ ] + asset_map['patch_tracker'] = { } # To help remove duplicate patches","def parse_inventory(email,data,params): + asset_map = {} + asset_map['owner'] = email + asset_map['host'] = host + asset_map['id'] = vmuuid + asset_map['name'] = host + asset_map['tags'] = [ ] + asset_map['patch_tracker'] = { } # To help remove duplicate patches" +34,https://:@github.com/Keeper-Security/Commander.git,9bd55c8dd48ab62759bbbb8dfcd38ab364cec2dc,"@@ -1550,7 +1550,7 @@ def prepare_record(params, record): + else: + if params.debug: print('Generated record key') + unencrypted_key = os.urandom(32) +- record_object['record_key'] = encrypt_aes(params.data_key, unencrypted_key) ++ record_object['record_key'] = encrypt_aes(unencrypted_key, params.data_key) + record_object['revision'] = 0 + + data['title'] = record.title +",keepercommander/api.py,"ArgSwap(idxs=0<->1 @(1553,38)->(1553,49))","def prepare_record(params, record): + else: + if params.debug: print('Generated record key') + unencrypted_key = os.urandom(32) + record_object['record_key'] = encrypt_aes(params.data_key, unencrypted_key) + record_object['revision'] = 0 + + data['title'] = record.title","def prepare_record(params, record): + else: + if params.debug: print('Generated record key') + unencrypted_key = os.urandom(32) + record_object['record_key'] = encrypt_aes(unencrypted_key, params.data_key) + record_object['revision'] = 0 + + data['title'] = record.title" +35,https://:@github.com/hpapaxen/rope.git,27d5085b30e89095e88339c96d9940e338482106,"@@ -69,7 +69,7 @@ class JobSet(object): + + def get_percent_done(self): + if self.count is not None and self.count > 0: +- percent = self.done * 100 / self.count ++ percent = self.done * 100 // self.count + return min(percent, 100) + + def get_name(self): +",rope/base/taskhandle.py,"ReplaceText(target='//' @(72,38)->(72,39))","class JobSet(object): + + def get_percent_done(self): + if self.count is not None and self.count > 0: + percent = self.done * 100 / self.count + return min(percent, 100) + + def get_name(self):","class JobSet(object): + + def get_percent_done(self): + if self.count is not None and self.count > 0: + percent = self.done * 100 // self.count + return min(percent, 100) + + def get_name(self):" +36,https://:@github.com/hpapaxen/rope.git,27d5085b30e89095e88339c96d9940e338482106,"@@ -524,7 +524,7 @@ class ProgressBar(object): + self.text['text'] = text + + def _draw_shape(self): +- width = int(self.canvas['width']) * self.percent / 100 ++ width = int(self.canvas['width']) * self.percent // 100 + self.canvas.create_rectangle(0, 0, width, self.canvas['height'], + fill=self.color) + total_width = self.canvas['width'] +",rope/ui/uihelpers.py,"ReplaceText(target='//' @(527,57)->(527,58))","class ProgressBar(object): + self.text['text'] = text + + def _draw_shape(self): + width = int(self.canvas['width']) * self.percent / 100 + self.canvas.create_rectangle(0, 0, width, self.canvas['height'], + fill=self.color) + total_width = self.canvas['width']","class ProgressBar(object): + self.text['text'] = text + + def _draw_shape(self): + width = int(self.canvas['width']) * self.percent // 100 + self.canvas.create_rectangle(0, 0, width, self.canvas['height'], + fill=self.color) + total_width = self.canvas['width']" +37,https://:@github.com/hpapaxen/rope.git,2720419618aceab7fba51aaa4d66f7eae005b22d,"@@ -129,7 +129,7 @@ class SimilarFinderTest(unittest.TestCase): + source = 'x.a = 1\n' + finder = similarfinder.SimilarFinder(source) + result = list(finder.get_matches('${a} = 1')) +- self.assertEquals(1, len(result)) ++ self.assertEquals(0, len(result)) + + def test_functions_not_matching_when_only_first_parameters(self): + source = 'f(1, 2)\n' +",ropetest/refactor/similarfindertest.py,"ReplaceText(target='0' @(132,26)->(132,27))","class SimilarFinderTest(unittest.TestCase): + source = 'x.a = 1\n' + finder = similarfinder.SimilarFinder(source) + result = list(finder.get_matches('${a} = 1')) + self.assertEquals(1, len(result)) + + def test_functions_not_matching_when_only_first_parameters(self): + source = 'f(1, 2)\n'","class SimilarFinderTest(unittest.TestCase): + source = 'x.a = 1\n' + finder = similarfinder.SimilarFinder(source) + result = list(finder.get_matches('${a} = 1')) + self.assertEquals(0, len(result)) + + def test_functions_not_matching_when_only_first_parameters(self): + source = 'f(1, 2)\n'" +38,https://:@github.com/hpapaxen/rope.git,0eb3cb58493cdaea83a4e24d47b5bd4dbd19f963,"@@ -32,7 +32,7 @@ class BuiltinModule(pyobjects.AbstractModule): + result.update(self.initial) + for modname in self.submodules: + name = modname.split('.')[-1] +- result[name] = BuiltinModule(name, self.submodules) ++ result[name] = BuiltinModule(modname, self.submodules) + return result + + @property +",rope/base/builtins.py,"ReplaceText(target='modname' @(35,41)->(35,45))","class BuiltinModule(pyobjects.AbstractModule): + result.update(self.initial) + for modname in self.submodules: + name = modname.split('.')[-1] + result[name] = BuiltinModule(name, self.submodules) + return result + + @property","class BuiltinModule(pyobjects.AbstractModule): + result.update(self.initial) + for modname in self.submodules: + name = modname.split('.')[-1] + result[name] = BuiltinModule(modname, self.submodules) + return result + + @property" +39,https://:@github.com/hpapaxen/rope.git,528744bb4bc1b8076680f7c2c1bfac508ddca4f9,"@@ -37,7 +37,7 @@ def relative(root, path): + if os.path.samefile(root, path): + return '/'.join(reversed(rel)) + parent = os.path.dirname(path) +- if not path or parent == path: ++ if not parent or parent == path: + break + rel.append(os.path.basename(path)) + path = parent +",rope/base/libutils.py,"ReplaceText(target='parent' @(40,15)->(40,19))","def relative(root, path): + if os.path.samefile(root, path): + return '/'.join(reversed(rel)) + parent = os.path.dirname(path) + if not path or parent == path: + break + rel.append(os.path.basename(path)) + path = parent","def relative(root, path): + if os.path.samefile(root, path): + return '/'.join(reversed(rel)) + parent = os.path.dirname(path) + if not parent or parent == path: + break + rel.append(os.path.basename(path)) + path = parent" +40,https://:@github.com/benjamincrom/baseball.git,6ef29729ad07458aebe709b4e42f56ecd3761ec4,"@@ -111,7 +111,7 @@ def write_game_svg_and_html(game_id, game, output_path): + html_filename = game_id + '.html' + + svg_text = game.get_svg_str() +- html_text = HTML_WRAPPER.format(title=game_id, filename=html_filename) ++ html_text = HTML_WRAPPER.format(title=game_id, filename=svg_filename) + + output_svg_path = join(output_path, svg_filename) + output_html_path = join(output_path, html_filename) +",fetch_game.py,"ReplaceText(target='svg_filename' @(114,60)->(114,73))","def write_game_svg_and_html(game_id, game, output_path): + html_filename = game_id + '.html' + + svg_text = game.get_svg_str() + html_text = HTML_WRAPPER.format(title=game_id, filename=html_filename) + + output_svg_path = join(output_path, svg_filename) + output_html_path = join(output_path, html_filename)","def write_game_svg_and_html(game_id, game, output_path): + html_filename = game_id + '.html' + + svg_text = game.get_svg_str() + html_text = HTML_WRAPPER.format(title=game_id, filename=svg_filename) + + output_svg_path = join(output_path, svg_filename) + output_html_path = join(output_path, html_filename)" +41,https://:@github.com/sporestack/bitcash.git,dbc65e1b47426e0e4d286db5b27216ec36cb32cf,"@@ -16,7 +16,7 @@ def test_set_fee_cache_time(): + + + def test_get_fee(): +- assert get_fee(fast=True) != get_fee(fast=False) ++ assert get_fee(fast=True) >= get_fee(fast=False) + + + class TestFeeCache: +",tests/network/test_fees.py,"ReplaceText(target='>=' @(19,30)->(19,32))","def test_set_fee_cache_time(): + + + def test_get_fee(): + assert get_fee(fast=True) != get_fee(fast=False) + + + class TestFeeCache:","def test_set_fee_cache_time(): + + + def test_get_fee(): + assert get_fee(fast=True) >= get_fee(fast=False) + + + class TestFeeCache:" +42,https://:@github.com/galaxy-genome-annotation/python-apollo.git,53e514b619844fa1f87179d738b9d29830027300,"@@ -29,7 +29,7 @@ class ApolloTestCase(unittest.TestCase): + """""" + + org_info = wa.organisms.show_organism(org_id) +- if 'directory' in org_info: ++ if 'directory' not in org_info: + time.sleep(1) + org_info = wa.organisms.show_organism(org_id) + +",test/__init__.py,"ReplaceText(target=' not in ' @(32,22)->(32,26))","class ApolloTestCase(unittest.TestCase): + """""" + + org_info = wa.organisms.show_organism(org_id) + if 'directory' in org_info: + time.sleep(1) + org_info = wa.organisms.show_organism(org_id) + ","class ApolloTestCase(unittest.TestCase): + """""" + + org_info = wa.organisms.show_organism(org_id) + if 'directory' not in org_info: + time.sleep(1) + org_info = wa.organisms.show_organism(org_id) + " +43,https://:@github.com/jakubplichta/grafana-dashboard-builder.git,3228e6950d65b9bd347cacb56a9e85ec410b14ce,"@@ -35,7 +35,7 @@ class Context(object): + formatter = string.Formatter() + (result, to_expand) = (formatter.vformat(to_expand, (), self._context), to_expand) + while result != to_expand: +- (result, to_expand) = (formatter.vformat(to_expand, (), self._context), result) ++ (result, to_expand) = (formatter.vformat(result, (), self._context), result) + return result + elif isinstance(to_expand, list): + return [self.expand_placeholders(value) for value in to_expand] +",grafana_dashboards/context.py,"ReplaceText(target='result' @(38,57)->(38,66))","class Context(object): + formatter = string.Formatter() + (result, to_expand) = (formatter.vformat(to_expand, (), self._context), to_expand) + while result != to_expand: + (result, to_expand) = (formatter.vformat(to_expand, (), self._context), result) + return result + elif isinstance(to_expand, list): + return [self.expand_placeholders(value) for value in to_expand]","class Context(object): + formatter = string.Formatter() + (result, to_expand) = (formatter.vformat(to_expand, (), self._context), to_expand) + while result != to_expand: + (result, to_expand) = (formatter.vformat(result, (), self._context), result) + return result + elif isinstance(to_expand, list): + return [self.expand_placeholders(value) for value in to_expand]" +44,https://:@github.com/Phylliade/ikpy.git,815dbff3a521532a7b792c309902ffea82abac85,"@@ -13,7 +13,7 @@ class TestFK(unittest.TestCase): + one_move[5] = np.pi / 4 + one_move[6] = -np.pi / 2 + one_move[4] = -np.pi / 2 +- self.test_pos = one_move ++ self.test_pos = all_zeros + + def test_fk_creature(self): + +",tests/test_fk.py,"ReplaceText(target='all_zeros' @(16,24)->(16,32))","class TestFK(unittest.TestCase): + one_move[5] = np.pi / 4 + one_move[6] = -np.pi / 2 + one_move[4] = -np.pi / 2 + self.test_pos = one_move + + def test_fk_creature(self): + ","class TestFK(unittest.TestCase): + one_move[5] = np.pi / 4 + one_move[6] = -np.pi / 2 + one_move[4] = -np.pi / 2 + self.test_pos = all_zeros + + def test_fk_creature(self): + " +45,https://:@github.com/tingbot/tingbot-python.git,5374186675f6809faf9ce953fc35c81217348753,"@@ -72,7 +72,7 @@ class RunLoop(object): + while self.running: + if len(self.timers) > 0: + try: +- self._wait(self.timers[0].next_fire_time) ++ self._wait(self.timers[-1].next_fire_time) + except Exception as e: + self._error(e) + continue +",tingbot/run_loop.py,"ReplaceText(target='-1' @(75,43)->(75,44))","class RunLoop(object): + while self.running: + if len(self.timers) > 0: + try: + self._wait(self.timers[0].next_fire_time) + except Exception as e: + self._error(e) + continue","class RunLoop(object): + while self.running: + if len(self.timers) > 0: + try: + self._wait(self.timers[-1].next_fire_time) + except Exception as e: + self._error(e) + continue" +46,https://:@github.com/nyoka-pmml/nyoka.git,8d5c0d31d0bf1e251abe686f06b614a16e5ffcfb,"@@ -74,7 +74,7 @@ class TestMethods(unittest.TestCase): + self.assertEqual(pmml_obj.NearestNeighborModel[0].ComparisonMeasure.kind, ""distance"") + + ##3 +- self.assertEqual(pmml_obj.steps[-1][-1].n_neighbors, pmml_obj.NearestNeighborModel[0].numberOfNeighbors) ++ self.assertEqual(pipeline_obj.steps[-1][-1].n_neighbors, pmml_obj.NearestNeighborModel[0].numberOfNeighbors) + + + def test_sklearn_03(self): +",nyoka/tests/skl_to_pmml_UnitTest.py,"ReplaceText(target='pipeline_obj' @(77,25)->(77,33))","class TestMethods(unittest.TestCase): + self.assertEqual(pmml_obj.NearestNeighborModel[0].ComparisonMeasure.kind, ""distance"") + + ##3 + self.assertEqual(pmml_obj.steps[-1][-1].n_neighbors, pmml_obj.NearestNeighborModel[0].numberOfNeighbors) + + + def test_sklearn_03(self):","class TestMethods(unittest.TestCase): + self.assertEqual(pmml_obj.NearestNeighborModel[0].ComparisonMeasure.kind, ""distance"") + + ##3 + self.assertEqual(pipeline_obj.steps[-1][-1].n_neighbors, pmml_obj.NearestNeighborModel[0].numberOfNeighbors) + + + def test_sklearn_03(self):" +47,https://:@github.com/iris-edu/pyweed.git,77d919acd8d54d4879d1a34598e9e04f16fdf708,"@@ -97,7 +97,7 @@ class WaveformEntry(AttribDict): + + self.error = None + +- self.start_time = self.distances.arrival + self.config.offsets[0] ++ self.start_time = self.distances.arrival - self.config.offsets[0] + self.end_time = self.distances.arrival + self.config.offsets[1] + + self.start_string = UTCDateTime(self.start_time).format_iris_web_service().replace(':', '_') +",pyweed/waveforms_handler.py,"ReplaceText(target='-' @(100,49)->(100,50))","class WaveformEntry(AttribDict): + + self.error = None + + self.start_time = self.distances.arrival + self.config.offsets[0] + self.end_time = self.distances.arrival + self.config.offsets[1] + + self.start_string = UTCDateTime(self.start_time).format_iris_web_service().replace(':', '_')","class WaveformEntry(AttribDict): + + self.error = None + + self.start_time = self.distances.arrival - self.config.offsets[0] + self.end_time = self.distances.arrival + self.config.offsets[1] + + self.start_string = UTCDateTime(self.start_time).format_iris_web_service().replace(':', '_')" +48,https://:@github.com/anaxilaus/coindata.git,2e5067311c4eed50eed41c45f43ad63e8973e579,"@@ -52,6 +52,6 @@ def dump_json(data, filepath): + + try: + with open(filepath, 'w') as file: +- json.dump(data, filepath) ++ json.dump(data, file) + except TypeError as e: + print(""Data isn't JSON compatible.\n"", e) +",coindata/utils.py,"ReplaceText(target='file' @(55,28)->(55,36))","def dump_json(data, filepath): + + try: + with open(filepath, 'w') as file: + json.dump(data, filepath) + except TypeError as e: + print(""Data isn't JSON compatible.\n"", e)","def dump_json(data, filepath): + + try: + with open(filepath, 'w') as file: + json.dump(data, file) + except TypeError as e: + print(""Data isn't JSON compatible.\n"", e)" +49,https://:@github.com/Pixelapse/pyglass.git,a31e95cbc259ce61f5851d6f0d769792aaa182fe,"@@ -20,7 +20,7 @@ def preview(src_path): + preview_path = thumbnail_preview(src_path) + + if preview_path: +- mimetype = magic.from_file(src_path, mime=True).lower() ++ mimetype = magic.from_file(preview_path, mime=True).lower() + if mimetype in [ExportMimeType.PNG, ExportMimeType.PDF]: + return preview_path + +",pyglass/quicklook/api.py,"ReplaceText(target='preview_path' @(23,31)->(23,39))","def preview(src_path): + preview_path = thumbnail_preview(src_path) + + if preview_path: + mimetype = magic.from_file(src_path, mime=True).lower() + if mimetype in [ExportMimeType.PNG, ExportMimeType.PDF]: + return preview_path + ","def preview(src_path): + preview_path = thumbnail_preview(src_path) + + if preview_path: + mimetype = magic.from_file(preview_path, mime=True).lower() + if mimetype in [ExportMimeType.PNG, ExportMimeType.PDF]: + return preview_path + " +50,https://:@github.com/erezsh/plyplus.git,8cc69bebfcb2cb0480ac66d07fe1f4b8637bba11,"@@ -784,7 +784,7 @@ class _Grammar(object): + subtree.extend(child.tail) + else: + subtree.append(child) +- p[0] = self.tree_class(rule_name, subtree, skip_adjustments=True) if len(subtree) > 1 else subtree[0] ++ p[0] = self.tree_class(rule_name, subtree, skip_adjustments=True) if len(subtree) != 1 else subtree[0] + else: + def p_rule(self, p): + p[0] = self.tree_class(rule_name, p[1:], skip_adjustments=True) +",plyplus/plyplus.py,"ReplaceText(target='!=' @(787,98)->(787,99))","class _Grammar(object): + subtree.extend(child.tail) + else: + subtree.append(child) + p[0] = self.tree_class(rule_name, subtree, skip_adjustments=True) if len(subtree) > 1 else subtree[0] + else: + def p_rule(self, p): + p[0] = self.tree_class(rule_name, p[1:], skip_adjustments=True)","class _Grammar(object): + subtree.extend(child.tail) + else: + subtree.append(child) + p[0] = self.tree_class(rule_name, subtree, skip_adjustments=True) if len(subtree) != 1 else subtree[0] + else: + def p_rule(self, p): + p[0] = self.tree_class(rule_name, p[1:], skip_adjustments=True)" +51,https://:@github.com/olls/graphics.git,877ef2670d4ad34c4fcf951dab0922419f081531,"@@ -22,7 +22,7 @@ def colorStr(text, color=WHITE): + return seq + sys.stdout.write(seq + '\n') + else: +- return seq ++ return text + sys.stdout.write(text + '\n') + + if __name__ == '__main__': +",colors.py,"ReplaceText(target='text' @(25,9)->(25,12))","def colorStr(text, color=WHITE): + return seq + sys.stdout.write(seq + '\n') + else: + return seq + sys.stdout.write(text + '\n') + + if __name__ == '__main__':","def colorStr(text, color=WHITE): + return seq + sys.stdout.write(seq + '\n') + else: + return text + sys.stdout.write(text + '\n') + + if __name__ == '__main__':" +52,https://:@github.com/hkwi/twink.git,5ef359deb609fc55659596a8cb327abb9c7e4653,"@@ -319,7 +319,7 @@ def ofp_action_set_field(message, offset): + cursor = _cursor(offset) + offset = cursor.offset + +- (type,len) = ofp_action_header(message, offset) ++ (type,len) = ofp_action_header(message, cursor) + field = message[cursor.offset:offset+len] + cursor.offset = offset+len + return namedtuple(""ofp_action_set_field"", +",twink/ofp4/parse.py,"ReplaceText(target='cursor' @(322,41)->(322,47))","def ofp_action_set_field(message, offset): + cursor = _cursor(offset) + offset = cursor.offset + + (type,len) = ofp_action_header(message, offset) + field = message[cursor.offset:offset+len] + cursor.offset = offset+len + return namedtuple(""ofp_action_set_field"",","def ofp_action_set_field(message, offset): + cursor = _cursor(offset) + offset = cursor.offset + + (type,len) = ofp_action_header(message, cursor) + field = message[cursor.offset:offset+len] + cursor.offset = offset+len + return namedtuple(""ofp_action_set_field""," +53,https://:@github.com/hkwi/twink.git,fc6f5ad63cb12f9caf5455e3179ecfd9cd9de060,"@@ -27,7 +27,7 @@ def _unpack(fmt, message, offset): + return struct.unpack_from(fmt, message, offset) + + def _align(length): +- return (length+7)/8*8 ++ return (length+7)//8*8 + + # 7.1 + def ofp_header(version, type, length, xid): +",twink/ofp4/build.py,"ReplaceText(target='//' @(30,18)->(30,19))","def _unpack(fmt, message, offset): + return struct.unpack_from(fmt, message, offset) + + def _align(length): + return (length+7)/8*8 + + # 7.1 + def ofp_header(version, type, length, xid):","def _unpack(fmt, message, offset): + return struct.unpack_from(fmt, message, offset) + + def _align(length): + return (length+7)//8*8 + + # 7.1 + def ofp_header(version, type, length, xid):" +54,https://:@github.com/biolab/orange3-datafusion.git,54f941a66a9b369a73190dfe2007e5b6dae1803a,"@@ -33,7 +33,7 @@ def _find_completion(fuser, relation): + for fuser_relation in fuser.fusion_graph.get_relations(relation.row_type, + relation.col_type): + if fuser_relation._id == relation._id: +- return fuser.complete(fuser_relation) ++ return fuser.complete(relation) + return None + + +",orangecontrib/datafusion/widgets/owcompletionscoring.py,"ReplaceText(target='relation' @(36,34)->(36,48))","def _find_completion(fuser, relation): + for fuser_relation in fuser.fusion_graph.get_relations(relation.row_type, + relation.col_type): + if fuser_relation._id == relation._id: + return fuser.complete(fuser_relation) + return None + + ","def _find_completion(fuser, relation): + for fuser_relation in fuser.fusion_graph.get_relations(relation.row_type, + relation.col_type): + if fuser_relation._id == relation._id: + return fuser.complete(relation) + return None + + " +55,https://:@github.com/aiqm/torchani.git,5bb6691515e5e56fbe4994b140dd40b73043a33f,"@@ -151,7 +151,7 @@ class PrepareInput(torch.nn.Module): + new_tensors = [] + for t in tensors: + new_tensors.append(t.index_select(1, reverse)) +- return (species, *tensors) ++ return (species, *new_tensors) + + def forward(self, species_coordinates): + species, coordinates = species_coordinates +",torchani/aev.py,"ReplaceText(target='new_tensors' @(154,26)->(154,33))","class PrepareInput(torch.nn.Module): + new_tensors = [] + for t in tensors: + new_tensors.append(t.index_select(1, reverse)) + return (species, *tensors) + + def forward(self, species_coordinates): + species, coordinates = species_coordinates","class PrepareInput(torch.nn.Module): + new_tensors = [] + for t in tensors: + new_tensors.append(t.index_select(1, reverse)) + return (species, *new_tensors) + + def forward(self, species_coordinates): + species, coordinates = species_coordinates" +56,https://:@github.com/aiqm/torchani.git,abc8f7f842ae4b273c6e867b392413dcadd9c921,"@@ -593,7 +593,7 @@ def collate_fn(data, chunk_threshold, properties_info): + if properties_info['padding_values'][i] is None: + prop = torch.stack(prop) + else: +- prop = torch.nn.utils.rnn.pad_sequence(batch_species, ++ prop = torch.nn.utils.rnn.pad_sequence(prop, + batch_first=True, + padding_value=properties_info['padding_values'][i]) + # sort with number of atoms +",torchani/data/new.py,"ReplaceText(target='prop' @(596,51)->(596,64))","def collate_fn(data, chunk_threshold, properties_info): + if properties_info['padding_values'][i] is None: + prop = torch.stack(prop) + else: + prop = torch.nn.utils.rnn.pad_sequence(batch_species, + batch_first=True, + padding_value=properties_info['padding_values'][i]) + # sort with number of atoms","def collate_fn(data, chunk_threshold, properties_info): + if properties_info['padding_values'][i] is None: + prop = torch.stack(prop) + else: + prop = torch.nn.utils.rnn.pad_sequence(prop, + batch_first=True, + padding_value=properties_info['padding_values'][i]) + # sort with number of atoms" +57,https://:@github.com/aiqm/torchani.git,c18f4a5ea1f9732cc07c8816caa401981e43dc48,"@@ -274,7 +274,7 @@ def compute_aev(species: Tensor, coordinates: Tensor, cell: Tensor, + num_atoms = species.shape[1] + num_species_pairs = angular_length // angular_sublength + # PBC calculation is bypassed if there are no shifts +- if shifts.numel() == 1: ++ if shifts.numel() == 0: + atom_index1, atom_index2, shifts = neighbor_pairs_nopbc(species == -1, coordinates, cell, shifts, Rcr) + else: + atom_index1, atom_index2, shifts = neighbor_pairs(species == -1, coordinates, cell, shifts, Rcr) +",torchani/aev.py,"ReplaceText(target='0' @(277,25)->(277,26))","def compute_aev(species: Tensor, coordinates: Tensor, cell: Tensor, + num_atoms = species.shape[1] + num_species_pairs = angular_length // angular_sublength + # PBC calculation is bypassed if there are no shifts + if shifts.numel() == 1: + atom_index1, atom_index2, shifts = neighbor_pairs_nopbc(species == -1, coordinates, cell, shifts, Rcr) + else: + atom_index1, atom_index2, shifts = neighbor_pairs(species == -1, coordinates, cell, shifts, Rcr)","def compute_aev(species: Tensor, coordinates: Tensor, cell: Tensor, + num_atoms = species.shape[1] + num_species_pairs = angular_length // angular_sublength + # PBC calculation is bypassed if there are no shifts + if shifts.numel() == 0: + atom_index1, atom_index2, shifts = neighbor_pairs_nopbc(species == -1, coordinates, cell, shifts, Rcr) + else: + atom_index1, atom_index2, shifts = neighbor_pairs(species == -1, coordinates, cell, shifts, Rcr)" +58,https://:@github.com/cs207group4/cs207-FinalProject.git,e7f1cc613ace275a8d259de7455ee39ca063e029,"@@ -120,7 +120,7 @@ class ChemSolver: + r.set_initial_value(y0, 0) + self._t = [0] + self._y = [y0] +- while r.successful() and r.t <= t1: ++ while r.successful() and r.t < t1: + self._t.append(r.t + dt) + self._y.append(r.integrate(r.t + dt)) + self._t = np.array(self._t) +",pychemkin/ChemSolver.py,"ReplaceText(target='<' @(123,37)->(123,39))","class ChemSolver: + r.set_initial_value(y0, 0) + self._t = [0] + self._y = [y0] + while r.successful() and r.t <= t1: + self._t.append(r.t + dt) + self._y.append(r.integrate(r.t + dt)) + self._t = np.array(self._t)","class ChemSolver: + r.set_initial_value(y0, 0) + self._t = [0] + self._y = [y0] + while r.successful() and r.t < t1: + self._t.append(r.t + dt) + self._y.append(r.integrate(r.t + dt)) + self._t = np.array(self._t)" +59,https://:@github.com/MrLeeh/pyads.git,d14fd2a7bb2d4b784a4f6a47b6981ba2a86b699c,"@@ -97,7 +97,7 @@ def set_local_address(ams_netid): + else: + ams_netid_st = ams_netid + +- assert isinstance(ams_netid, SAmsNetId) ++ assert isinstance(ams_netid_st, SAmsNetId) + + if linux: + return adsSetLocalAddress(ams_netid_st) +",pyads/ads.py,"ReplaceText(target='ams_netid_st' @(100,22)->(100,31))","def set_local_address(ams_netid): + else: + ams_netid_st = ams_netid + + assert isinstance(ams_netid, SAmsNetId) + + if linux: + return adsSetLocalAddress(ams_netid_st)","def set_local_address(ams_netid): + else: + ams_netid_st = ams_netid + + assert isinstance(ams_netid_st, SAmsNetId) + + if linux: + return adsSetLocalAddress(ams_netid_st)" +60,https://:@github.com/pytorch/fairseq.git,0a836276129ef71fa6c44975dd02ab70bccc496d,"@@ -58,7 +58,7 @@ class FConvEncoder(FairseqEncoder): + self.projections = nn.ModuleList() + self.convolutions = nn.ModuleList() + for (out_channels, kernel_size) in convolutions: +- pad = (kernel_size - 1) // 2 ++ pad = (kernel_size - 1) / 2 + self.projections.append(Linear(in_channels, out_channels) + if in_channels != out_channels else None) + self.convolutions.append( +",fairseq/models/fconv.py,"ReplaceText(target='/' @(61,36)->(61,38))","class FConvEncoder(FairseqEncoder): + self.projections = nn.ModuleList() + self.convolutions = nn.ModuleList() + for (out_channels, kernel_size) in convolutions: + pad = (kernel_size - 1) // 2 + self.projections.append(Linear(in_channels, out_channels) + if in_channels != out_channels else None) + self.convolutions.append(","class FConvEncoder(FairseqEncoder): + self.projections = nn.ModuleList() + self.convolutions = nn.ModuleList() + for (out_channels, kernel_size) in convolutions: + pad = (kernel_size - 1) / 2 + self.projections.append(Linear(in_channels, out_channels) + if in_channels != out_channels else None) + self.convolutions.append(" +61,https://:@github.com/pytorch/fairseq.git,f68a44359b6596997b931d2e662a899ffba9d407,"@@ -62,7 +62,7 @@ class SinusoidalPositionalEmbedding(nn.Module): + # recompute/expand embeddings if needed + bsz, seq_len = input.size() + max_pos = self.padding_idx + 1 + seq_len +- if seq_len > self.weights.size(0): ++ if max_pos > self.weights.size(0): + self.weights = SinusoidalPositionalEmbedding.get_embedding( + max_pos, + self.embedding_dim, +",fairseq/modules/sinusoidal_positional_embedding.py,"ReplaceText(target='max_pos' @(65,11)->(65,18))","class SinusoidalPositionalEmbedding(nn.Module): + # recompute/expand embeddings if needed + bsz, seq_len = input.size() + max_pos = self.padding_idx + 1 + seq_len + if seq_len > self.weights.size(0): + self.weights = SinusoidalPositionalEmbedding.get_embedding( + max_pos, + self.embedding_dim,","class SinusoidalPositionalEmbedding(nn.Module): + # recompute/expand embeddings if needed + bsz, seq_len = input.size() + max_pos = self.padding_idx + 1 + seq_len + if max_pos > self.weights.size(0): + self.weights = SinusoidalPositionalEmbedding.get_embedding( + max_pos, + self.embedding_dim," +62,https://:@github.com/pytorch/fairseq.git,762956a559e65e1e48df8f8b4df515d23b66fddb,"@@ -82,7 +82,7 @@ def main(args): + train_meter.start() + valid_losses = [None] + valid_subsets = args.valid_subset.split(',') +- while lr > args.min_lr and epoch_itr.epoch <= max_epoch and trainer.get_num_updates() < max_update: ++ while lr > args.min_lr and epoch_itr.epoch < max_epoch and trainer.get_num_updates() < max_update: + # train for one epoch + train(args, trainer, task, epoch_itr) + +",train.py,"ReplaceText(target='<' @(85,47)->(85,49))","def main(args): + train_meter.start() + valid_losses = [None] + valid_subsets = args.valid_subset.split(',') + while lr > args.min_lr and epoch_itr.epoch <= max_epoch and trainer.get_num_updates() < max_update: + # train for one epoch + train(args, trainer, task, epoch_itr) + ","def main(args): + train_meter.start() + valid_losses = [None] + valid_subsets = args.valid_subset.split(',') + while lr > args.min_lr and epoch_itr.epoch < max_epoch and trainer.get_num_updates() < max_update: + # train for one epoch + train(args, trainer, task, epoch_itr) + " +63,https://:@github.com/pytorch/fairseq.git,e9967cd334783f5da50deadc17cf8a4fc3380171,"@@ -82,7 +82,7 @@ def main(args): + train_meter.start() + valid_losses = [None] + valid_subsets = args.valid_subset.split(',') +- while lr > args.min_lr and epoch_itr.epoch <= max_epoch and trainer.get_num_updates() < max_update: ++ while lr > args.min_lr and epoch_itr.epoch < max_epoch and trainer.get_num_updates() < max_update: + # train for one epoch + train(args, trainer, task, epoch_itr) + +",train.py,"ReplaceText(target='<' @(85,47)->(85,49))","def main(args): + train_meter.start() + valid_losses = [None] + valid_subsets = args.valid_subset.split(',') + while lr > args.min_lr and epoch_itr.epoch <= max_epoch and trainer.get_num_updates() < max_update: + # train for one epoch + train(args, trainer, task, epoch_itr) + ","def main(args): + train_meter.start() + valid_losses = [None] + valid_subsets = args.valid_subset.split(',') + while lr > args.min_lr and epoch_itr.epoch < max_epoch and trainer.get_num_updates() < max_update: + # train for one epoch + train(args, trainer, task, epoch_itr) + " +64,https://:@github.com/pytorch/fairseq.git,7bcb487aad8504043d13c9b869d555aa565a46c7,"@@ -49,7 +49,7 @@ class LabelSmoothedCrossEntropyCriterion(FairseqCriterion): + sample_size = sample['target'].size(0) if self.args.sentence_avg else sample['ntokens'] + logging_output = { + 'loss': utils.item(loss.data) if reduce else loss.data, +- 'nll_loss': utils.item(nll_loss.data) if reduce else loss.data, ++ 'nll_loss': utils.item(nll_loss.data) if reduce else nll_loss.data, + 'ntokens': sample['ntokens'], + 'sample_size': sample_size, + } +",fairseq/criterions/label_smoothed_cross_entropy.py,"ReplaceText(target='nll_loss' @(52,65)->(52,69))","class LabelSmoothedCrossEntropyCriterion(FairseqCriterion): + sample_size = sample['target'].size(0) if self.args.sentence_avg else sample['ntokens'] + logging_output = { + 'loss': utils.item(loss.data) if reduce else loss.data, + 'nll_loss': utils.item(nll_loss.data) if reduce else loss.data, + 'ntokens': sample['ntokens'], + 'sample_size': sample_size, + }","class LabelSmoothedCrossEntropyCriterion(FairseqCriterion): + sample_size = sample['target'].size(0) if self.args.sentence_avg else sample['ntokens'] + logging_output = { + 'loss': utils.item(loss.data) if reduce else loss.data, + 'nll_loss': utils.item(nll_loss.data) if reduce else nll_loss.data, + 'ntokens': sample['ntokens'], + 'sample_size': sample_size, + }" +65,https://:@github.com/pytorch/fairseq.git,74efc21403477d103bd426ae64c37b7a30d8f4bf,"@@ -154,7 +154,7 @@ class TestIncrementalDecoder(FairseqIncrementalDecoder): + probs[:, i, self.dictionary.eos()] = 1.0 + + # random attention +- attn = torch.rand(bbsz, src_len, tgt_len) ++ attn = torch.rand(bbsz, tgt_len, src_len) + + return Variable(probs), Variable(attn) + +",tests/utils.py,"ArgSwap(idxs=1<->2 @(157,15)->(157,25))","class TestIncrementalDecoder(FairseqIncrementalDecoder): + probs[:, i, self.dictionary.eos()] = 1.0 + + # random attention + attn = torch.rand(bbsz, src_len, tgt_len) + + return Variable(probs), Variable(attn) + ","class TestIncrementalDecoder(FairseqIncrementalDecoder): + probs[:, i, self.dictionary.eos()] = 1.0 + + # random attention + attn = torch.rand(bbsz, tgt_len, src_len) + + return Variable(probs), Variable(attn) + " +66,https://:@github.com/pytorch/fairseq.git,dfd77717b91a6e233829735795ab49d6fd85c0b3,"@@ -93,7 +93,7 @@ class CosineSchedule(FairseqLRScheduler): + else: + i = math.floor(curr_updates / self.period) + t_i = self.period +- t_curr = num_updates - (self.period * i) ++ t_curr = curr_updates - (self.period * i) + + lr_shrink = self.lr_shrink ** i + min_lr = self.min_lr * lr_shrink +",fairseq/optim/lr_scheduler/cosine_lr_scheduler.py,"ReplaceText(target='curr_updates' @(96,25)->(96,36))","class CosineSchedule(FairseqLRScheduler): + else: + i = math.floor(curr_updates / self.period) + t_i = self.period + t_curr = num_updates - (self.period * i) + + lr_shrink = self.lr_shrink ** i + min_lr = self.min_lr * lr_shrink","class CosineSchedule(FairseqLRScheduler): + else: + i = math.floor(curr_updates / self.period) + t_i = self.period + t_curr = curr_updates - (self.period * i) + + lr_shrink = self.lr_shrink ** i + min_lr = self.min_lr * lr_shrink" +67,https://:@github.com/pytorch/fairseq.git,0eea6923b9d7f408e667714709b070171ac7fe05,"@@ -312,7 +312,7 @@ def make_positions(tensor, padding_idx, left_pad, onnx_trace=False): + positions = range_buf.expand_as(tensor) + if left_pad: + positions = positions - mask.size(1) + mask.long().sum(dim=1).unsqueeze(1) +- return positions * mask.long() + positions * (1 - mask.long()) ++ return positions * mask.long() + padding_idx * (1 - mask.long()) + + max_pos = padding_idx + 1 + tensor.size(1) + if not hasattr(make_positions, 'range_buf'): +",fairseq/utils.py,"ReplaceText(target='padding_idx' @(315,41)->(315,50))","def make_positions(tensor, padding_idx, left_pad, onnx_trace=False): + positions = range_buf.expand_as(tensor) + if left_pad: + positions = positions - mask.size(1) + mask.long().sum(dim=1).unsqueeze(1) + return positions * mask.long() + positions * (1 - mask.long()) + + max_pos = padding_idx + 1 + tensor.size(1) + if not hasattr(make_positions, 'range_buf'):","def make_positions(tensor, padding_idx, left_pad, onnx_trace=False): + positions = range_buf.expand_as(tensor) + if left_pad: + positions = positions - mask.size(1) + mask.long().sum(dim=1).unsqueeze(1) + return positions * mask.long() + padding_idx * (1 - mask.long()) + + max_pos = padding_idx + 1 + tensor.size(1) + if not hasattr(make_positions, 'range_buf'):" +68,https://:@github.com/pytorch/fairseq.git,4d3401b09f155995cd81fd394dfa50bf65ee8e5f,"@@ -183,7 +183,7 @@ class Sampling(Search): + lprobs = lprobs[:, ::beam_size, :].contiguous() + + # we exclude the first two vocab items, one of which is pad +- assert self.pad == 1, 'sampling assumes the first two symbols can be ignored' ++ assert self.pad <= 1, 'sampling assumes the first two symbols can be ignored' + lprobs_nopad = lprobs[:, :, 2:] + + # only sample from top-k candidates +",fairseq/search.py,"ReplaceText(target='<=' @(186,24)->(186,26))","class Sampling(Search): + lprobs = lprobs[:, ::beam_size, :].contiguous() + + # we exclude the first two vocab items, one of which is pad + assert self.pad == 1, 'sampling assumes the first two symbols can be ignored' + lprobs_nopad = lprobs[:, :, 2:] + + # only sample from top-k candidates","class Sampling(Search): + lprobs = lprobs[:, ::beam_size, :].contiguous() + + # we exclude the first two vocab items, one of which is pad + assert self.pad <= 1, 'sampling assumes the first two symbols can be ignored' + lprobs_nopad = lprobs[:, :, 2:] + + # only sample from top-k candidates" +69,https://:@github.com/pytorch/fairseq.git,2340832fdd7acaaaf07626daa6a0cef6fda06cd1,"@@ -160,7 +160,7 @@ def main(args): + )) + + # update running id counter +- start_id += len(results) ++ start_id += len(inputs) + + + def cli_main(): +",interactive.py,"ReplaceText(target='inputs' @(163,24)->(163,31))","def main(args): + )) + + # update running id counter + start_id += len(results) + + + def cli_main():","def main(args): + )) + + # update running id counter + start_id += len(inputs) + + + def cli_main():" +70,https://:@github.com/pytorch/fairseq.git,39a60b844aad67aa59267d873edeb4948f6f0af9,"@@ -351,7 +351,7 @@ class LSTMDecoder(FairseqIncrementalDecoder): + self.additional_fc = Linear(hidden_size, out_embed_dim) + if adaptive_softmax_cutoff is not None: + # setting adaptive_softmax dropout to dropout_out for now but can be redefined +- self.adaptive_softmax = AdaptiveSoftmax(num_embeddings, embed_dim, adaptive_softmax_cutoff, ++ self.adaptive_softmax = AdaptiveSoftmax(num_embeddings, hidden_size, adaptive_softmax_cutoff, + dropout=dropout_out) + elif not self.share_input_output_embed: + self.fc_out = Linear(out_embed_dim, num_embeddings, dropout=dropout_out) +",fairseq/models/lstm.py,"ReplaceText(target='hidden_size' @(354,68)->(354,77))","class LSTMDecoder(FairseqIncrementalDecoder): + self.additional_fc = Linear(hidden_size, out_embed_dim) + if adaptive_softmax_cutoff is not None: + # setting adaptive_softmax dropout to dropout_out for now but can be redefined + self.adaptive_softmax = AdaptiveSoftmax(num_embeddings, embed_dim, adaptive_softmax_cutoff, + dropout=dropout_out) + elif not self.share_input_output_embed: + self.fc_out = Linear(out_embed_dim, num_embeddings, dropout=dropout_out)","class LSTMDecoder(FairseqIncrementalDecoder): + self.additional_fc = Linear(hidden_size, out_embed_dim) + if adaptive_softmax_cutoff is not None: + # setting adaptive_softmax dropout to dropout_out for now but can be redefined + self.adaptive_softmax = AdaptiveSoftmax(num_embeddings, hidden_size, adaptive_softmax_cutoff, + dropout=dropout_out) + elif not self.share_input_output_embed: + self.fc_out = Linear(out_embed_dim, num_embeddings, dropout=dropout_out)" +71,https://:@github.com/pytorch/fairseq.git,49177c99c45f7d6e99a8f1500d16396e2d7b4519,"@@ -498,7 +498,7 @@ class TransformerDecoder(FairseqIncrementalDecoder): + del state_dict[k] + + version_key = '{}.version'.format(name) +- if utils.item(state_dict.get(version_key, torch.Tensor([1]))[0]) < 2: ++ if utils.item(state_dict.get(version_key, torch.Tensor([1]))[0]) <= 2: + # earlier checkpoints did not normalize after the stack of layers + self.layer_norm = None + self.normalize = False +",fairseq/models/transformer.py,"ReplaceText(target='<=' @(501,73)->(501,74))","class TransformerDecoder(FairseqIncrementalDecoder): + del state_dict[k] + + version_key = '{}.version'.format(name) + if utils.item(state_dict.get(version_key, torch.Tensor([1]))[0]) < 2: + # earlier checkpoints did not normalize after the stack of layers + self.layer_norm = None + self.normalize = False","class TransformerDecoder(FairseqIncrementalDecoder): + del state_dict[k] + + version_key = '{}.version'.format(name) + if utils.item(state_dict.get(version_key, torch.Tensor([1]))[0]) <= 2: + # earlier checkpoints did not normalize after the stack of layers + self.layer_norm = None + self.normalize = False" +72,https://:@github.com/pytorch/fairseq.git,5d7a81099462e9f19715ce5fa37c03816a750e12,"@@ -412,7 +412,7 @@ class LevenshteinTransformerModel(FairseqNATModel): + max_lens = torch.zeros_like(output_tokens).fill_(255) + else: + if encoder_out.encoder_padding_mask is None: +- max_src_len = encoder_out.encoder_out.size(1) ++ max_src_len = encoder_out.encoder_out.size(0) + src_lens = encoder_out.encoder_out.new(bsz).fill_(max_src_len) + else: + src_lens = (~encoder_out.encoder_padding_mask).sum(1) +",fairseq/models/nat/levenshtein_transformer.py,"ReplaceText(target='0' @(415,59)->(415,60))","class LevenshteinTransformerModel(FairseqNATModel): + max_lens = torch.zeros_like(output_tokens).fill_(255) + else: + if encoder_out.encoder_padding_mask is None: + max_src_len = encoder_out.encoder_out.size(1) + src_lens = encoder_out.encoder_out.new(bsz).fill_(max_src_len) + else: + src_lens = (~encoder_out.encoder_padding_mask).sum(1)","class LevenshteinTransformerModel(FairseqNATModel): + max_lens = torch.zeros_like(output_tokens).fill_(255) + else: + if encoder_out.encoder_padding_mask is None: + max_src_len = encoder_out.encoder_out.size(0) + src_lens = encoder_out.encoder_out.new(bsz).fill_(max_src_len) + else: + src_lens = (~encoder_out.encoder_padding_mask).sum(1)" +73,https://:@github.com/pytorch/fairseq.git,431d604f696a15c06fceab56b4ace271bb85e74b,"@@ -331,7 +331,7 @@ class SequenceGenerator(object): + avg_attn_scores = avg_attn_scores[0] + if avg_attn_scores is not None: + if attn is None: +- attn = scores.new(bsz * beam_size, src_tokens.size(1), max_len + 2) ++ attn = scores.new(bsz * beam_size, avg_attn_scores.size(1), max_len + 2) + attn_buf = attn.clone() + attn[:, :, step + 1].copy_(avg_attn_scores) + +",fairseq/sequence_generator.py,"ReplaceText(target='avg_attn_scores' @(334,55)->(334,65))","class SequenceGenerator(object): + avg_attn_scores = avg_attn_scores[0] + if avg_attn_scores is not None: + if attn is None: + attn = scores.new(bsz * beam_size, src_tokens.size(1), max_len + 2) + attn_buf = attn.clone() + attn[:, :, step + 1].copy_(avg_attn_scores) + ","class SequenceGenerator(object): + avg_attn_scores = avg_attn_scores[0] + if avg_attn_scores is not None: + if attn is None: + attn = scores.new(bsz * beam_size, avg_attn_scores.size(1), max_len + 2) + attn_buf = attn.clone() + attn[:, :, step + 1].copy_(avg_attn_scores) + " +74,https://:@github.com/pytorch/fairseq.git,4f8b0643c80d6a41039ae29e94fca6b44de8791a,"@@ -138,7 +138,7 @@ def should_stop_early(args, valid_loss): + return False + else: + should_stop_early.num_runs += 1 +- return should_stop_early.num_runs > args.patience ++ return should_stop_early.num_runs >= args.patience + + + @metrics.aggregate('train') +",fairseq_cli/train.py,"ReplaceText(target='>=' @(141,42)->(141,43))","def should_stop_early(args, valid_loss): + return False + else: + should_stop_early.num_runs += 1 + return should_stop_early.num_runs > args.patience + + + @metrics.aggregate('train')","def should_stop_early(args, valid_loss): + return False + else: + should_stop_early.num_runs += 1 + return should_stop_early.num_runs >= args.patience + + + @metrics.aggregate('train')" +75,https://:@github.com/pytorch/fairseq.git,9a718e29855713a51877237b2dcc25e39c234c82,"@@ -110,5 +110,5 @@ class TranslationFromPretrainedBARTTask(TranslationTask): + for s_t in src_tokens: + s_t = torch.cat([s_t, s_t.new(1).fill_(src_lang_id)]) + source_tokens.append(s_t) +- dataset = LanguagePairDataset(src_tokens, src_lengths, self.source_dictionary) ++ dataset = LanguagePairDataset(source_tokens, src_lengths, self.source_dictionary) + return dataset +",fairseq/tasks/translation_from_pretrained_bart.py,"ReplaceText(target='source_tokens' @(113,38)->(113,48))","class TranslationFromPretrainedBARTTask(TranslationTask): + for s_t in src_tokens: + s_t = torch.cat([s_t, s_t.new(1).fill_(src_lang_id)]) + source_tokens.append(s_t) + dataset = LanguagePairDataset(src_tokens, src_lengths, self.source_dictionary) + return dataset","class TranslationFromPretrainedBARTTask(TranslationTask): + for s_t in src_tokens: + s_t = torch.cat([s_t, s_t.new(1).fill_(src_lang_id)]) + source_tokens.append(s_t) + dataset = LanguagePairDataset(source_tokens, src_lengths, self.source_dictionary) + return dataset" +76,https://:@github.com/pytorch/fairseq.git,b689b6ff3ab7b806217b8aa41821bb8fc85f7cd8,"@@ -264,7 +264,7 @@ class LanguagePairDataset(FairseqDataset): + tgt_item = torch.cat([torch.LongTensor([bos]), self.tgt[index]]) + + bos = self.src_dict.bos() +- if self.src[index][-1] != bos: ++ if self.src[index][0] != bos: + src_item = torch.cat([torch.LongTensor([bos]), self.src[index]]) + + if self.remove_eos_from_source: +",fairseq/data/language_pair_dataset.py,"ReplaceText(target='0' @(267,31)->(267,33))","class LanguagePairDataset(FairseqDataset): + tgt_item = torch.cat([torch.LongTensor([bos]), self.tgt[index]]) + + bos = self.src_dict.bos() + if self.src[index][-1] != bos: + src_item = torch.cat([torch.LongTensor([bos]), self.src[index]]) + + if self.remove_eos_from_source:","class LanguagePairDataset(FairseqDataset): + tgt_item = torch.cat([torch.LongTensor([bos]), self.tgt[index]]) + + bos = self.src_dict.bos() + if self.src[index][0] != bos: + src_item = torch.cat([torch.LongTensor([bos]), self.src[index]]) + + if self.remove_eos_from_source:" +77,https://:@github.com/prprprus/PyMySQLPool.git,66b07cdf844554245cf209a72de89bd17133269c,"@@ -169,7 +169,7 @@ class Pool(object): + if self.ping_check: + now = int(time()) + timeout = now +- if isinstance(int, self.ping_check): ++ if isinstance(self.ping_check, int): + timeout = timeout - self.ping_check + if not hasattr(c, '__ping_check_timestamp'): + c.__ping_check_timestamp = now +",pymysqlpool/pool.py,"ArgSwap(idxs=0<->1 @(172,15)->(172,25))","class Pool(object): + if self.ping_check: + now = int(time()) + timeout = now + if isinstance(int, self.ping_check): + timeout = timeout - self.ping_check + if not hasattr(c, '__ping_check_timestamp'): + c.__ping_check_timestamp = now","class Pool(object): + if self.ping_check: + now = int(time()) + timeout = now + if isinstance(self.ping_check, int): + timeout = timeout - self.ping_check + if not hasattr(c, '__ping_check_timestamp'): + c.__ping_check_timestamp = now" +78,https://:@github.com/dailymuse/oz.git,a15adf73c721d07b9dac886fcc27145e2449563c,"@@ -173,7 +173,7 @@ class S3File(CDNFile): + + def copy(self, new_path, replace=False): + """"""Uses boto to copy the file to the new path instead of uploading another file to the new key"""""" +- if replace or get_file(new_path).exists(): ++ if replace or not get_file(new_path).exists(): + self.key.copy(self.key.bucket, new_path) + return True + return False +",oz/aws_cdn/__init__.py,"ReplaceText(target='not ' @(176,22)->(176,22))","class S3File(CDNFile): + + def copy(self, new_path, replace=False): + """"""Uses boto to copy the file to the new path instead of uploading another file to the new key"""""" + if replace or get_file(new_path).exists(): + self.key.copy(self.key.bucket, new_path) + return True + return False","class S3File(CDNFile): + + def copy(self, new_path, replace=False): + """"""Uses boto to copy the file to the new path instead of uploading another file to the new key"""""" + if replace or not get_file(new_path).exists(): + self.key.copy(self.key.bucket, new_path) + return True + return False" +79,https://:@github.com/juju/amulet.git,016bfab60aca89cbcb58e80f4103e371a77b06ba,"@@ -77,7 +77,7 @@ class Deployment(object): + pass # Copy the current parent directory to temp and deploy that + elif self.charm_name: + if charm_name == self.charm_name: +- charm = os.getcwd() ++ charm_branch = os.getcwd() + + self.services[service] = {'branch': charm_branch} + if units > 1: +",amulet/deployer.py,"ReplaceText(target='charm_branch' @(80,16)->(80,21))","class Deployment(object): + pass # Copy the current parent directory to temp and deploy that + elif self.charm_name: + if charm_name == self.charm_name: + charm = os.getcwd() + + self.services[service] = {'branch': charm_branch} + if units > 1:","class Deployment(object): + pass # Copy the current parent directory to temp and deploy that + elif self.charm_name: + if charm_name == self.charm_name: + charm_branch = os.getcwd() + + self.services[service] = {'branch': charm_branch} + if units > 1:" +80,https://:@github.com/gitpython-developers/gitdb.git,ca829e0b341dd5c3ae1408b24702f2c75db6ec73,"@@ -445,7 +445,7 @@ class DeltaApplyReader(LazyMixin): + + + #{ Configuration +- if not has_perf_mod: ++ if has_perf_mod: + _set_cache_ = _set_cache_brute_ + else: + _set_cache_ = _set_cache_too_slow_without_c +",stream.py,"ReplaceText(target='' @(448,4)->(448,8))","class DeltaApplyReader(LazyMixin): + + + #{ Configuration + if not has_perf_mod: + _set_cache_ = _set_cache_brute_ + else: + _set_cache_ = _set_cache_too_slow_without_c","class DeltaApplyReader(LazyMixin): + + + #{ Configuration + if has_perf_mod: + _set_cache_ = _set_cache_brute_ + else: + _set_cache_ = _set_cache_too_slow_without_c" +81,https://:@github.com/longld/peda.git,82fcb5a12c92c27fc5722772a84df47b996d3d03,"@@ -4746,7 +4746,7 @@ class PEDACmd(object): + + step = peda.intsize() + if not peda.is_address(address): # cannot determine address +- msg(""Invalid $SP address: 0x%x"" % sp, ""red"") ++ msg(""Invalid $SP address: 0x%x"" % address, ""red"") + return + for i in range(count): + if not peda.execute(""x/%sx 0x%x"" % (""g"" if step == 8 else ""w"", address + i*step)): +",peda.py,"ReplaceText(target='address' @(4749,46)->(4749,48))","class PEDACmd(object): + + step = peda.intsize() + if not peda.is_address(address): # cannot determine address + msg(""Invalid $SP address: 0x%x"" % sp, ""red"") + return + for i in range(count): + if not peda.execute(""x/%sx 0x%x"" % (""g"" if step == 8 else ""w"", address + i*step)):","class PEDACmd(object): + + step = peda.intsize() + if not peda.is_address(address): # cannot determine address + msg(""Invalid $SP address: 0x%x"" % address, ""red"") + return + for i in range(count): + if not peda.execute(""x/%sx 0x%x"" % (""g"" if step == 8 else ""w"", address + i*step)):" +82,https://:@github.com/TheGhouls/oct.git,1f9ea29181962353fe0ea275cb4ba4ec9ae93142,"@@ -18,7 +18,7 @@ class Report(object): + self.set_statics() + + def set_statics(self): +- if os.path.exists(self.results_dir): ++ if not os.path.exists(self.results_dir): + return + try: + shutil.copytree(os.path.join(self.templates_dir, 'css'), os.path.join(self.results_dir, 'css')) +",oct/results/reportwriter.py,"ReplaceText(target='not ' @(21,11)->(21,11))","class Report(object): + self.set_statics() + + def set_statics(self): + if os.path.exists(self.results_dir): + return + try: + shutil.copytree(os.path.join(self.templates_dir, 'css'), os.path.join(self.results_dir, 'css'))","class Report(object): + self.set_statics() + + def set_statics(self): + if not os.path.exists(self.results_dir): + return + try: + shutil.copytree(os.path.join(self.templates_dir, 'css'), os.path.join(self.results_dir, 'css'))" +83,https://:@github.com/ASPP/pelita.git,bee6872dbd95a1e526305ef39f42ac537fd2f708,"@@ -105,7 +105,7 @@ def create_maze(layout_mesh): + Mesh of lists of MazeComponents + + """""" +- maze_mesh = Mesh(layout_mesh.height, layout_mesh.width, ++ maze_mesh = Mesh(layout_mesh.width, layout_mesh.height, + data=[[] for i in range(len(layout_mesh))]) + for index in maze_mesh.iterkeys(): + if layout_mesh[index] == CTFUniverse.wall: +",pelita/universe.py,"ArgSwap(idxs=0<->1 @(108,16)->(108,20))","def create_maze(layout_mesh): + Mesh of lists of MazeComponents + + """""" + maze_mesh = Mesh(layout_mesh.height, layout_mesh.width, + data=[[] for i in range(len(layout_mesh))]) + for index in maze_mesh.iterkeys(): + if layout_mesh[index] == CTFUniverse.wall:","def create_maze(layout_mesh): + Mesh of lists of MazeComponents + + """""" + maze_mesh = Mesh(layout_mesh.width, layout_mesh.height, + data=[[] for i in range(len(layout_mesh))]) + for index in maze_mesh.iterkeys(): + if layout_mesh[index] == CTFUniverse.wall:" +84,https://:@github.com/ASPP/pelita.git,508cd180dce7b72ab248211c977c8525a9c023de,"@@ -31,7 +31,7 @@ def __init__(self, index, initial_pos, team, homezone, + + @property + def in_own_zone(self): +- return self.homezone[0] <= self.current_pos[1] <= self.homezone[1] ++ return self.homezone[0] <= self.current_pos[0] <= self.homezone[1] + + def move(self, new_pos): + self.current_pos = new_pos +",pelita/universe.py,"ReplaceText(target='0' @(34,52)->(34,53))","def __init__(self, index, initial_pos, team, homezone, + + @property + def in_own_zone(self): + return self.homezone[0] <= self.current_pos[1] <= self.homezone[1] + + def move(self, new_pos): + self.current_pos = new_pos","def __init__(self, index, initial_pos, team, homezone, + + @property + def in_own_zone(self): + return self.homezone[0] <= self.current_pos[0] <= self.homezone[1] + + def move(self, new_pos): + self.current_pos = new_pos" +85,https://:@github.com/ASPP/pelita.git,6b76e416da2dc0d18224e47d7b176dad967e15b2,"@@ -182,7 +182,7 @@ def a_star(self, initial, target): + else: + seen.append(current) + for pos in self.adjacency[current]: +- heapq.heappush(to_visit, (datamodel.manhattan_dist(current, pos), (pos))) ++ heapq.heappush(to_visit, (datamodel.manhattan_dist(target, pos), (pos))) + + # Now back-track using seen to determine how we got here. + # Initialise the path with current node, i.e. position of food. +",pelita/game_master.py,"ReplaceText(target='target' @(185,71)->(185,78))","def a_star(self, initial, target): + else: + seen.append(current) + for pos in self.adjacency[current]: + heapq.heappush(to_visit, (datamodel.manhattan_dist(current, pos), (pos))) + + # Now back-track using seen to determine how we got here. + # Initialise the path with current node, i.e. position of food.","def a_star(self, initial, target): + else: + seen.append(current) + for pos in self.adjacency[current]: + heapq.heappush(to_visit, (datamodel.manhattan_dist(target, pos), (pos))) + + # Now back-track using seen to determine how we got here. + # Initialise the path with current node, i.e. position of food." +86,https://:@github.com/ASPP/pelita.git,fa2505d44ae3d3724f7fa979c0167f03bf7424f7,"@@ -136,7 +136,7 @@ def play(self): + if self.universe.teams[0].score < self.universe.teams[1].score: + events.append(datamodel.TeamWins(1)) + elif self.universe.teams[0].score > self.universe.teams[1].score: +- events.append(datamodel.TeamWins(1)) ++ events.append(datamodel.TeamWins(0)) + else: + events.append(datamodel.GameDraw()) + self.send_to_viewers(round_index, None, events) +",pelita/game_master.py,"ReplaceText(target='0' @(139,45)->(139,46))","def play(self): + if self.universe.teams[0].score < self.universe.teams[1].score: + events.append(datamodel.TeamWins(1)) + elif self.universe.teams[0].score > self.universe.teams[1].score: + events.append(datamodel.TeamWins(1)) + else: + events.append(datamodel.GameDraw()) + self.send_to_viewers(round_index, None, events)","def play(self): + if self.universe.teams[0].score < self.universe.teams[1].score: + events.append(datamodel.TeamWins(1)) + elif self.universe.teams[0].score > self.universe.teams[1].score: + events.append(datamodel.TeamWins(0)) + else: + events.append(datamodel.GameDraw()) + self.send_to_viewers(round_index, None, events)" +87,https://:@github.com/ASPP/pelita.git,4044f845e54c2077d6896010c25fcc123fc10203,"@@ -78,7 +78,7 @@ def test_equal_positions(self): + layout = create_layout(layout_str) + assert layout.bots == [(1, 1), (1, 1)] + assert layout.enemy == [(1, 1), (1, 1)] +- setup_test_game(layout=layout) ++ setup_test_game(layout=layout_str) + + def test_define_after(self): + layout = create_layout(self.layout, food=[(1, 1)], bots=[None, None], enemy=None) +",test/test_team.py,"ReplaceText(target='layout_str' @(81,31)->(81,37))","def test_equal_positions(self): + layout = create_layout(layout_str) + assert layout.bots == [(1, 1), (1, 1)] + assert layout.enemy == [(1, 1), (1, 1)] + setup_test_game(layout=layout) + + def test_define_after(self): + layout = create_layout(self.layout, food=[(1, 1)], bots=[None, None], enemy=None)","def test_equal_positions(self): + layout = create_layout(layout_str) + assert layout.bots == [(1, 1), (1, 1)] + assert layout.enemy == [(1, 1), (1, 1)] + setup_test_game(layout=layout_str) + + def test_define_after(self): + layout = create_layout(self.layout, food=[(1, 1)], bots=[None, None], enemy=None)" +88,https://:@github.com/ASPP/pelita.git,6fd0a9d2af44c491c1cc6774c3a169e97e2040be,"@@ -398,7 +398,7 @@ def _team(self): + @property + def turn(self): + """""" The turn of our bot. """""" +- return self.bot_index // 2 ++ return self.bot_index % 2 + + @property + def other(self): +",pelita/player/team.py,"ReplaceText(target='%' @(401,30)->(401,32))","def _team(self): + @property + def turn(self): + """""" The turn of our bot. """""" + return self.bot_index // 2 + + @property + def other(self):","def _team(self): + @property + def turn(self): + """""" The turn of our bot. """""" + return self.bot_index % 2 + + @property + def other(self):" +89,https://:@github.com/iotaledger/ccurl.interface.py.git,eb7f9190d24995d3f8d03a8350382ab6045a6e67,"@@ -44,7 +44,7 @@ gta = api.get_transactions_to_approve(depth=3) # get tips to be approved by your + + mwm = 14 # target is mainnet + +-bundle = entangled_interface.local_attach_to_tangle(pb, gta['trunkTransaction'], gta['branchTransaction'], mwm) ++bundle = entangled_interface.local_attach_to_tangle(pb, gta['branchTransaction'],gta['trunkTransaction'], mwm) + + bundle_trytes = [ x.as_tryte_string() for x in pb._transactions ] + +",examples/with_entangled.py,"ArgSwap(idxs=1<->2 @(47,9)->(47,51))","gta = api.get_transactions_to_approve(depth=3) # get tips to be approved by your + + mwm = 14 # target is mainnet + + bundle = entangled_interface.local_attach_to_tangle(pb, gta['trunkTransaction'], gta['branchTransaction'], mwm) + + bundle_trytes = [ x.as_tryte_string() for x in pb._transactions ] + ","gta = api.get_transactions_to_approve(depth=3) # get tips to be approved by your + + mwm = 14 # target is mainnet + + bundle = entangled_interface.local_attach_to_tangle(pb, gta['branchTransaction'],gta['trunkTransaction'], mwm) + + bundle_trytes = [ x.as_tryte_string() for x in pb._transactions ] + " +90,https://:@github.com/softlayer/softlayer-python.git,53731de7e51d31475cc224aceb0f3ff7217cdafd,"@@ -153,7 +153,7 @@ class NetworkManager(object): + ('privateResidenceFlag', private_residence), + ('state', state), + ('postalCode', postal_code)]: +- if key is not None: ++ if value is not None: + update[key] = value + + # If there's anything to update, update it +",SoftLayer/managers/network.py,"ReplaceText(target='value' @(156,15)->(156,18))","class NetworkManager(object): + ('privateResidenceFlag', private_residence), + ('state', state), + ('postalCode', postal_code)]: + if key is not None: + update[key] = value + + # If there's anything to update, update it","class NetworkManager(object): + ('privateResidenceFlag', private_residence), + ('state', state), + ('postalCode', postal_code)]: + if value is not None: + update[key] = value + + # If there's anything to update, update it" +91,https://:@github.com/softlayer/softlayer-python.git,dcf66e15711e47c594f20ffac7605bfc6d1a8746,"@@ -15,7 +15,7 @@ import click + type=click.Choice(['vs', 'vlan', 'server']), + help='Firewall type', + required=True) +-@click.option('--high-availability', '--ha', ++@click.option('--ha', '--high-availability', + is_flag=True, + help='High available firewall option') + @environment.pass_env +",SoftLayer/CLI/firewall/add.py,"ArgSwap(idxs=0<->1 @(18,1)->(18,13))","import click + type=click.Choice(['vs', 'vlan', 'server']), + help='Firewall type', + required=True) + @click.option('--high-availability', '--ha', + is_flag=True, + help='High available firewall option') + @environment.pass_env","import click + type=click.Choice(['vs', 'vlan', 'server']), + help='Firewall type', + required=True) + @click.option('--ha', '--high-availability', + is_flag=True, + help='High available firewall option') + @environment.pass_env" +92,https://:@github.com/softlayer/softlayer-python.git,f0840e302d486d6002a14419bbde85c1deedaf6a,"@@ -271,7 +271,7 @@ class BlockStorageManager(utils.IdentifierMixin, object): + package, + 'performance_storage_iscsi' + ), +- storage_utils.find_performance_space_price(package, iops), ++ storage_utils.find_performance_space_price(package, size), + storage_utils.find_performance_iops_price(package, size, iops), + ] + elif storage_type == 'storage_service_enterprise': +",SoftLayer/managers/block.py,"ReplaceText(target='size' @(274,68)->(274,72))","class BlockStorageManager(utils.IdentifierMixin, object): + package, + 'performance_storage_iscsi' + ), + storage_utils.find_performance_space_price(package, iops), + storage_utils.find_performance_iops_price(package, size, iops), + ] + elif storage_type == 'storage_service_enterprise':","class BlockStorageManager(utils.IdentifierMixin, object): + package, + 'performance_storage_iscsi' + ), + storage_utils.find_performance_space_price(package, size), + storage_utils.find_performance_iops_price(package, size, iops), + ] + elif storage_type == 'storage_service_enterprise':" +93,https://:@github.com/softlayer/softlayer-python.git,4418057fc0e3632aba2d89b6e42494c79cadd16a,"@@ -367,7 +367,7 @@ class VSManager(utils.IdentifierMixin, object): + if datacenter: + data[""datacenter""] = {""name"": datacenter} + +- if private_vlan and public_vlan: ++ if private_vlan or public_vlan: + network_components = self._create_network_components(public_vlan, private_vlan, + private_subnet, public_subnet) + data.update(network_components) +",SoftLayer/managers/vs.py,"ReplaceText(target='or' @(370,24)->(370,27))","class VSManager(utils.IdentifierMixin, object): + if datacenter: + data[""datacenter""] = {""name"": datacenter} + + if private_vlan and public_vlan: + network_components = self._create_network_components(public_vlan, private_vlan, + private_subnet, public_subnet) + data.update(network_components)","class VSManager(utils.IdentifierMixin, object): + if datacenter: + data[""datacenter""] = {""name"": datacenter} + + if private_vlan or public_vlan: + network_components = self._create_network_components(public_vlan, private_vlan, + private_subnet, public_subnet) + data.update(network_components)" +94,https://:@github.com/softlayer/softlayer-python.git,58b27c6bf5400a717acd00b7866964ef11f36e59,"@@ -87,6 +87,6 @@ def cli(env, identifier): + for guest in guests: + real_guest = guest.get('virtualGuest') + member_table.add_row([ +- guest.get('id'), real_guest.get('hostname'), utils.clean_time(real_guest.get('provisionDate')) ++ real_guest.get('id'), real_guest.get('hostname'), utils.clean_time(real_guest.get('provisionDate')) + ]) + env.fout(member_table) +",SoftLayer/CLI/autoscale/detail.py,"ReplaceText(target='real_guest' @(90,12)->(90,17))","def cli(env, identifier): + for guest in guests: + real_guest = guest.get('virtualGuest') + member_table.add_row([ + guest.get('id'), real_guest.get('hostname'), utils.clean_time(real_guest.get('provisionDate')) + ]) + env.fout(member_table)","def cli(env, identifier): + for guest in guests: + real_guest = guest.get('virtualGuest') + member_table.add_row([ + real_guest.get('id'), real_guest.get('hostname'), utils.clean_time(real_guest.get('provisionDate')) + ]) + env.fout(member_table)" +95,https://:@github.com/data-8/datascience.git,fd9aceb598290fb89a0f3131c3fb39dde18ef543,"@@ -446,7 +446,7 @@ class Table(collections.abc.Mapping): + count | points + 9 | 10 + """""" +- percentiles = [percentile(self[column_name], p) for column_name in self] ++ percentiles = [percentile(p, self[column_name]) for column_name in self] + return Table(percentiles, self.column_labels) + ################## + # Export/Display # +",datascience/tables.py,"ArgSwap(idxs=0<->1 @(449,23)->(449,33))","class Table(collections.abc.Mapping): + count | points + 9 | 10 + """""" + percentiles = [percentile(self[column_name], p) for column_name in self] + return Table(percentiles, self.column_labels) + ################## + # Export/Display #","class Table(collections.abc.Mapping): + count | points + 9 | 10 + """""" + percentiles = [percentile(p, self[column_name]) for column_name in self] + return Table(percentiles, self.column_labels) + ################## + # Export/Display #" +96,https://:@github.com/data-8/datascience.git,084450f127ecc490b887cad82fa43cda5f9b32fe,"@@ -2255,7 +2255,7 @@ class Table(collections.abc.MutableMapping): + space_count[labels[i]] += 1 + return updated_labels + return labels +- yticks = make_unique_labels(labels) ++ yticks = make_unique_labels(yticks) + + print(""yticks: "" + str(yticks)) + print(""ylabel: "" + str(ylabel)) +",datascience/tables.py,"ReplaceText(target='yticks' @(2258,36)->(2258,42))","class Table(collections.abc.MutableMapping): + space_count[labels[i]] += 1 + return updated_labels + return labels + yticks = make_unique_labels(labels) + + print(""yticks: "" + str(yticks)) + print(""ylabel: "" + str(ylabel))","class Table(collections.abc.MutableMapping): + space_count[labels[i]] += 1 + return updated_labels + return labels + yticks = make_unique_labels(yticks) + + print(""yticks: "" + str(yticks)) + print(""ylabel: "" + str(ylabel))" +97,https://:@github.com/dnaeon/py-vpoller.git,81769f6f8d9cb0dfc8cbc39a44027afa7d459636,"@@ -51,6 +51,6 @@ def task(name, required=None): + result = {'success': 1, 'msg': e.message} + finally: + return result +- registry.register(name=name, fn=fn, required=required) ++ registry.register(name=name, fn=wrapper, required=required) + return wrapper + return decorator +",src/vpoller/decorators.py,"ReplaceText(target='wrapper' @(54,40)->(54,42))","def task(name, required=None): + result = {'success': 1, 'msg': e.message} + finally: + return result + registry.register(name=name, fn=fn, required=required) + return wrapper + return decorator","def task(name, required=None): + result = {'success': 1, 'msg': e.message} + finally: + return result + registry.register(name=name, fn=wrapper, required=required) + return wrapper + return decorator" +98,https://:@github.com/enthought/qt_binder.git,68381b406035f2ce9666cb8ef1ab2e8e57cf8bf8,"@@ -58,4 +58,4 @@ else: + loader = RecordingUiLoader() + ui = loader.load(path) + +- return ui, ui.to_be_bound() ++ return ui, loader.to_be_bound() +",qt_binder/qt/ui_loader.py,"ReplaceText(target='loader' @(61,19)->(61,21))","else: + loader = RecordingUiLoader() + ui = loader.load(path) + + return ui, ui.to_be_bound()","else: + loader = RecordingUiLoader() + ui = loader.load(path) + + return ui, loader.to_be_bound()" +99,https://:@github.com/ggozad/behaving.git,1bc546aa03f9d42ff78a0a79e0894e488edc9add,"@@ -40,7 +40,7 @@ def should_receive_email(context, address): + def click_link_in_email(context, address): + mails = context.mail.user_messages(address) + assert mails, u'message not found' +- mail = email.message_from_string(mails[-1]) ++ mail = email.message_from_string(mails[0]) + links = URL_RE.findall(str(mail).replace('=\n', '')) + assert links, u'link not found' + url = links[0] +",src/behaving/mail/steps.py,"ReplaceText(target='0' @(43,43)->(43,45))","def should_receive_email(context, address): + def click_link_in_email(context, address): + mails = context.mail.user_messages(address) + assert mails, u'message not found' + mail = email.message_from_string(mails[-1]) + links = URL_RE.findall(str(mail).replace('=\n', '')) + assert links, u'link not found' + url = links[0]","def should_receive_email(context, address): + def click_link_in_email(context, address): + mails = context.mail.user_messages(address) + assert mails, u'message not found' + mail = email.message_from_string(mails[0]) + links = URL_RE.findall(str(mail).replace('=\n', '')) + assert links, u'link not found' + url = links[0]" +100,https://:@github.com/allenai/SciSpaCy.git,d0d1d525943e051762ea5482ba82c9a4718285c0,"@@ -58,7 +58,7 @@ def train_parser_and_tagger(train_json_path: str, + parser = nlp.get_pipe('parser') + + train_corpus = GoldCorpus(train_json_path, dev_json_path) +- test_corpus = GoldCorpus(train_json_path, dev_json_path) ++ test_corpus = GoldCorpus(train_json_path, test_json_path) + + if ontonotes_path: + onto_train_path = os.path.join(ontonotes_path, ""train"") +",scripts/train_parser_and_tagger.py,"ReplaceText(target='test_json_path' @(61,46)->(61,59))","def train_parser_and_tagger(train_json_path: str, + parser = nlp.get_pipe('parser') + + train_corpus = GoldCorpus(train_json_path, dev_json_path) + test_corpus = GoldCorpus(train_json_path, dev_json_path) + + if ontonotes_path: + onto_train_path = os.path.join(ontonotes_path, ""train"")","def train_parser_and_tagger(train_json_path: str, + parser = nlp.get_pipe('parser') + + train_corpus = GoldCorpus(train_json_path, dev_json_path) + test_corpus = GoldCorpus(train_json_path, test_json_path) + + if ontonotes_path: + onto_train_path = os.path.join(ontonotes_path, ""train"")" +101,https://:@github.com/allenai/SciSpaCy.git,e15e9b7913459b6139d4f30030a502f30479cfd5,"@@ -190,7 +190,7 @@ def train_parser_and_tagger(train_json_path: str, + print(""Token acc:"", scorer_onto_retrained.token_acc) + + with open(os.path.join(model_output_dir, ""ontonotes_test.json"")) as metric_file: +- json.dump(scorer.scores, metric_file) ++ json.dump(scorer_onto_retrained.scores, metric_file) + if __name__ == ""__main__"": + parser = argparse.ArgumentParser() + +",scripts/train_parser_and_tagger.py,"ReplaceText(target='scorer_onto_retrained' @(193,22)->(193,28))","def train_parser_and_tagger(train_json_path: str, + print(""Token acc:"", scorer_onto_retrained.token_acc) + + with open(os.path.join(model_output_dir, ""ontonotes_test.json"")) as metric_file: + json.dump(scorer.scores, metric_file) + if __name__ == ""__main__"": + parser = argparse.ArgumentParser() + ","def train_parser_and_tagger(train_json_path: str, + print(""Token acc:"", scorer_onto_retrained.token_acc) + + with open(os.path.join(model_output_dir, ""ontonotes_test.json"")) as metric_file: + json.dump(scorer_onto_retrained.scores, metric_file) + if __name__ == ""__main__"": + parser = argparse.ArgumentParser() + " +102,https://:@github.com/allenai/SciSpaCy.git,47400cbed4d4943f6bba7ed013bf80110f738f2e,"@@ -679,7 +679,7 @@ def eval_candidate_generation_and_linking(examples: List[data_util.MedMentionExa + if generate_linking_classifier_training_data: + for candidates, mention_types_for_mention in zip(candidates_by_mention, mention_types_by_mention): + for candidate_id, candidate in candidates.items(): +- classifier_example = linker.classifier_example(candidate_id, candidate, mention_text, mention_types) ++ classifier_example = linker.classifier_example(candidate_id, candidate, mention_text, mention_types_for_mention) + classifier_example['label'] = int(gold_entity.umls_id == candidate_id) + linking_classifier_training_data.append(classifier_example) + +",scripts/linking.py,"ReplaceText(target='mention_types_for_mention' @(682,118)->(682,131))","def eval_candidate_generation_and_linking(examples: List[data_util.MedMentionExa + if generate_linking_classifier_training_data: + for candidates, mention_types_for_mention in zip(candidates_by_mention, mention_types_by_mention): + for candidate_id, candidate in candidates.items(): + classifier_example = linker.classifier_example(candidate_id, candidate, mention_text, mention_types) + classifier_example['label'] = int(gold_entity.umls_id == candidate_id) + linking_classifier_training_data.append(classifier_example) + ","def eval_candidate_generation_and_linking(examples: List[data_util.MedMentionExa + if generate_linking_classifier_training_data: + for candidates, mention_types_for_mention in zip(candidates_by_mention, mention_types_by_mention): + for candidate_id, candidate in candidates.items(): + classifier_example = linker.classifier_example(candidate_id, candidate, mention_text, mention_types_for_mention) + classifier_example['label'] = int(gold_entity.umls_id == candidate_id) + linking_classifier_training_data.append(classifier_example) + " +103,https://:@github.com/Burnysc2/python-sc2.git,c3f5b0de304727914a2a59d5cfde6dda04071686,"@@ -381,7 +381,7 @@ class BotAI(object): + return ActionResult.CantFindPlacementLocation + + unit = unit or self.select_build_worker(p) +- if unit is None or self.can_afford(building): ++ if unit is None or not self.can_afford(building): + return ActionResult.Error + return await self.do(unit.build(building, p)) + +",sc2/bot_ai.py,"ReplaceText(target='not ' @(384,27)->(384,27))","class BotAI(object): + return ActionResult.CantFindPlacementLocation + + unit = unit or self.select_build_worker(p) + if unit is None or self.can_afford(building): + return ActionResult.Error + return await self.do(unit.build(building, p)) + ","class BotAI(object): + return ActionResult.CantFindPlacementLocation + + unit = unit or self.select_build_worker(p) + if unit is None or not self.can_afford(building): + return ActionResult.Error + return await self.do(unit.build(building, p)) + " +104,https://:@github.com/Burnysc2/python-sc2.git,20468d57d6fd5cc80c9e7757d75e987bd81e632a,"@@ -185,7 +185,7 @@ class Point2(Pointlike): + Used in ramp finding """""" + assert self != p + distanceBetweenPoints = self.distance_to(p) +- assert r > distanceBetweenPoints / 2 ++ assert r >= distanceBetweenPoints / 2 + # remaining distance from center towards the intersection, using pythagoras + remainingDistanceFromCenter = (r ** 2 - (distanceBetweenPoints / 2) ** 2) ** 0.5 + # center of both points +",sc2/position.py,"ReplaceText(target='>=' @(188,17)->(188,18))","class Point2(Pointlike): + Used in ramp finding """""" + assert self != p + distanceBetweenPoints = self.distance_to(p) + assert r > distanceBetweenPoints / 2 + # remaining distance from center towards the intersection, using pythagoras + remainingDistanceFromCenter = (r ** 2 - (distanceBetweenPoints / 2) ** 2) ** 0.5 + # center of both points","class Point2(Pointlike): + Used in ramp finding """""" + assert self != p + distanceBetweenPoints = self.distance_to(p) + assert r >= distanceBetweenPoints / 2 + # remaining distance from center towards the intersection, using pythagoras + remainingDistanceFromCenter = (r ** 2 - (distanceBetweenPoints / 2) ** 2) ** 0.5 + # center of both points" +105,https://:@github.com/Burnysc2/python-sc2.git,9470180d3caaa18098ebffea220719ad6083afbe,"@@ -185,7 +185,7 @@ class Point2(Pointlike): + Used in ramp finding """""" + assert self != p + distanceBetweenPoints = self.distance_to(p) +- assert r > distanceBetweenPoints / 2 ++ assert r >= distanceBetweenPoints / 2 + # remaining distance from center towards the intersection, using pythagoras + remainingDistanceFromCenter = (r ** 2 - (distanceBetweenPoints / 2) ** 2) ** 0.5 + # center of both points +",sc2/position.py,"ReplaceText(target='>=' @(188,17)->(188,18))","class Point2(Pointlike): + Used in ramp finding """""" + assert self != p + distanceBetweenPoints = self.distance_to(p) + assert r > distanceBetweenPoints / 2 + # remaining distance from center towards the intersection, using pythagoras + remainingDistanceFromCenter = (r ** 2 - (distanceBetweenPoints / 2) ** 2) ** 0.5 + # center of both points","class Point2(Pointlike): + Used in ramp finding """""" + assert self != p + distanceBetweenPoints = self.distance_to(p) + assert r >= distanceBetweenPoints / 2 + # remaining distance from center towards the intersection, using pythagoras + remainingDistanceFromCenter = (r ** 2 - (distanceBetweenPoints / 2) ** 2) ** 0.5 + # center of both points" +106,https://:@github.com/Burnysc2/python-sc2.git,9c59f42e1722e1141a51300d472b0385d64f1640,"@@ -86,7 +86,7 @@ class Units(list): + return self[0] + + def take(self, n: int) -> ""Units"": +- if self.amount >= n: ++ if self.amount <= n: + return self + else: + return self.subgroup(self[:n]) +",sc2/units.py,"ReplaceText(target='<=' @(89,23)->(89,25))","class Units(list): + return self[0] + + def take(self, n: int) -> ""Units"": + if self.amount >= n: + return self + else: + return self.subgroup(self[:n])","class Units(list): + return self[0] + + def take(self, n: int) -> ""Units"": + if self.amount <= n: + return self + else: + return self.subgroup(self[:n])" +107,https://:@github.com/kenjyco/beu.git,4aea6146fc5f01df3e344b9fadddf28b795dac89,"@@ -36,7 +36,7 @@ def _get_settings_file(): + if not os.path.exists(home_config_dir): + os.makedirs(home_config_dir) + copyfile(sample_file, settings_file) +- print('\nCopied settings to {}'.format(repr(home_config_dir))) ++ print('\nCopied settings to {}'.format(repr(settings_file))) + return settings_file + + +",beu/__init__.py,"ReplaceText(target='settings_file' @(39,48)->(39,63))","def _get_settings_file(): + if not os.path.exists(home_config_dir): + os.makedirs(home_config_dir) + copyfile(sample_file, settings_file) + print('\nCopied settings to {}'.format(repr(home_config_dir))) + return settings_file + + ","def _get_settings_file(): + if not os.path.exists(home_config_dir): + os.makedirs(home_config_dir) + copyfile(sample_file, settings_file) + print('\nCopied settings to {}'.format(repr(settings_file))) + return settings_file + + " +108,https://:@github.com/WattTime/pyiso.git,009316799f872c90f50b73e41f3a6f9021f8b2cc,"@@ -111,7 +111,7 @@ class BaseClient(object): + self.options.update(kwargs) + + # check start_at and end_at args +- if self.options.get('start_at', None) and self.options.get('end_at', None): ++ if self.options.get('start_at', None) or self.options.get('end_at', None): + assert self.options['start_at'] < self.options['end_at'] + self.options['start_at'] = self.utcify(self.options['start_at']) + self.options['end_at'] = self.utcify(self.options['end_at']) +",pyiso/base.py,"ReplaceText(target='or' @(114,46)->(114,49))","class BaseClient(object): + self.options.update(kwargs) + + # check start_at and end_at args + if self.options.get('start_at', None) and self.options.get('end_at', None): + assert self.options['start_at'] < self.options['end_at'] + self.options['start_at'] = self.utcify(self.options['start_at']) + self.options['end_at'] = self.utcify(self.options['end_at'])","class BaseClient(object): + self.options.update(kwargs) + + # check start_at and end_at args + if self.options.get('start_at', None) or self.options.get('end_at', None): + assert self.options['start_at'] < self.options['end_at'] + self.options['start_at'] = self.utcify(self.options['start_at']) + self.options['end_at'] = self.utcify(self.options['end_at'])" +109,https://:@github.com/WattTime/pyiso.git,31c2680f1e96d6affbbef6dc75b9ab3724a7d8b9,"@@ -117,7 +117,7 @@ class BaseClient(object): + self.options.update(kwargs) + + # check start_at and end_at args +- if self.options.get('start_at', None) or self.options.get('end_at', None): ++ if self.options.get('start_at', None) and self.options.get('end_at', None): + assert self.options['start_at'] < self.options['end_at'] + self.options['start_at'] = self.utcify(self.options['start_at']) + self.options['end_at'] = self.utcify(self.options['end_at']) +",pyiso/base.py,"ReplaceText(target='and' @(120,46)->(120,48))","class BaseClient(object): + self.options.update(kwargs) + + # check start_at and end_at args + if self.options.get('start_at', None) or self.options.get('end_at', None): + assert self.options['start_at'] < self.options['end_at'] + self.options['start_at'] = self.utcify(self.options['start_at']) + self.options['end_at'] = self.utcify(self.options['end_at'])","class BaseClient(object): + self.options.update(kwargs) + + # check start_at and end_at args + if self.options.get('start_at', None) and self.options.get('end_at', None): + assert self.options['start_at'] < self.options['end_at'] + self.options['start_at'] = self.utcify(self.options['start_at']) + self.options['end_at'] = self.utcify(self.options['end_at'])" +110,https://:@github.com/WattTime/pyiso.git,14fd34daa69230352ecb651ee8f30a4566ab6c59,"@@ -18,7 +18,7 @@ class TestGenerationTask(TestCase): + expected = client_factory(ba).get_generation(**kwargs) + received = tasks.get_generation(ba, **kwargs) + +- for i in range(len(expected)): ++ for i in range(len(received)): + if expected[i]['timestamp'] == received[i]['timestamp']: + self.assertEqual(expected[i]['gen_MW'], received[i]['gen_MW']) + self.assertEqual(expected[i]['fuel_name'], received[i]['fuel_name']) +",tests/test_tasks.py,"ReplaceText(target='received' @(21,27)->(21,35))","class TestGenerationTask(TestCase): + expected = client_factory(ba).get_generation(**kwargs) + received = tasks.get_generation(ba, **kwargs) + + for i in range(len(expected)): + if expected[i]['timestamp'] == received[i]['timestamp']: + self.assertEqual(expected[i]['gen_MW'], received[i]['gen_MW']) + self.assertEqual(expected[i]['fuel_name'], received[i]['fuel_name'])","class TestGenerationTask(TestCase): + expected = client_factory(ba).get_generation(**kwargs) + received = tasks.get_generation(ba, **kwargs) + + for i in range(len(received)): + if expected[i]['timestamp'] == received[i]['timestamp']: + self.assertEqual(expected[i]['gen_MW'], received[i]['gen_MW']) + self.assertEqual(expected[i]['fuel_name'], received[i]['fuel_name'])" +111,https://:@github.com/TTWShell/hobbit-core.git,b51217f7fc8cb238c1dc09e8932178cda40cf2b4,"@@ -133,4 +133,4 @@ class TestTransaction(BaseTest): + + with pytest.raises(Exception): + view_func2() +- assert len(User.query.all()) == 1 ++ assert len(User.query.all()) == 0 +",tests/test_db.py,"ReplaceText(target='0' @(136,40)->(136,41))","class TestTransaction(BaseTest): + + with pytest.raises(Exception): + view_func2() + assert len(User.query.all()) == 1","class TestTransaction(BaseTest): + + with pytest.raises(Exception): + view_func2() + assert len(User.query.all()) == 0" +112,https://:@github.com/ktdreyer/jenkins-job-wrecker.git,3be4ea2d49a46cec8223361142305107b88ca889,"@@ -162,7 +162,7 @@ def prebuildcleanup(top, parent): + pass + else: + raise NotImplementedError(""cannot handle "" +- ""XML %s"" % subelement.tag) ++ ""XML %s"" % element.tag) + + for rule in preclean_patterns: + if preclean_patterns[rule] is not None and len(preclean_patterns[rule]) > 0: +",jenkins_job_wrecker/modules/buildwrappers.py,"ReplaceText(target='element' @(165,49)->(165,59))","def prebuildcleanup(top, parent): + pass + else: + raise NotImplementedError(""cannot handle "" + ""XML %s"" % subelement.tag) + + for rule in preclean_patterns: + if preclean_patterns[rule] is not None and len(preclean_patterns[rule]) > 0:","def prebuildcleanup(top, parent): + pass + else: + raise NotImplementedError(""cannot handle "" + ""XML %s"" % element.tag) + + for rule in preclean_patterns: + if preclean_patterns[rule] is not None and len(preclean_patterns[rule]) > 0:" +113,https://:@github.com/Sage-Bionetworks/Genie.git,7a6ff590425d32fd596687bd0d35bc98680fc5b8,"@@ -379,7 +379,7 @@ class clinical(example_filetype_format.FileTypeFormat): + patient_patients = clinicalDF[patientId][clinicalDF[patientId] != """"] + # #CHECK: All samples must have associated patient data (GENIE requires patient data) + if not all(sample_patients.isin(patient_patients)): +- total_error += ""Sample: All samples must have associated patient information. These samples are missing patient data: %s\n"" % "", "".join(clinicalSampleDF[patientId][~clinicalSampleDF[patientId].isin(clinicalDF[patientId])]) ++ total_error += ""Sample: All samples must have associated patient information. These samples are missing patient data: %s\n"" % "", "".join(clinicalSampleDF[sampleId][~clinicalSampleDF[patientId].isin(clinicalDF[patientId])]) + #CHECK: All patients must have associated sample data + if not all(patient_patients.isin(sample_patients)): + ### MAKE WARNING FOR NOW### +",processing/clinical.py,"ReplaceText(target='sampleId' @(382,157)->(382,166))","class clinical(example_filetype_format.FileTypeFormat): + patient_patients = clinicalDF[patientId][clinicalDF[patientId] != """"] + # #CHECK: All samples must have associated patient data (GENIE requires patient data) + if not all(sample_patients.isin(patient_patients)): + total_error += ""Sample: All samples must have associated patient information. These samples are missing patient data: %s\n"" % "", "".join(clinicalSampleDF[patientId][~clinicalSampleDF[patientId].isin(clinicalDF[patientId])]) + #CHECK: All patients must have associated sample data + if not all(patient_patients.isin(sample_patients)): + ### MAKE WARNING FOR NOW###","class clinical(example_filetype_format.FileTypeFormat): + patient_patients = clinicalDF[patientId][clinicalDF[patientId] != """"] + # #CHECK: All samples must have associated patient data (GENIE requires patient data) + if not all(sample_patients.isin(patient_patients)): + total_error += ""Sample: All samples must have associated patient information. These samples are missing patient data: %s\n"" % "", "".join(clinicalSampleDF[sampleId][~clinicalSampleDF[patientId].isin(clinicalDF[patientId])]) + #CHECK: All patients must have associated sample data + if not all(patient_patients.isin(sample_patients)): + ### MAKE WARNING FOR NOW###" +114,https://:@github.com/Sage-Bionetworks/Genie.git,b5b670e4a5797ba2a66caa517bbe2160fec645f7,"@@ -209,7 +209,7 @@ def createMafDatabase(syn, databaseToSynIdMappingDf,testing=False,staging=False) + #Make sure to store the newly created maf db synid into the staging synapse mapping + databaseToSynIdMapping = syn.tableQuery(""SELECT * FROM syn12094210 where Database = 'vcf2maf'"") + databaseToSynIdMappingDf = databaseToSynIdMapping.asDataFrame() +- databaseToSynIdMapping['Id'][0] = newMafDb.id ++ databaseToSynIdMappingDf['Id'][0] = newMafDb.id + syn.store(synapseclient.Table(""syn12094210"",databaseToSynIdMappingDf)) + #Move and archive old mafdatabase + mafDatabaseEnt.parentId = ""syn7208886"" +",processing/input_to_database.py,"ReplaceText(target='databaseToSynIdMappingDf' @(212,2)->(212,24))","def createMafDatabase(syn, databaseToSynIdMappingDf,testing=False,staging=False) + #Make sure to store the newly created maf db synid into the staging synapse mapping + databaseToSynIdMapping = syn.tableQuery(""SELECT * FROM syn12094210 where Database = 'vcf2maf'"") + databaseToSynIdMappingDf = databaseToSynIdMapping.asDataFrame() + databaseToSynIdMapping['Id'][0] = newMafDb.id + syn.store(synapseclient.Table(""syn12094210"",databaseToSynIdMappingDf)) + #Move and archive old mafdatabase + mafDatabaseEnt.parentId = ""syn7208886""","def createMafDatabase(syn, databaseToSynIdMappingDf,testing=False,staging=False) + #Make sure to store the newly created maf db synid into the staging synapse mapping + databaseToSynIdMapping = syn.tableQuery(""SELECT * FROM syn12094210 where Database = 'vcf2maf'"") + databaseToSynIdMappingDf = databaseToSynIdMapping.asDataFrame() + databaseToSynIdMappingDf['Id'][0] = newMafDb.id + syn.store(synapseclient.Table(""syn12094210"",databaseToSynIdMappingDf)) + #Move and archive old mafdatabase + mafDatabaseEnt.parentId = ""syn7208886""" +115,https://:@github.com/Sage-Bionetworks/Genie.git,78fcacd10d4c44c90f41893a161de24ff13ea774,"@@ -311,7 +311,7 @@ class clinical(FileTypeFormat): + haveColumn = process_functions.checkColExist(clinicalDF, ""SEQ_ASSAY_ID"") + if haveColumn: + if not all([i != """" for i in clinicalDF['SEQ_ASSAY_ID']]): +- total_error += ""Sample: Please double check your SEQ_ASSAY_ID columns, there are empty rows.\n"" ++ warning += ""Sample: Please double check your SEQ_ASSAY_ID columns, there are empty rows.\n"" + #must remove empty seq assay ids first + #Checking if seq assay ids start with the center name + seqAssayIds = clinicalDF.SEQ_ASSAY_ID[clinicalDF.SEQ_ASSAY_ID != """"] +",genie/clinical.py,"ReplaceText(target='warning' @(314,4)->(314,15))","class clinical(FileTypeFormat): + haveColumn = process_functions.checkColExist(clinicalDF, ""SEQ_ASSAY_ID"") + if haveColumn: + if not all([i != """" for i in clinicalDF['SEQ_ASSAY_ID']]): + total_error += ""Sample: Please double check your SEQ_ASSAY_ID columns, there are empty rows.\n"" + #must remove empty seq assay ids first + #Checking if seq assay ids start with the center name + seqAssayIds = clinicalDF.SEQ_ASSAY_ID[clinicalDF.SEQ_ASSAY_ID != """"]","class clinical(FileTypeFormat): + haveColumn = process_functions.checkColExist(clinicalDF, ""SEQ_ASSAY_ID"") + if haveColumn: + if not all([i != """" for i in clinicalDF['SEQ_ASSAY_ID']]): + warning += ""Sample: Please double check your SEQ_ASSAY_ID columns, there are empty rows.\n"" + #must remove empty seq assay ids first + #Checking if seq assay ids start with the center name + seqAssayIds = clinicalDF.SEQ_ASSAY_ID[clinicalDF.SEQ_ASSAY_ID != """"]" +116,https://:@github.com/Sage-Bionetworks/Genie.git,e115f3884db224a231c87b346f04d6edbf66d6bb,"@@ -87,7 +87,7 @@ class vcf(maf.maf): + tumor = ""TUMOR"" + normal = ""NORMAL"" + # ### If the tumor name isn't TUMOR, set the sample id to be the tumor name +- if tumor != ""TUMOR"": ++ if tumor == ""TUMOR"": + tumorName = vcfName.replace("".vcf"","""") + else: + tumorName = tumor +",genie/vcf.py,"ReplaceText(target='==' @(90,12)->(90,14))","class vcf(maf.maf): + tumor = ""TUMOR"" + normal = ""NORMAL"" + # ### If the tumor name isn't TUMOR, set the sample id to be the tumor name + if tumor != ""TUMOR"": + tumorName = vcfName.replace("".vcf"","""") + else: + tumorName = tumor","class vcf(maf.maf): + tumor = ""TUMOR"" + normal = ""NORMAL"" + # ### If the tumor name isn't TUMOR, set the sample id to be the tumor name + if tumor == ""TUMOR"": + tumorName = vcfName.replace("".vcf"","""") + else: + tumorName = tumor" +117,https://:@github.com/Sage-Bionetworks/Genie.git,4c861c5eccebb0d0a402d85b658924df1e6a8819,"@@ -247,7 +247,7 @@ def validation(syn, center, process, center_mapping_df, databaseToSynIdMappingDf + duplicatedFiles = duplicatedFiles.append(cbsSegFiles) + clinical_bool = [""clinical"" in i for i in inputValidStatus['name']] + clinical_files = inputValidStatus[clinical_bool] +- if len(clinical_bool) > 2: ++ if len(clinical_files) > 2: + duplicatedFiles = duplicatedFiles.append(clinical_files) + + # nodups = [""data_mutations_extended""] +",genie/input_to_database.py,"ReplaceText(target='clinical_files' @(250,15)->(250,28))","def validation(syn, center, process, center_mapping_df, databaseToSynIdMappingDf + duplicatedFiles = duplicatedFiles.append(cbsSegFiles) + clinical_bool = [""clinical"" in i for i in inputValidStatus['name']] + clinical_files = inputValidStatus[clinical_bool] + if len(clinical_bool) > 2: + duplicatedFiles = duplicatedFiles.append(clinical_files) + + # nodups = [""data_mutations_extended""]","def validation(syn, center, process, center_mapping_df, databaseToSynIdMappingDf + duplicatedFiles = duplicatedFiles.append(cbsSegFiles) + clinical_bool = [""clinical"" in i for i in inputValidStatus['name']] + clinical_files = inputValidStatus[clinical_bool] + if len(clinical_files) > 2: + duplicatedFiles = duplicatedFiles.append(clinical_files) + + # nodups = [""data_mutations_extended""]" +118,https://:@github.com/Sage-Bionetworks/Genie.git,39f33cd754223ee515b8d790c0cd96b32f36b88e,"@@ -270,7 +270,7 @@ def validatefile(syn, entities, validation_status_table, error_tracker_table, + input_status_list, invalid_errors_list = _get_status_and_error_list( + valid, message, entities) + # Send email the first time the file is invalid +- if invalid_errors_list: ++ if not invalid_errors_list: + _send_validation_error_email(syn, filenames, message, file_users) + else: + input_status_list = [ +",genie/input_to_database.py,"ReplaceText(target='not ' @(273,11)->(273,11))","def validatefile(syn, entities, validation_status_table, error_tracker_table, + input_status_list, invalid_errors_list = _get_status_and_error_list( + valid, message, entities) + # Send email the first time the file is invalid + if invalid_errors_list: + _send_validation_error_email(syn, filenames, message, file_users) + else: + input_status_list = [","def validatefile(syn, entities, validation_status_table, error_tracker_table, + input_status_list, invalid_errors_list = _get_status_and_error_list( + valid, message, entities) + # Send email the first time the file is invalid + if not invalid_errors_list: + _send_validation_error_email(syn, filenames, message, file_users) + else: + input_status_list = [" +119,https://:@github.com/Sage-Bionetworks/Genie.git,e140dee708542afa35c5d1e30671d8083fcbcd29,"@@ -512,7 +512,7 @@ class bed(FileTypeFormat): + string: Path to new bed file + """""" + final_beddf = self._process(beddf, seq_assay_id, newPath, parentId) +- process_functions.updateData(self.syn, databaseSynId, beddf, ++ process_functions.updateData(self.syn, databaseSynId, final_beddf, + seq_assay_id, + filterByColumn=""SEQ_ASSAY_ID"", + toDelete=True) +",genie/bed.py,"ReplaceText(target='final_beddf' @(515,62)->(515,67))","class bed(FileTypeFormat): + string: Path to new bed file + """""" + final_beddf = self._process(beddf, seq_assay_id, newPath, parentId) + process_functions.updateData(self.syn, databaseSynId, beddf, + seq_assay_id, + filterByColumn=""SEQ_ASSAY_ID"", + toDelete=True)","class bed(FileTypeFormat): + string: Path to new bed file + """""" + final_beddf = self._process(beddf, seq_assay_id, newPath, parentId) + process_functions.updateData(self.syn, databaseSynId, final_beddf, + seq_assay_id, + filterByColumn=""SEQ_ASSAY_ID"", + toDelete=True)" +120,https://:@github.com/Libensemble/libensemble.git,a7175c6bf59803deb4a52aaf8c0185b93874ff21,"@@ -96,7 +96,7 @@ def decide_work_and_resources(active_w, idle_w, H, H_ind, sim_specs, gen_specs): + 'form_subcomm': [], + 'calc_in': H[sim_specs['in']][inds_to_send], + 'calc_out': sim_specs['out'], +- 'calc_info': {'type':'sim', 'pt_ids': q_inds}, ++ 'calc_info': {'type':'sim', 'pt_ids': inds_to_send}, + } + + update_history_x_out(H, q_inds, Work[i]['calc_in'], i, sim_specs['params']) +",code/src/libE_manager.py,"ReplaceText(target='inds_to_send' @(99,61)->(99,67))","def decide_work_and_resources(active_w, idle_w, H, H_ind, sim_specs, gen_specs): + 'form_subcomm': [], + 'calc_in': H[sim_specs['in']][inds_to_send], + 'calc_out': sim_specs['out'], + 'calc_info': {'type':'sim', 'pt_ids': q_inds}, + } + + update_history_x_out(H, q_inds, Work[i]['calc_in'], i, sim_specs['params'])","def decide_work_and_resources(active_w, idle_w, H, H_ind, sim_specs, gen_specs): + 'form_subcomm': [], + 'calc_in': H[sim_specs['in']][inds_to_send], + 'calc_out': sim_specs['out'], + 'calc_info': {'type':'sim', 'pt_ids': inds_to_send}, + } + + update_history_x_out(H, q_inds, Work[i]['calc_in'], i, sim_specs['params'])" +121,https://:@github.com/Libensemble/libensemble.git,ad5e021d040efd28a61d6afa2be908e25f363bd4,"@@ -52,7 +52,7 @@ def worker_main(c, sim_specs, gen_specs): + + if tag_out == STOP_TAG: break + +- comm.send(obj=data_out, dest=0, tag=calc_tag) ++ comm.send(obj=data_out, dest=0, tag=tag_out) + + # Clean up + for loc in locations.values(): +",code/src/libE_worker.py,"ReplaceText(target='tag_out' @(55,44)->(55,52))","def worker_main(c, sim_specs, gen_specs): + + if tag_out == STOP_TAG: break + + comm.send(obj=data_out, dest=0, tag=calc_tag) + + # Clean up + for loc in locations.values():","def worker_main(c, sim_specs, gen_specs): + + if tag_out == STOP_TAG: break + + comm.send(obj=data_out, dest=0, tag=tag_out) + + # Clean up + for loc in locations.values():" +122,https://:@github.com/Libensemble/libensemble.git,2b33970bdac3034cc7799c2849eae09f9c22fcf6,"@@ -40,7 +40,7 @@ class MPIComm(Comm): + def kill_pending(self): + ""Make sure pending requests are cancelled if the comm is killed."" + for req in self._outbox: +- if req.Test(): ++ if not req.Test(): + req.Cancel() + self._outbox = [] + +",libensemble/mpi_comms.py,"ReplaceText(target='not ' @(43,15)->(43,15))","class MPIComm(Comm): + def kill_pending(self): + ""Make sure pending requests are cancelled if the comm is killed."" + for req in self._outbox: + if req.Test(): + req.Cancel() + self._outbox = [] + ","class MPIComm(Comm): + def kill_pending(self): + ""Make sure pending requests are cancelled if the comm is killed."" + for req in self._outbox: + if not req.Test(): + req.Cancel() + self._outbox = [] + " +123,https://:@github.com/Libensemble/libensemble.git,155ba0c0517046e8ec305e76862bc6f0a44fafc7,"@@ -136,7 +136,7 @@ class EnvResources: + nidstr = splitstr[1].strip(""]"") + nidlst = EnvResources._noderange_append(prefix, nidstr) + else: # Multiple Partitions +- splitgroups = [str.split('[', 1) for str in splitstr] ++ splitgroups = [str.split('[', 1) for str in part_splitstr] + prefixgroups = [group[0] for group in splitgroups] + nodegroups = [group[1].strip(']') for group in splitgroups] + nidlst = [] +",libensemble/env_resources.py,"ReplaceText(target='part_splitstr' @(139,56)->(139,64))","class EnvResources: + nidstr = splitstr[1].strip(""]"") + nidlst = EnvResources._noderange_append(prefix, nidstr) + else: # Multiple Partitions + splitgroups = [str.split('[', 1) for str in splitstr] + prefixgroups = [group[0] for group in splitgroups] + nodegroups = [group[1].strip(']') for group in splitgroups] + nidlst = []","class EnvResources: + nidstr = splitstr[1].strip(""]"") + nidlst = EnvResources._noderange_append(prefix, nidstr) + else: # Multiple Partitions + splitgroups = [str.split('[', 1) for str in part_splitstr] + prefixgroups = [group[0] for group in splitgroups] + nodegroups = [group[1].strip(']') for group in splitgroups] + nidlst = []" +124,https://:@github.com/Libensemble/libensemble.git,c89e4f0b72361ba84884a3c691d73d8f62b98014,"@@ -108,7 +108,7 @@ def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + last_size = persis_info.get('last_size') + if len(H): + # Don't give gen instances in batch mode if points are unfinished +- if (gen_specs['user'].get('batch_mode') ++ if (alloc_specs['user'].get('batch_mode') + and not all(np.logical_or(H['returned'][last_size:], + H['paused'][last_size:]))): + break +",libensemble/alloc_funcs/fast_alloc_and_pausing.py,"ReplaceText(target='alloc_specs' @(111,20)->(111,29))","def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + last_size = persis_info.get('last_size') + if len(H): + # Don't give gen instances in batch mode if points are unfinished + if (gen_specs['user'].get('batch_mode') + and not all(np.logical_or(H['returned'][last_size:], + H['paused'][last_size:]))): + break","def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + last_size = persis_info.get('last_size') + if len(H): + # Don't give gen instances in batch mode if points are unfinished + if (alloc_specs['user'].get('batch_mode') + and not all(np.logical_or(H['returned'][last_size:], + H['paused'][last_size:]))): + break" +125,https://:@github.com/Libensemble/libensemble.git,c89e4f0b72361ba84884a3c691d73d8f62b98014,"@@ -33,7 +33,7 @@ def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + last_size = persis_info.get('last_size') + if len(H): + # Don't give gen instances in batch mode if points are unfinished +- if (gen_specs['user'].get('batch_mode') ++ if (alloc_specs['user'].get('batch_mode') + and not all(np.logical_or(H['returned'][last_size:], + H['paused'][last_size:]))): + break +",libensemble/alloc_funcs/fast_alloc_to_aposmm.py,"ReplaceText(target='alloc_specs' @(36,20)->(36,29))","def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + last_size = persis_info.get('last_size') + if len(H): + # Don't give gen instances in batch mode if points are unfinished + if (gen_specs['user'].get('batch_mode') + and not all(np.logical_or(H['returned'][last_size:], + H['paused'][last_size:]))): + break","def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + last_size = persis_info.get('last_size') + if len(H): + # Don't give gen instances in batch mode if points are unfinished + if (alloc_specs['user'].get('batch_mode') + and not all(np.logical_or(H['returned'][last_size:], + H['paused'][last_size:]))): + break" +126,https://:@github.com/Libensemble/libensemble.git,c89e4f0b72361ba84884a3c691d73d8f62b98014,"@@ -73,7 +73,7 @@ def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + + # No gen instances in batch mode if workers still working + still_working = ~H['returned'] +- if gen_specs['user'].get('batch_mode') and np.any(still_working): ++ if alloc_specs['user'].get('batch_mode') and np.any(still_working): + break + + # Give gen work +",libensemble/alloc_funcs/give_sim_work_first.py,"ReplaceText(target='alloc_specs' @(76,15)->(76,24))","def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + + # No gen instances in batch mode if workers still working + still_working = ~H['returned'] + if gen_specs['user'].get('batch_mode') and np.any(still_working): + break + + # Give gen work","def give_sim_work_first(W, H, sim_specs, gen_specs, alloc_specs, persis_info): + + # No gen instances in batch mode if workers still working + still_working = ~H['returned'] + if alloc_specs['user'].get('batch_mode') and np.any(still_working): + break + + # Give gen work" +127,https://:@github.com/Libensemble/libensemble.git,55f4a8f05ade4709b53cbe9ef92fe00a0e2e9a79,"@@ -59,7 +59,7 @@ def try_and_run_nlopt(H, gen_specs, libE_info): + gen_specs['user']['ub'], gen_specs['user']['lb'], local=True, active=True) + tag, Work, calc_in = sendrecv_mgr_worker_msg(comm, H_o) + if tag in [STOP_TAG, PERSIS_STOP]: +- nlopt.forced_stop.message = 'tag=' + str(tag) ++ nlopt.forced_stop.message = 'tag=' + str(Work) + raise nlopt.forced_stop + + # Return function value (and maybe gradient) +",libensemble/gen_funcs/uniform_or_localopt.py,"ReplaceText(target='Work' @(62,53)->(62,56))","def try_and_run_nlopt(H, gen_specs, libE_info): + gen_specs['user']['ub'], gen_specs['user']['lb'], local=True, active=True) + tag, Work, calc_in = sendrecv_mgr_worker_msg(comm, H_o) + if tag in [STOP_TAG, PERSIS_STOP]: + nlopt.forced_stop.message = 'tag=' + str(tag) + raise nlopt.forced_stop + + # Return function value (and maybe gradient)","def try_and_run_nlopt(H, gen_specs, libE_info): + gen_specs['user']['ub'], gen_specs['user']['lb'], local=True, active=True) + tag, Work, calc_in = sendrecv_mgr_worker_msg(comm, H_o) + if tag in [STOP_TAG, PERSIS_STOP]: + nlopt.forced_stop.message = 'tag=' + str(Work) + raise nlopt.forced_stop + + # Return function value (and maybe gradient)" +128,https://:@github.com/Libensemble/libensemble.git,c090514bb370c6960db4c8be2ae643534def8d2b,"@@ -24,4 +24,4 @@ def persistent_uniform(H, persis_info, gen_specs, libE_info): + H_o['x'] = persis_info['rand_stream'].uniform(lb, ub, (b, n)) + tag, Work, calc_in = sendrecv_mgr_worker_msg(libE_info['comm'], H_o) + +- return H_o, persis_info, tag ++ return H_o, persis_info, Work +",libensemble/gen_funcs/persistent_uniform_sampling.py,"ReplaceText(target='Work' @(27,29)->(27,32))","def persistent_uniform(H, persis_info, gen_specs, libE_info): + H_o['x'] = persis_info['rand_stream'].uniform(lb, ub, (b, n)) + tag, Work, calc_in = sendrecv_mgr_worker_msg(libE_info['comm'], H_o) + + return H_o, persis_info, tag","def persistent_uniform(H, persis_info, gen_specs, libE_info): + H_o['x'] = persis_info['rand_stream'].uniform(lb, ub, (b, n)) + tag, Work, calc_in = sendrecv_mgr_worker_msg(libE_info['comm'], H_o) + + return H_o, persis_info, Work" +129,https://:@github.com/davedittrich/python_secrets.git,3a477f63bb9d0417e63254ba993025a8666c3e1d,"@@ -181,7 +181,7 @@ class PythonSecretsApp(App): + self.environment = self.options.environment + self.secrets_basedir = self.options.secrets_basedir + # Don't output error messages when ""complete"" command used +- if cmd.cmd_name == 'complete': ++ if cmd.cmd_name != 'complete': + SecretsEnvironment.permissions_check( + self.secrets_basedir, + verbose_level=self.options.verbose_level, +",psec/main.py,"ReplaceText(target='!=' @(184,24)->(184,26))","class PythonSecretsApp(App): + self.environment = self.options.environment + self.secrets_basedir = self.options.secrets_basedir + # Don't output error messages when ""complete"" command used + if cmd.cmd_name == 'complete': + SecretsEnvironment.permissions_check( + self.secrets_basedir, + verbose_level=self.options.verbose_level,","class PythonSecretsApp(App): + self.environment = self.options.environment + self.secrets_basedir = self.options.secrets_basedir + # Don't output error messages when ""complete"" command used + if cmd.cmd_name != 'complete': + SecretsEnvironment.permissions_check( + self.secrets_basedir, + verbose_level=self.options.verbose_level," +130,https://:@github.com/junzis/pyModeS.git,b2940af6efe4cb6d99bca8a1f1f214292acf3e6a,"@@ -79,7 +79,7 @@ def cpr2position(cprlat0, cprlat1, cprlon0, cprlon1, t0, t1): + cprlat_even = cprlat0 / 131072.0 + cprlat_odd = cprlat1 / 131072.0 + cprlon_even = cprlon0 / 131072.0 +- cprlon_odd = cprlon0 / 131072.0 ++ cprlon_odd = cprlon1 / 131072.0 + + air_d_lat_even = 360.0 / 60 + air_d_lat_odd = 360.0 / 59 +",decoder.py,"ReplaceText(target='cprlon1' @(82,18)->(82,25))","def cpr2position(cprlat0, cprlat1, cprlon0, cprlon1, t0, t1): + cprlat_even = cprlat0 / 131072.0 + cprlat_odd = cprlat1 / 131072.0 + cprlon_even = cprlon0 / 131072.0 + cprlon_odd = cprlon0 / 131072.0 + + air_d_lat_even = 360.0 / 60 + air_d_lat_odd = 360.0 / 59 ","def cpr2position(cprlat0, cprlat1, cprlon0, cprlon1, t0, t1): + cprlat_even = cprlat0 / 131072.0 + cprlat_odd = cprlat1 / 131072.0 + cprlon_even = cprlon0 / 131072.0 + cprlon_odd = cprlon1 / 131072.0 + + air_d_lat_even = 360.0 / 60 + air_d_lat_odd = 360.0 / 59 " +131,https://:@github.com/icb-dcm/pyabc.git,2df9fbbc034ecad45cde0e14d0205fc70ae9b90b,"@@ -456,5 +456,5 @@ class ABCSMC: + return + + for m in self.history.alive_models(t - 1): +- particles, w = self.history.get_distribution(t - 1, m) ++ particles, w = self.history.get_distribution(m, t - 1) + self.transitions[m].fit(particles, w) +",pyabc/smc.py,"ArgSwap(idxs=0<->1 @(459,27)->(459,56))","class ABCSMC: + return + + for m in self.history.alive_models(t - 1): + particles, w = self.history.get_distribution(t - 1, m) + self.transitions[m].fit(particles, w)","class ABCSMC: + return + + for m in self.history.alive_models(t - 1): + particles, w = self.history.get_distribution(m, t - 1) + self.transitions[m].fit(particles, w)" +132,https://:@github.com/icb-dcm/pyabc.git,2df9fbbc034ecad45cde0e14d0205fc70ae9b90b,"@@ -108,7 +108,7 @@ def abc_model(abc_id, model_id, t): + t = history.max_t + else: + t = int(t) +- df, w = history.get_distribution(t, model_id) ++ df, w = history.get_distribution(model_id, t) + df[""CDF""] = w + tabs = [] + +",pyabc/visserver/server.py,"ArgSwap(idxs=0<->1 @(111,12)->(111,36))","def abc_model(abc_id, model_id, t): + t = history.max_t + else: + t = int(t) + df, w = history.get_distribution(t, model_id) + df[""CDF""] = w + tabs = [] + ","def abc_model(abc_id, model_id, t): + t = history.max_t + else: + t = int(t) + df, w = history.get_distribution(model_id, t) + df[""CDF""] = w + tabs = [] + " +133,https://:@github.com/icb-dcm/pyabc.git,2df9fbbc034ecad45cde0e14d0205fc70ae9b90b,"@@ -122,7 +122,7 @@ def test_dataframe_storage_readout(): + for m in range(5): + pop = pops[(h, m, t)] + expected_particles_list = [p.parameter for p in pop] +- pars_df, w = h.get_distribution(t, m) ++ pars_df, w = h.get_distribution(m, t) + # use range(len and not zip on dataframe to not stop early + # in case of population not completely stored + assert np.isclose(w.sum(), 1) +",test/test_storage.py,"ArgSwap(idxs=0<->1 @(125,29)->(125,47))","def test_dataframe_storage_readout(): + for m in range(5): + pop = pops[(h, m, t)] + expected_particles_list = [p.parameter for p in pop] + pars_df, w = h.get_distribution(t, m) + # use range(len and not zip on dataframe to not stop early + # in case of population not completely stored + assert np.isclose(w.sum(), 1)","def test_dataframe_storage_readout(): + for m in range(5): + pop = pops[(h, m, t)] + expected_particles_list = [p.parameter for p in pop] + pars_df, w = h.get_distribution(m, t) + # use range(len and not zip on dataframe to not stop early + # in case of population not completely stored + assert np.isclose(w.sum(), 1)" +134,https://:@github.com/llllllllll/codetransformer.git,7c327683df810265d01a995d2704c9f8218b0ef7,"@@ -141,7 +141,7 @@ class Instruction(InstructionMeta._marker, metaclass=InstructionMeta): + 'little', + ) + +- yield cls(arg) ++ yield instr(arg) + + @classmethod + def from_opcode(cls, opcode): +",codetransformer/instructions.py,"ReplaceText(target='instr' @(144,18)->(144,21))","class Instruction(InstructionMeta._marker, metaclass=InstructionMeta): + 'little', + ) + + yield cls(arg) + + @classmethod + def from_opcode(cls, opcode):","class Instruction(InstructionMeta._marker, metaclass=InstructionMeta): + 'little', + ) + + yield instr(arg) + + @classmethod + def from_opcode(cls, opcode):" +135,https://:@github.com/richardkiss/pycoin.git,c6b3b2e0d7167d4566dc1d90258d6b98dba8bb65,"@@ -197,7 +197,7 @@ def eval_script(script, signature_for_hash_type_f, lock_time, expected_hash_type + # Subset of script starting at the most recent codeseparator + op_checksig(stack, signature_for_hash_type_f, expected_hash_type, script[begin_code_hash:], flags) + if opcode == opcodes.OP_CHECKSIGVERIFY: +- if bool_from_script_bytes(stack.pop()): ++ if not bool_from_script_bytes(stack.pop()): + raise ScriptError(""VERIFY failed at %d"" % (pc-1)) + continue + +",pycoin/tx/script/vm.py,"ReplaceText(target='not ' @(200,23)->(200,23))","def eval_script(script, signature_for_hash_type_f, lock_time, expected_hash_type + # Subset of script starting at the most recent codeseparator + op_checksig(stack, signature_for_hash_type_f, expected_hash_type, script[begin_code_hash:], flags) + if opcode == opcodes.OP_CHECKSIGVERIFY: + if bool_from_script_bytes(stack.pop()): + raise ScriptError(""VERIFY failed at %d"" % (pc-1)) + continue + ","def eval_script(script, signature_for_hash_type_f, lock_time, expected_hash_type + # Subset of script starting at the most recent codeseparator + op_checksig(stack, signature_for_hash_type_f, expected_hash_type, script[begin_code_hash:], flags) + if opcode == opcodes.OP_CHECKSIGVERIFY: + if not bool_from_script_bytes(stack.pop()): + raise ScriptError(""VERIFY failed at %d"" % (pc-1)) + continue + " +136,https://:@github.com/richardkiss/pycoin.git,6d1df60ddb054d1510f38231a529ccf35a73525a,"@@ -302,7 +302,7 @@ def generate_output(args, output_dict, output_order): + + if len(output_order) == 0: + print(""no output: use -j option to see keys"") +- elif len(output_order) == 1: ++ elif len(output_dict) == 1: + print(output_dict[output_order[0][0]]) + else: + dump_output(output_dict, output_order) +",pycoin/cmds/ku.py,"ReplaceText(target='output_dict' @(305,13)->(305,25))","def generate_output(args, output_dict, output_order): + + if len(output_order) == 0: + print(""no output: use -j option to see keys"") + elif len(output_order) == 1: + print(output_dict[output_order[0][0]]) + else: + dump_output(output_dict, output_order)","def generate_output(args, output_dict, output_order): + + if len(output_order) == 0: + print(""no output: use -j option to see keys"") + elif len(output_dict) == 1: + print(output_dict[output_order[0][0]]) + else: + dump_output(output_dict, output_order)" +137,https://:@github.com/richardkiss/pycoin.git,02a225ef6056cc5a7fa19a731e14fbda94522c55,"@@ -37,7 +37,7 @@ def deterministic_generate_k(generator_order, secret_exponent, val, hash_f=hashl + shift = 8 * hash_size - bln + if shift > 0: + val >>= shift +- if val > n: ++ if val >= n: + val -= n + h1 = intstream.to_bytes(val, length=order_size) + k = hmac.new(k, v + b'\x00' + priv + h1, hash_f).digest() +",pycoin/ecdsa/rfc6979.py,"ReplaceText(target='>=' @(40,11)->(40,12))","def deterministic_generate_k(generator_order, secret_exponent, val, hash_f=hashl + shift = 8 * hash_size - bln + if shift > 0: + val >>= shift + if val > n: + val -= n + h1 = intstream.to_bytes(val, length=order_size) + k = hmac.new(k, v + b'\x00' + priv + h1, hash_f).digest()","def deterministic_generate_k(generator_order, secret_exponent, val, hash_f=hashl + shift = 8 * hash_size - bln + if shift > 0: + val >>= shift + if val >= n: + val -= n + h1 = intstream.to_bytes(val, length=order_size) + k = hmac.new(k, v + b'\x00' + priv + h1, hash_f).digest()" +138,https://:@github.com/er1iang/hfut-stu-lib.git,6bdc0e5591564da7b5fe2acd60bde0cb8b2b46f6,"@@ -60,7 +60,7 @@ class TestUtil(TestBase): + '172.18.6.98', + '172.18.6.99' + ]) +- assert len(r) == 1 ++ assert len(r) <= 1 + with pytest.raises(ValueError): + util.get_host_speed_rank(['qq.com']) + assert util.get_host_speed_rank(timeout=0) == [] +",tests/test_util.py,"ReplaceText(target='<=' @(63,22)->(63,24))","class TestUtil(TestBase): + '172.18.6.98', + '172.18.6.99' + ]) + assert len(r) == 1 + with pytest.raises(ValueError): + util.get_host_speed_rank(['qq.com']) + assert util.get_host_speed_rank(timeout=0) == []","class TestUtil(TestBase): + '172.18.6.98', + '172.18.6.99' + ]) + assert len(r) <= 1 + with pytest.raises(ValueError): + util.get_host_speed_rank(['qq.com']) + assert util.get_host_speed_rank(timeout=0) == []" +139,https://:@github.com/acorg/dark-matter.git,7837baf17ff17925b5a56178358b3ec478635c9b,"@@ -109,7 +109,7 @@ def main(): + consensus.id = args.id + elif args.idLambda is not None: + idLambda = eval(args.idLambda) +- consensus.id = idLambda(args.id) ++ consensus.id = idLambda(consensus.id) + + print(consensus.toString('fasta'), end='') + +",bin/make-consensus.py,"ReplaceText(target='consensus' @(112,32)->(112,36))","def main(): + consensus.id = args.id + elif args.idLambda is not None: + idLambda = eval(args.idLambda) + consensus.id = idLambda(args.id) + + print(consensus.toString('fasta'), end='') + ","def main(): + consensus.id = args.id + elif args.idLambda is not None: + idLambda = eval(args.idLambda) + consensus.id = idLambda(consensus.id) + + print(consensus.toString('fasta'), end='') + " +140,https://:@github.com/Netflix/security_monkey.git,b6356189f8c9e407e4c017bbbf31d8f32aa004a9,"@@ -122,7 +122,7 @@ class SNSAuditor(Auditor): + else: + arn = ARN(princ_aws) + if arn.error: +- self.add_issue(3, 'Auditor could not parse ARN', snsitem, notes=entry) ++ self.add_issue(3, 'Auditor could not parse ARN', snsitem, notes=princ_aws) + else: + account_numbers.append(arn.account_number) + +",security_monkey/auditors/sns.py,"ReplaceText(target='princ_aws' @(125,88)->(125,93))","class SNSAuditor(Auditor): + else: + arn = ARN(princ_aws) + if arn.error: + self.add_issue(3, 'Auditor could not parse ARN', snsitem, notes=entry) + else: + account_numbers.append(arn.account_number) + ","class SNSAuditor(Auditor): + else: + arn = ARN(princ_aws) + if arn.error: + self.add_issue(3, 'Auditor could not parse ARN', snsitem, notes=princ_aws) + else: + account_numbers.append(arn.account_number) + " +141,https://:@github.com/SetBased/py-stratum.git,0a4f1f580810e466e6384395832353a77b8e909f,"@@ -26,7 +26,7 @@ class Connection: + else: + return_value = config.get(section, option, fallback=fallback) + +- if fallback is not None and return_value is None: ++ if fallback is None and return_value is None: + raise KeyError(""Option '%s' is not found in section '%s'."" % (option, section)) + + return return_value +",pystratum/Connection.py,"ReplaceText(target=' is ' @(29,19)->(29,27))","class Connection: + else: + return_value = config.get(section, option, fallback=fallback) + + if fallback is not None and return_value is None: + raise KeyError(""Option '%s' is not found in section '%s'."" % (option, section)) + + return return_value","class Connection: + else: + return_value = config.get(section, option, fallback=fallback) + + if fallback is None and return_value is None: + raise KeyError(""Option '%s' is not found in section '%s'."" % (option, section)) + + return return_value" +142,https://:@github.com/awslabs/aws-service-catalog-puppet-framework.git,8ec184735fbc4d8f72484d5baa0e357bbdbeb9d8,"@@ -85,7 +85,7 @@ def test_deploy_launches_task_builder_for_account_launch_region(sut, mocker, sha + assert len(actual_all_tasks.keys()) == 1 + assert actual_all_tasks == expected_all_tasks + mocked_get_required_params.assert_called_once_with( +- region_name, launch_details.get('portfolio'), launch_details.get('product'), launch_details.get('version'), puppet_account_id ++ region_name, launch_details.get('portfolio'), launch_details.get('product'), launch_details.get('version'), account_id + ) + mocked_get_parameters_for_launch.assert_called_once_with( + required_parameters, +",servicecatalog_puppet/cli_command_helpers_unit_test.py,"ReplaceText(target='account_id' @(88,116)->(88,133))","def test_deploy_launches_task_builder_for_account_launch_region(sut, mocker, sha + assert len(actual_all_tasks.keys()) == 1 + assert actual_all_tasks == expected_all_tasks + mocked_get_required_params.assert_called_once_with( + region_name, launch_details.get('portfolio'), launch_details.get('product'), launch_details.get('version'), puppet_account_id + ) + mocked_get_parameters_for_launch.assert_called_once_with( + required_parameters,","def test_deploy_launches_task_builder_for_account_launch_region(sut, mocker, sha + assert len(actual_all_tasks.keys()) == 1 + assert actual_all_tasks == expected_all_tasks + mocked_get_required_params.assert_called_once_with( + region_name, launch_details.get('portfolio'), launch_details.get('product'), launch_details.get('version'), account_id + ) + mocked_get_parameters_for_launch.assert_called_once_with( + required_parameters," +143,https://:@github.com/kivy-garden/graph.git,b6ec8765b231bfbc1cf0c585243eb43379bb8946,"@@ -448,7 +448,7 @@ class Graph(Widget): + ymin = self.ymin + ymax = self.ymax + if ylog: +- xmin = log10(ymin) ++ ymin = log10(ymin) + ymax = log10(ymax) + if len(xpoints): + top = size[3] if self.x_grid else metrics.dp(12) + size[1] +",__init__.py,"ReplaceText(target='ymin' @(451,12)->(451,16))","class Graph(Widget): + ymin = self.ymin + ymax = self.ymax + if ylog: + xmin = log10(ymin) + ymax = log10(ymax) + if len(xpoints): + top = size[3] if self.x_grid else metrics.dp(12) + size[1]","class Graph(Widget): + ymin = self.ymin + ymax = self.ymax + if ylog: + ymin = log10(ymin) + ymax = log10(ymax) + if len(xpoints): + top = size[3] if self.x_grid else metrics.dp(12) + size[1]" +144,https://:@github.com/irmen/synthesizer.git,e1da70408c0fce248edc4542e2f94e8ea6ea72b9,"@@ -31,7 +31,7 @@ class DecodedSoundFile: + self.sample_format = sample_format # one of the ma_format_ values + self.sample_format_name = ffi.string(lib.ma_get_format_name(sample_format)).decode() + self.samples = samples +- self.num_frames = len(samples) / self.nchannels ++ self.num_frames = len(samples) // self.nchannels + self.duration = self.num_frames / self.sample_rate + + +",pyminiaudio/miniaudio.py,"ReplaceText(target='//' @(34,39)->(34,40))","class DecodedSoundFile: + self.sample_format = sample_format # one of the ma_format_ values + self.sample_format_name = ffi.string(lib.ma_get_format_name(sample_format)).decode() + self.samples = samples + self.num_frames = len(samples) / self.nchannels + self.duration = self.num_frames / self.sample_rate + + ","class DecodedSoundFile: + self.sample_format = sample_format # one of the ma_format_ values + self.sample_format_name = ffi.string(lib.ma_get_format_name(sample_format)).decode() + self.samples = samples + self.num_frames = len(samples) // self.nchannels + self.duration = self.num_frames / self.sample_rate + + " +145,https://:@github.com/pydata/numexpr.git,d11ef8a9dec059b679e773ad8fa54dd4f462d2e8,"@@ -304,7 +304,7 @@ class test_numexpr(TestCase): + assert_equal(res, b) + a = False + res = evaluate('where(a, b, c)') +- assert_equal(res, b) ++ assert_equal(res, c) + + + +",numexpr/tests/test_numexpr.py,"ReplaceText(target='c' @(307,26)->(307,27))","class test_numexpr(TestCase): + assert_equal(res, b) + a = False + res = evaluate('where(a, b, c)') + assert_equal(res, b) + + + ","class test_numexpr(TestCase): + assert_equal(res, b) + a = False + res = evaluate('where(a, b, c)') + assert_equal(res, c) + + + " +146,https://:@github.com/aio-libs/aiozipkin.git,73a9594e475a65d11f32ae1ec48d3a324d2cb2b2,"@@ -23,7 +23,7 @@ class Transport: + self._queue.append(data) + + async def _sender_loop(self): +- while self._ender.done(): ++ while not self._ender.done(): + if len(self._queue) != 0: + await self._send() + +",aiozipkin/transport.py,"ReplaceText(target='not ' @(26,14)->(26,14))","class Transport: + self._queue.append(data) + + async def _sender_loop(self): + while self._ender.done(): + if len(self._queue) != 0: + await self._send() + ","class Transport: + self._queue.append(data) + + async def _sender_loop(self): + while not self._ender.done(): + if len(self._queue) != 0: + await self._send() + " +147,https://:@gitlab.com/deliberist/xdgenvpy.git,cce7b99c90cd770aee31195f98e23169405d31c2,"@@ -96,7 +96,7 @@ def print_vars(xdg, variables): + :param list variables: A sequence of XDG variables to print. + """""" + for var in variables: +- if not (str(var).startswith('XDG_') or hasattr(xdg, var)): ++ if not (str(var).startswith('XDG_') and hasattr(xdg, var)): + LOG.error('Invalid XDG variable: %s', var) + else: + value = getattr(xdg, var) +",xdgenvpy/__main__.py,"ReplaceText(target='and' @(99,44)->(99,46))","def print_vars(xdg, variables): + :param list variables: A sequence of XDG variables to print. + """""" + for var in variables: + if not (str(var).startswith('XDG_') or hasattr(xdg, var)): + LOG.error('Invalid XDG variable: %s', var) + else: + value = getattr(xdg, var)","def print_vars(xdg, variables): + :param list variables: A sequence of XDG variables to print. + """""" + for var in variables: + if not (str(var).startswith('XDG_') and hasattr(xdg, var)): + LOG.error('Invalid XDG variable: %s', var) + else: + value = getattr(xdg, var)" +148,https://:@github.com/theislab/anndata.git,908bbbd7c0ad3e61e7db0441fbe9ec93091a0dd5,"@@ -850,7 +850,7 @@ class AnnData(IndexMixin): + categories=ddata[k]) + if k_stripped in var: + var[k_stripped] = pd.Categorical.from_codes( +- codes=smp[k_stripped].values, ++ codes=var[k_stripped].values, + categories=ddata[k]) + k_to_delete.append(k) + +",anndata/anndata.py,"ReplaceText(target='var' @(853,34)->(853,37))","class AnnData(IndexMixin): + categories=ddata[k]) + if k_stripped in var: + var[k_stripped] = pd.Categorical.from_codes( + codes=smp[k_stripped].values, + categories=ddata[k]) + k_to_delete.append(k) + ","class AnnData(IndexMixin): + categories=ddata[k]) + if k_stripped in var: + var[k_stripped] = pd.Categorical.from_codes( + codes=var[k_stripped].values, + categories=ddata[k]) + k_to_delete.append(k) + " +149,https://:@github.com/theislab/anndata.git,0c6ad8700a028675f25e6a769aaf39db3f2b8893,"@@ -104,7 +104,7 @@ def write_loom( + elif len(adata.obsm.keys()) > 0 or len(adata.varm.keys()) > 0: + logger.warning( + f'The loom file will lack these fields:\n' +- f'{adata.obsm.keys() + adata.varm.keys()}\n' ++ f'{adata.obsm.keys() | adata.varm.keys()}\n' + f'Use write_obsm_varm=True to export multi-dimensional annotations' + ) + +",anndata/readwrite/write.py,"ReplaceText(target='|' @(107,33)->(107,34))","def write_loom( + elif len(adata.obsm.keys()) > 0 or len(adata.varm.keys()) > 0: + logger.warning( + f'The loom file will lack these fields:\n' + f'{adata.obsm.keys() + adata.varm.keys()}\n' + f'Use write_obsm_varm=True to export multi-dimensional annotations' + ) + ","def write_loom( + elif len(adata.obsm.keys()) > 0 or len(adata.varm.keys()) > 0: + logger.warning( + f'The loom file will lack these fields:\n' + f'{adata.obsm.keys() | adata.varm.keys()}\n' + f'Use write_obsm_varm=True to export multi-dimensional annotations' + ) + " +150,https://:@github.com/atarashansky/self-assembling-manifold.git,a8a2172a308d8fb99fc3981e64c1cc358d4d3355,"@@ -965,7 +965,7 @@ class SAMGUI(object): + else: + return; #quit + +- markers = ut.find_corr_genes(s,txt).flatten() ++ markers = ut.find_corr_genes(gene,txt).flatten() + _,i = np.unique(markers,return_index=True) + markers=markers[np.sort(i)] + self.marker_genes[self.stab.selected_index] = markers +",SAMGUI.py,"ReplaceText(target='gene' @(968,37)->(968,38))","class SAMGUI(object): + else: + return; #quit + + markers = ut.find_corr_genes(s,txt).flatten() + _,i = np.unique(markers,return_index=True) + markers=markers[np.sort(i)] + self.marker_genes[self.stab.selected_index] = markers","class SAMGUI(object): + else: + return; #quit + + markers = ut.find_corr_genes(gene,txt).flatten() + _,i = np.unique(markers,return_index=True) + markers=markers[np.sort(i)] + self.marker_genes[self.stab.selected_index] = markers" +151,https://:@github.com/atarashansky/self-assembling-manifold.git,6539b0d87edc6dd18bd1bd3709fc41ad2c51b3f3,"@@ -248,7 +248,7 @@ def search_string(vec, s, case_sensitive=False, invert=False): + i = len(V) + V = np.concatenate(V); M = np.concatenate(M); + if i > 1: +- ix = np.sort(np.unique(V,return_index=True)[1]) ++ ix = np.sort(np.unique(M,return_index=True)[1]) + V=V[ix]; M=M[ix]; + return V,M + else: +",samalg/utilities.py,"ReplaceText(target='M' @(251,35)->(251,36))","def search_string(vec, s, case_sensitive=False, invert=False): + i = len(V) + V = np.concatenate(V); M = np.concatenate(M); + if i > 1: + ix = np.sort(np.unique(V,return_index=True)[1]) + V=V[ix]; M=M[ix]; + return V,M + else:","def search_string(vec, s, case_sensitive=False, invert=False): + i = len(V) + V = np.concatenate(V); M = np.concatenate(M); + if i > 1: + ix = np.sort(np.unique(M,return_index=True)[1]) + V=V[ix]; M=M[ix]; + return V,M + else:" +152,https://:@github.com/den4uk/andriller.git,a5af3433a9caa6f05d8d43aef5abc8f405349f67,"@@ -379,7 +379,7 @@ class MainWindow(BaseWindow): + self.menubar.add_cascade(menu=menu_help, label='Help', underline=0) + menu_help.add_command(label='Visit website') + menu_help.add_separator() +- if getattr(sys, 'frozen', False): ++ if not getattr(sys, 'frozen', False): + menu_help.add_command(label='Run Update', command=lambda: self.conf.upgrade_package(logger=self.logger)) + menu_help.add_separator() + menu_help.add_command(label='About', command=self.about_msg) +",andriller/windows.py,"ReplaceText(target='not ' @(382,11)->(382,11))","class MainWindow(BaseWindow): + self.menubar.add_cascade(menu=menu_help, label='Help', underline=0) + menu_help.add_command(label='Visit website') + menu_help.add_separator() + if getattr(sys, 'frozen', False): + menu_help.add_command(label='Run Update', command=lambda: self.conf.upgrade_package(logger=self.logger)) + menu_help.add_separator() + menu_help.add_command(label='About', command=self.about_msg)","class MainWindow(BaseWindow): + self.menubar.add_cascade(menu=menu_help, label='Help', underline=0) + menu_help.add_command(label='Visit website') + menu_help.add_separator() + if not getattr(sys, 'frozen', False): + menu_help.add_command(label='Run Update', command=lambda: self.conf.upgrade_package(logger=self.logger)) + menu_help.add_separator() + menu_help.add_command(label='About', command=self.about_msg)" +153,https://:@github.com/fabiencro/knmt.git,26b7b1ed8dfbc0e82804e86c149926fc96cd8d84,"@@ -699,7 +699,7 @@ def do_eval(config_eval): + assert len(encdec_list) == 1 + scorer = encdec_list[0].nbest_scorer(src_batch, src_mask) + +- nb_batches = (len(tgt_list) + mb_size - 1) / mb_size ++ nb_batches = (len(tgt_list) + mb_size - 1) // mb_size + for num_batch in six.moves.range(nb_batches): + tgt_batch, arg_sort = utils.make_batch_tgt(tgt_list[num_batch * nb_batches: (num_batch + 1) * nb_batches], + eos_idx=eos_idx, gpu=gpu, volatile=""on"", need_arg_sort=True) +",nmt_chainer/translation/eval.py,"ReplaceText(target='//' @(702,55)->(702,56))","def do_eval(config_eval): + assert len(encdec_list) == 1 + scorer = encdec_list[0].nbest_scorer(src_batch, src_mask) + + nb_batches = (len(tgt_list) + mb_size - 1) / mb_size + for num_batch in six.moves.range(nb_batches): + tgt_batch, arg_sort = utils.make_batch_tgt(tgt_list[num_batch * nb_batches: (num_batch + 1) * nb_batches], + eos_idx=eos_idx, gpu=gpu, volatile=""on"", need_arg_sort=True)","def do_eval(config_eval): + assert len(encdec_list) == 1 + scorer = encdec_list[0].nbest_scorer(src_batch, src_mask) + + nb_batches = (len(tgt_list) + mb_size - 1) // mb_size + for num_batch in six.moves.range(nb_batches): + tgt_batch, arg_sort = utils.make_batch_tgt(tgt_list[num_batch * nb_batches: (num_batch + 1) * nb_batches], + eos_idx=eos_idx, gpu=gpu, volatile=""on"", need_arg_sort=True)" +154,https://:@github.com/fabiencro/knmt.git,8ca17b7d3b52100a3c36ae7a380efbf0ce42107d,"@@ -699,7 +699,7 @@ def do_eval(config_eval): + assert len(encdec_list) == 1 + scorer = encdec_list[0].nbest_scorer(src_batch, src_mask) + +- nb_batches = (len(tgt_list) + mb_size - 1) / mb_size ++ nb_batches = (len(tgt_list) + mb_size - 1) // mb_size + for num_batch in six.moves.range(nb_batches): + tgt_batch, arg_sort = utils.make_batch_tgt(tgt_list[num_batch * nb_batches: (num_batch + 1) * nb_batches], + eos_idx=eos_idx, gpu=gpu, volatile=""on"", need_arg_sort=True) +",nmt_chainer/translation/eval.py,"ReplaceText(target='//' @(702,55)->(702,56))","def do_eval(config_eval): + assert len(encdec_list) == 1 + scorer = encdec_list[0].nbest_scorer(src_batch, src_mask) + + nb_batches = (len(tgt_list) + mb_size - 1) / mb_size + for num_batch in six.moves.range(nb_batches): + tgt_batch, arg_sort = utils.make_batch_tgt(tgt_list[num_batch * nb_batches: (num_batch + 1) * nb_batches], + eos_idx=eos_idx, gpu=gpu, volatile=""on"", need_arg_sort=True)","def do_eval(config_eval): + assert len(encdec_list) == 1 + scorer = encdec_list[0].nbest_scorer(src_batch, src_mask) + + nb_batches = (len(tgt_list) + mb_size - 1) // mb_size + for num_batch in six.moves.range(nb_batches): + tgt_batch, arg_sort = utils.make_batch_tgt(tgt_list[num_batch * nb_batches: (num_batch + 1) * nb_batches], + eos_idx=eos_idx, gpu=gpu, volatile=""on"", need_arg_sort=True)" +155,https://:@github.com/fabiencro/knmt.git,b091633d528161ceba3b63c501774627a2c927aa,"@@ -1127,7 +1127,7 @@ def build_dataset_one_side_pp(src_fn, src_pp, max_nb_ex=None, make_constraints=N + # print(len(sentence_tgt), len(sentence_src)) + seq_src = src_pp.convert(sentence_src, stats=stats_src) + if make_constraints is not None: +- constraints_fn = make_constraints(src, seq_src) ++ constraints_fn = make_constraints(sentence_src, seq_src) + constraints_list.append(constraints_fn) + res.append(seq_src) + if make_constraints is not None: +",nmt_chainer/dataprocessing/processors.py,"ReplaceText(target='sentence_src' @(1130,46)->(1130,49))","def build_dataset_one_side_pp(src_fn, src_pp, max_nb_ex=None, make_constraints=N + # print(len(sentence_tgt), len(sentence_src)) + seq_src = src_pp.convert(sentence_src, stats=stats_src) + if make_constraints is not None: + constraints_fn = make_constraints(src, seq_src) + constraints_list.append(constraints_fn) + res.append(seq_src) + if make_constraints is not None:","def build_dataset_one_side_pp(src_fn, src_pp, max_nb_ex=None, make_constraints=N + # print(len(sentence_tgt), len(sentence_src)) + seq_src = src_pp.convert(sentence_src, stats=stats_src) + if make_constraints is not None: + constraints_fn = make_constraints(sentence_src, seq_src) + constraints_list.append(constraints_fn) + res.append(seq_src) + if make_constraints is not None:" +156,https://:@github.com/biocore/emperor.git,dedef9ab8d8578dd9d8d002dfa2dde254f27b133,"@@ -100,7 +100,7 @@ def main(): + sids_intersection = len(set(zip(*mapping_data)[0]) & set(parsed_coords[0])) + + # sample ids must be shared between files +- if sids_intersection > 0: ++ if sids_intersection <= 0: + option_parser.error('The sample identifiers in the coordinates file ' + 'must have at least one match with the data contained in mapping ' + 'file. Verify you are using a coordinates file and a mapping file ' +",scripts/make_emperor.py,"ReplaceText(target='<=' @(103,25)->(103,26))","def main(): + sids_intersection = len(set(zip(*mapping_data)[0]) & set(parsed_coords[0])) + + # sample ids must be shared between files + if sids_intersection > 0: + option_parser.error('The sample identifiers in the coordinates file ' + 'must have at least one match with the data contained in mapping ' + 'file. Verify you are using a coordinates file and a mapping file '","def main(): + sids_intersection = len(set(zip(*mapping_data)[0]) & set(parsed_coords[0])) + + # sample ids must be shared between files + if sids_intersection <= 0: + option_parser.error('The sample identifiers in the coordinates file ' + 'must have at least one match with the data contained in mapping ' + 'file. Verify you are using a coordinates file and a mapping file '" +157,https://:@github.com/juanpex/django-model-report.git,0aa6d98497f25d178fe48ed9185b77e8d62e722b,"@@ -58,7 +58,7 @@ class ExcelExporter(Exporter): + + for g, rows in report_rows: + if g: +- sheet1.write(row_index, 0, u'%s' % x, stylebold) ++ sheet1.write(row_index, 0, u'%s' % g, stylebold) + row_index += 1 + for row in list(rows): + if row.is_value(): +",model_report/exporters/excel.py,"ReplaceText(target='g' @(61,51)->(61,52))","class ExcelExporter(Exporter): + + for g, rows in report_rows: + if g: + sheet1.write(row_index, 0, u'%s' % x, stylebold) + row_index += 1 + for row in list(rows): + if row.is_value():","class ExcelExporter(Exporter): + + for g, rows in report_rows: + if g: + sheet1.write(row_index, 0, u'%s' % g, stylebold) + row_index += 1 + for row in list(rows): + if row.is_value():" +158,https://:@github.com/hclivess/Bismuth.git,a969c471f3d255e9cd139c100ac942c441c51aa0,"@@ -120,7 +120,7 @@ def difficulty(c): + + time_now = time.time() + if time_now > timestamp_last + 300: #if 5 minutes have passed +- difficulty2 = percentage(97,diff_block_previous) ++ difficulty2 = percentage(97,difficulty) + else: + difficulty2 = difficulty + +",gui.py,"ReplaceText(target='difficulty' @(123,36)->(123,55))","def difficulty(c): + + time_now = time.time() + if time_now > timestamp_last + 300: #if 5 minutes have passed + difficulty2 = percentage(97,diff_block_previous) + else: + difficulty2 = difficulty + ","def difficulty(c): + + time_now = time.time() + if time_now > timestamp_last + 300: #if 5 minutes have passed + difficulty2 = percentage(97,difficulty) + else: + difficulty2 = difficulty + " +159,https://:@github.com/hclivess/Bismuth.git,75e47ec06ac2c83df3fbe413086393d265f27f1c,"@@ -1097,7 +1097,7 @@ def manager(c, conn): + app_log.warning(""Only {} connections active, resetting the connection history"".format(len(connection_pool))) + del tried[:] + +- if nodes_ban_reset and len(connection_pool) < len(banlist) and int(time.time() - reset_time) > 60*10: #do not reset too often. 10 minutes here ++ if nodes_ban_reset and len(connection_pool) <= len(banlist) and int(time.time() - reset_time) > 60*10: #do not reset too often. 10 minutes here + app_log.warning(""Less active connections ({}) than banlist ({}), resetting banlist and tried"" .format(len(connection_pool), len(banlist))) + del banlist[:] + banlist.extend(config.banlist) # reset to config version +",node.py,"ReplaceText(target='<=' @(1100,52)->(1100,53))","def manager(c, conn): + app_log.warning(""Only {} connections active, resetting the connection history"".format(len(connection_pool))) + del tried[:] + + if nodes_ban_reset and len(connection_pool) < len(banlist) and int(time.time() - reset_time) > 60*10: #do not reset too often. 10 minutes here + app_log.warning(""Less active connections ({}) than banlist ({}), resetting banlist and tried"" .format(len(connection_pool), len(banlist))) + del banlist[:] + banlist.extend(config.banlist) # reset to config version","def manager(c, conn): + app_log.warning(""Only {} connections active, resetting the connection history"".format(len(connection_pool))) + del tried[:] + + if nodes_ban_reset and len(connection_pool) <= len(banlist) and int(time.time() - reset_time) > 60*10: #do not reset too often. 10 minutes here + app_log.warning(""Less active connections ({}) than banlist ({}), resetting banlist and tried"" .format(len(connection_pool), len(banlist))) + del banlist[:] + banlist.extend(config.banlist) # reset to config version" +160,https://:@github.com/hclivess/Bismuth.git,34d72e31b605ce74fc26bd9dac9cedd0c659d5b0,"@@ -204,7 +204,7 @@ class MainHandler(tornado.web.RequestHandler): + html.append("""") + + html.append("""") +- html.append("""".format(transferred_total)) ++ html.append("""".format(data_total)) + html.append("""".format(tx_count)) + html.append("""".format(tx_count/500)) + html.append("""".format(transferred_total)) +",ledger_explorer.py,"ReplaceText(target='data_total' @(207,77)->(207,94))","class MainHandler(tornado.web.RequestHandler): + html.append(""
Statistics for the last 500 blocks
Kilobytes transferred: {}
Kilobytes transferred: {}
Transactions: {}
Transactions per block: {}
Total BIS transferred {}
"") + + html.append("""") + html.append("""".format(transferred_total)) + html.append("""".format(tx_count)) + html.append("""".format(tx_count/500)) + html.append("""".format(transferred_total))","class MainHandler(tornado.web.RequestHandler): + html.append(""
Statistics for the last 500 blocks
Kilobytes transferred: {}
Transactions: {}
Transactions per block: {}
Total BIS transferred {}
"") + + html.append("""") + html.append("""".format(data_total)) + html.append("""".format(tx_count)) + html.append("""".format(tx_count/500)) + html.append("""".format(transferred_total))" +161,https://:@github.com/hclivess/Bismuth.git,e6dd78e38707d04ea401ef86960e9deb08ea59b7,"@@ -520,7 +520,7 @@ def difficulty(c, mode): + block_height = int(result[0]) + timestamp_before_last = Decimal(c.fetchone()[1]) + +- if block_height > 427000: #remove code ABOVE after hf ++ if block_height >= 427000: #remove code ABOVE after hf + execute(c, ""SELECT * FROM transactions WHERE reward != 0 ORDER BY block_height DESC LIMIT 2"") + result = c.fetchone() + timestamp_last = Decimal(result[1]) +",node.py,"ReplaceText(target='>=' @(523,20)->(523,21))","def difficulty(c, mode): + block_height = int(result[0]) + timestamp_before_last = Decimal(c.fetchone()[1]) + + if block_height > 427000: #remove code ABOVE after hf + execute(c, ""SELECT * FROM transactions WHERE reward != 0 ORDER BY block_height DESC LIMIT 2"") + result = c.fetchone() + timestamp_last = Decimal(result[1])","def difficulty(c, mode): + block_height = int(result[0]) + timestamp_before_last = Decimal(c.fetchone()[1]) + + if block_height >= 427000: #remove code ABOVE after hf + execute(c, ""SELECT * FROM transactions WHERE reward != 0 ORDER BY block_height DESC LIMIT 2"") + result = c.fetchone() + timestamp_last = Decimal(result[1])" +162,https://:@github.com/hclivess/Bismuth.git,01139c3f9457e2c4dbe7e143c47aa8475f7433cc,"@@ -9,7 +9,7 @@ def keys_load(privkey_file, pubkey_file): + pubkey_loaded = open(pubkey_file, 'rb').read() + pubkey = VerifyingKey.from_string(pubkey_loaded, curve=SECP256k1) + +- address = blake2b(privkey.to_string(), digest_size=20).hexdigest() ++ address = blake2b(pubkey.to_string(), digest_size=20).hexdigest() + + return privkey, pubkey, address + +",bisecdsa.py,"ReplaceText(target='pubkey' @(12,22)->(12,29))","def keys_load(privkey_file, pubkey_file): + pubkey_loaded = open(pubkey_file, 'rb').read() + pubkey = VerifyingKey.from_string(pubkey_loaded, curve=SECP256k1) + + address = blake2b(privkey.to_string(), digest_size=20).hexdigest() + + return privkey, pubkey, address + ","def keys_load(privkey_file, pubkey_file): + pubkey_loaded = open(pubkey_file, 'rb').read() + pubkey = VerifyingKey.from_string(pubkey_loaded, curve=SECP256k1) + + address = blake2b(pubkey.to_string(), digest_size=20).hexdigest() + + return privkey, pubkey, address + " +163,https://:@github.com/hclivess/Bismuth.git,b4f1e59d63db962b8f674dc2f4e6e0df34e8404d,"@@ -9,7 +9,7 @@ def keys_load(privkey_file, pubkey_file): + pubkey_loaded = open(pubkey_file, 'rb').read() + pubkey = VerifyingKey.from_string(pubkey_loaded, curve=SECP256k1) + +- address = blake2b(pubkey.to_string(), digest_size=20).hexdigest() ++ address = blake2b(privkey.to_string(), digest_size=20).hexdigest() + + return privkey, pubkey, address + +",bisecdsa.py,"ReplaceText(target='privkey' @(12,22)->(12,28))","def keys_load(privkey_file, pubkey_file): + pubkey_loaded = open(pubkey_file, 'rb').read() + pubkey = VerifyingKey.from_string(pubkey_loaded, curve=SECP256k1) + + address = blake2b(pubkey.to_string(), digest_size=20).hexdigest() + + return privkey, pubkey, address + ","def keys_load(privkey_file, pubkey_file): + pubkey_loaded = open(pubkey_file, 'rb').read() + pubkey = VerifyingKey.from_string(pubkey_loaded, curve=SECP256k1) + + address = blake2b(privkey.to_string(), digest_size=20).hexdigest() + + return privkey, pubkey, address + " +164,https://:@github.com/hclivess/Bismuth.git,081200edc97ae9d5e35156d634037844835c7205,"@@ -1192,7 +1192,7 @@ def digest_block(data, sdef, peer_ip, conn, c, hdd, h, hdd2, h2, h3, index, inde + + # if (q_time_now < q_received_timestamp + 432000) and not quicksync: + # balance_pre = quantize_eight(credit_ledger - debit_ledger - fees + rewards) # without projection +- balance_pre = ledger_balance3(db_address, h2, balances) ++ balance_pre = ledger_balance3(db_address, c, balances) + # balance = quantize_eight(credit - debit - fees + rewards) + balance = quantize_eight(balance_pre - block_debit_address) + # app_log.info(""Digest: Projected transaction address balance: "" + str(balance)) +",node.py,"ReplaceText(target='c' @(1195,62)->(1195,64))","def digest_block(data, sdef, peer_ip, conn, c, hdd, h, hdd2, h2, h3, index, inde + + # if (q_time_now < q_received_timestamp + 432000) and not quicksync: + # balance_pre = quantize_eight(credit_ledger - debit_ledger - fees + rewards) # without projection + balance_pre = ledger_balance3(db_address, h2, balances) + # balance = quantize_eight(credit - debit - fees + rewards) + balance = quantize_eight(balance_pre - block_debit_address) + # app_log.info(""Digest: Projected transaction address balance: "" + str(balance))","def digest_block(data, sdef, peer_ip, conn, c, hdd, h, hdd2, h2, h3, index, inde + + # if (q_time_now < q_received_timestamp + 432000) and not quicksync: + # balance_pre = quantize_eight(credit_ledger - debit_ledger - fees + rewards) # without projection + balance_pre = ledger_balance3(db_address, c, balances) + # balance = quantize_eight(credit - debit - fees + rewards) + balance = quantize_eight(balance_pre - block_debit_address) + # app_log.info(""Digest: Projected transaction address balance: "" + str(balance))" +165,https://:@github.com/RDCH106/parallel_foreach_submodule.git,714ddc620894fbc6fefac093fe9323a9429f85a8,"@@ -23,7 +23,7 @@ class PFSProcess(object): + if self.__output_filter == """": + self.__output += self.__p.communicate()[0].decode('utf-8') # stdoutdata + else: +- if str(self.__p.communicate()[0].decode('utf-8')).find(self.__output_filter) != -1: ++ if str(self.__p.communicate()[0].decode('utf-8')).find(self.__output_filter) == -1: + self.__output += self.__p.communicate()[0].decode('utf-8') + + if self.__p.communicate()[1]: # stderrdata +",parallelforeachsubmodule/process.py,"ReplaceText(target='==' @(26,89)->(26,91))","class PFSProcess(object): + if self.__output_filter == """": + self.__output += self.__p.communicate()[0].decode('utf-8') # stdoutdata + else: + if str(self.__p.communicate()[0].decode('utf-8')).find(self.__output_filter) != -1: + self.__output += self.__p.communicate()[0].decode('utf-8') + + if self.__p.communicate()[1]: # stderrdata","class PFSProcess(object): + if self.__output_filter == """": + self.__output += self.__p.communicate()[0].decode('utf-8') # stdoutdata + else: + if str(self.__p.communicate()[0].decode('utf-8')).find(self.__output_filter) == -1: + self.__output += self.__p.communicate()[0].decode('utf-8') + + if self.__p.communicate()[1]: # stderrdata" +166,https://:@github.com/rsokl/noggin.git,2f9ec33b6807cf8ff00169a284a2e1c3a77db137,"@@ -71,7 +71,7 @@ class LivePlot(LiveLogger): + if ( + not isinstance(size, Sequence) + or len(size) != 2 +- or not all(isinstance(x, Real) and x >= 0 for x in size) ++ or not all(isinstance(x, Real) and x > 0 for x in size) + ): + raise ValueError( + f""`size` must be a length-2 sequence of "" +",src/liveplot/plotter.py,"ReplaceText(target='>' @(74,49)->(74,51))","class LivePlot(LiveLogger): + if ( + not isinstance(size, Sequence) + or len(size) != 2 + or not all(isinstance(x, Real) and x >= 0 for x in size) + ): + raise ValueError( + f""`size` must be a length-2 sequence of ""","class LivePlot(LiveLogger): + if ( + not isinstance(size, Sequence) + or len(size) != 2 + or not all(isinstance(x, Real) and x > 0 for x in size) + ): + raise ValueError( + f""`size` must be a length-2 sequence of """ +167,https://:@github.com/ome/ome-model.git,99bf44c7c5f8661d4c073b98dcafa980abd44920,"@@ -366,5 +366,5 @@ class OMEModel(object): + substitutionGroupName = self.opts.lang.substitutionGroup(element.getName()) + self.substitutionElement_map[substitutionGroupName] = element + continue +- if len(self.opts.lang.getSubstitutionTypes()) >= 0: ++ if len(self.opts.lang.getSubstitutionTypes()) > 0: + config.METADATA_OBJECT_IGNORE.remove('BinData') +",components/xsd-fu/python/ome/modeltools/model.py,"ReplaceText(target='>' @(369,54)->(369,56))","class OMEModel(object): + substitutionGroupName = self.opts.lang.substitutionGroup(element.getName()) + self.substitutionElement_map[substitutionGroupName] = element + continue + if len(self.opts.lang.getSubstitutionTypes()) >= 0: + config.METADATA_OBJECT_IGNORE.remove('BinData')","class OMEModel(object): + substitutionGroupName = self.opts.lang.substitutionGroup(element.getName()) + self.substitutionElement_map[substitutionGroupName] = element + continue + if len(self.opts.lang.getSubstitutionTypes()) > 0: + config.METADATA_OBJECT_IGNORE.remove('BinData')" +168,https://:@github.com/ome/ome-model.git,49d212302bd30541e55ef64409b14377b069cd3a,"@@ -135,7 +135,7 @@ class Image(object): + assert (len(self.data[""Channels""]) <= sizeC), str(self.data) + channel_samples = sum([int(x.data['SamplesPerPixel']) + for x in self.data[""Channels""]]) +- assert channel_samples < sizeC, str(self.data) ++ assert channel_samples <= sizeC, str(self.data) + return self.data + + +",ome_model/experimental.py,"ReplaceText(target='<=' @(138,31)->(138,32))","class Image(object): + assert (len(self.data[""Channels""]) <= sizeC), str(self.data) + channel_samples = sum([int(x.data['SamplesPerPixel']) + for x in self.data[""Channels""]]) + assert channel_samples < sizeC, str(self.data) + return self.data + + ","class Image(object): + assert (len(self.data[""Channels""]) <= sizeC), str(self.data) + channel_samples = sum([int(x.data['SamplesPerPixel']) + for x in self.data[""Channels""]]) + assert channel_samples <= sizeC, str(self.data) + return self.data + + " +169,https://:@github.com/uber/causalml.git,3c085167f8fbf6a07ef53ad84f36682e015ff320,"@@ -966,7 +966,7 @@ class UpliftTreeClassifier: + rightNodeSummary = self.tree_node_summary(w_r, y_r, + min_samples_treatment=min_samples_treatment, + n_reg=n_reg, +- parentNodeSummary=parentNodeSummary) ++ parentNodeSummary=currentNodeSummary) + + # check the split validity on min_samples_treatment + if set(leftNodeSummary.keys()) != set(rightNodeSummary.keys()): +",causalml/inference/tree/models.py,"ReplaceText(target='currentNodeSummary' @(969,76)->(969,93))","class UpliftTreeClassifier: + rightNodeSummary = self.tree_node_summary(w_r, y_r, + min_samples_treatment=min_samples_treatment, + n_reg=n_reg, + parentNodeSummary=parentNodeSummary) + + # check the split validity on min_samples_treatment + if set(leftNodeSummary.keys()) != set(rightNodeSummary.keys()):","class UpliftTreeClassifier: + rightNodeSummary = self.tree_node_summary(w_r, y_r, + min_samples_treatment=min_samples_treatment, + n_reg=n_reg, + parentNodeSummary=currentNodeSummary) + + # check the split validity on min_samples_treatment + if set(leftNodeSummary.keys()) != set(rightNodeSummary.keys()):" +170,https://:@github.com/pypa/setuptools_scm.git,3e2ee4c2c77900f2d20241f489a670f7cb512e98,"@@ -77,7 +77,7 @@ def test_version_from_hg_id(tmpdir, get_log_version): + hg('add test.txt', cwd) + hg('commit -m commit -u test -d ""0 0""', cwd) + +- after_first_commit = get_log_version(tmpdir) ++ after_first_commit = get_log_version(cwd) + + assert after_first_commit.startswith('0.0.post1-') + +",test_hgdistver.py,"ReplaceText(target='cwd' @(80,41)->(80,47))","def test_version_from_hg_id(tmpdir, get_log_version): + hg('add test.txt', cwd) + hg('commit -m commit -u test -d ""0 0""', cwd) + + after_first_commit = get_log_version(tmpdir) + + assert after_first_commit.startswith('0.0.post1-') + ","def test_version_from_hg_id(tmpdir, get_log_version): + hg('add test.txt', cwd) + hg('commit -m commit -u test -d ""0 0""', cwd) + + after_first_commit = get_log_version(cwd) + + assert after_first_commit.startswith('0.0.post1-') + " +171,https://:@github.com/pypa/setuptools_scm.git,340b2356e8ab2e6525ef1a07d17155db2788ed50,"@@ -50,6 +50,6 @@ def scm_find_files(path, scm_files, scm_dirs): + # dirpath + filename with symlinks preserved + fullfilename = os.path.join(dirpath, filename) + if os.path.normcase(os.path.realpath(fullfilename)) in scm_files: +- res.append(os.path.join(path, os.path.relpath(fullfilename, path))) ++ res.append(os.path.join(path, os.path.relpath(fullfilename, realpath))) + seen.add(realdirpath) + return res +",src/setuptools_scm/file_finder.py,"ReplaceText(target='realpath' @(53,76)->(53,80))","def scm_find_files(path, scm_files, scm_dirs): + # dirpath + filename with symlinks preserved + fullfilename = os.path.join(dirpath, filename) + if os.path.normcase(os.path.realpath(fullfilename)) in scm_files: + res.append(os.path.join(path, os.path.relpath(fullfilename, path))) + seen.add(realdirpath) + return res","def scm_find_files(path, scm_files, scm_dirs): + # dirpath + filename with symlinks preserved + fullfilename = os.path.join(dirpath, filename) + if os.path.normcase(os.path.realpath(fullfilename)) in scm_files: + res.append(os.path.join(path, os.path.relpath(fullfilename, realpath))) + seen.add(realdirpath) + return res" +172,https://:@github.com/alphaomega-technology/Equation.git,66e92f5b6ab584b7e7ac3bb7c328ff4ea410f88e,"@@ -600,7 +600,7 @@ class Expression( object ): + continue + fs = self.__getfunction(op) + while True: +- if (fn['prec'] <= fs['prec']): ++ if (fn['prec'] >= fs['prec']): + self.__expr.append(ExpressionFunction(fs['func'],fs['args'],fs['str'],fs['latex'],op[0],False)) + if len(stack) == 0: + stack.append(v) +",Equation/core.py,"ReplaceText(target='>=' @(603,35)->(603,37))","class Expression( object ): + continue + fs = self.__getfunction(op) + while True: + if (fn['prec'] <= fs['prec']): + self.__expr.append(ExpressionFunction(fs['func'],fs['args'],fs['str'],fs['latex'],op[0],False)) + if len(stack) == 0: + stack.append(v)","class Expression( object ): + continue + fs = self.__getfunction(op) + while True: + if (fn['prec'] >= fs['prec']): + self.__expr.append(ExpressionFunction(fs['func'],fs['args'],fs['str'],fs['latex'],op[0],False)) + if len(stack) == 0: + stack.append(v)" +173,https://:@github.com/Azure/azure-uamqp-python.git,29706fc2599f09f186f85fd15bf243b5ed60477f,"@@ -499,7 +499,7 @@ class SendClient(AMQPClient): + message.state = constants.MessageState.SendComplete + message._response = errors.MessageAlreadySettled() # pylint: disable=protected-access + if message.on_send_complete: +- message.on_send_complete(result, delivery_state) ++ message.on_send_complete(result, exception) + + def _filter_pending(self, message): + if message.state in constants.DONE_STATES: +",uamqp/client.py,"ReplaceText(target='exception' @(502,45)->(502,59))","class SendClient(AMQPClient): + message.state = constants.MessageState.SendComplete + message._response = errors.MessageAlreadySettled() # pylint: disable=protected-access + if message.on_send_complete: + message.on_send_complete(result, delivery_state) + + def _filter_pending(self, message): + if message.state in constants.DONE_STATES:","class SendClient(AMQPClient): + message.state = constants.MessageState.SendComplete + message._response = errors.MessageAlreadySettled() # pylint: disable=protected-access + if message.on_send_complete: + message.on_send_complete(result, exception) + + def _filter_pending(self, message): + if message.state in constants.DONE_STATES:" +174,https://:@github.com/MITHaystack/digital_rf.git,fe9ab29c4bc9584474f264516130c1c92b43e0d3,"@@ -418,7 +418,7 @@ class Thor(object): + # set master clock rate + clock_rate = op.clock_rates[mb_num] + if clock_rate is not None: +- op.set_clock_rate(clock_rate, mb_num) ++ u.set_clock_rate(clock_rate, mb_num) + op.clock_rates[mb_num] = u.get_clock_rate(mb_num) + + # set clock source +",python/tools/thor.py,"ReplaceText(target='u' @(421,16)->(421,18))","class Thor(object): + # set master clock rate + clock_rate = op.clock_rates[mb_num] + if clock_rate is not None: + op.set_clock_rate(clock_rate, mb_num) + op.clock_rates[mb_num] = u.get_clock_rate(mb_num) + + # set clock source","class Thor(object): + # set master clock rate + clock_rate = op.clock_rates[mb_num] + if clock_rate is not None: + u.set_clock_rate(clock_rate, mb_num) + op.clock_rates[mb_num] = u.get_clock_rate(mb_num) + + # set clock source" +175,https://:@github.com/rm-hull/luma.core.git,dca2765dc5f02941a5f5668ed65f60650a95d929,"@@ -40,7 +40,7 @@ def show_message(device, msg, y_offset=0, fill=None, font=None, scroll_delay=0.0 + text(draw, (x, y_offset), msg, font=font, fill=fill) + + i = 0 +- while i < w + x: ++ while i <= w + x: + virtual.set_position((i, 0)) + regulator.sleep() + i += 1 +",luma/core/legacy/__init__.py,"ReplaceText(target='<=' @(43,12)->(43,13))","def show_message(device, msg, y_offset=0, fill=None, font=None, scroll_delay=0.0 + text(draw, (x, y_offset), msg, font=font, fill=fill) + + i = 0 + while i < w + x: + virtual.set_position((i, 0)) + regulator.sleep() + i += 1","def show_message(device, msg, y_offset=0, fill=None, font=None, scroll_delay=0.0 + text(draw, (x, y_offset), msg, font=font, fill=fill) + + i = 0 + while i <= w + x: + virtual.set_position((i, 0)) + regulator.sleep() + i += 1" +176,https://:@github.com/gforcada/flake8-builtins.git,da932110850fae82bdc56cb2e5b5fed2ff228e3c,"@@ -211,7 +211,7 @@ class BuiltinsChecker(object): + if not message: + message = self.assign_msg + if not variable: +- column = statement.id ++ variable = statement.id + if not line: + line = statement.lineno + if not column: +",flake8_builtins.py,"ReplaceText(target='variable' @(214,12)->(214,18))","class BuiltinsChecker(object): + if not message: + message = self.assign_msg + if not variable: + column = statement.id + if not line: + line = statement.lineno + if not column:","class BuiltinsChecker(object): + if not message: + message = self.assign_msg + if not variable: + variable = statement.id + if not line: + line = statement.lineno + if not column:" +177,https://:@github.com/European-XFEL/h5glance.git,23bcd02f8a36c9fd1f623e6627a7d6960669e06c,"@@ -157,7 +157,7 @@ class TreeViewBuilder: + if obj.id.get_create_plist().get_layout() == h5py.h5d.VIRTUAL: + detail += ' virtual' + elif isinstance(obj, h5py.Group): +- if max_depth > 1: ++ if max_depth >= 1: + children += [self.group_item_node(obj, key, max_depth - 1) + for key in obj] + else: +",h5glance/terminal.py,"ReplaceText(target='>=' @(160,25)->(160,26))","class TreeViewBuilder: + if obj.id.get_create_plist().get_layout() == h5py.h5d.VIRTUAL: + detail += ' virtual' + elif isinstance(obj, h5py.Group): + if max_depth > 1: + children += [self.group_item_node(obj, key, max_depth - 1) + for key in obj] + else:","class TreeViewBuilder: + if obj.id.get_create_plist().get_layout() == h5py.h5d.VIRTUAL: + detail += ' virtual' + elif isinstance(obj, h5py.Group): + if max_depth >= 1: + children += [self.group_item_node(obj, key, max_depth - 1) + for key in obj] + else:" +178,https://:@github.com/camptocamp/c2cgeoform.git,98126ec7859b1bc5b1b2b720fea1c5d5ca9bbbef,"@@ -224,7 +224,7 @@ class AbstractViews(): + if field.id() == sort: + criterion = field.sort_column() + if order == 'desc': +- criterion = desc(sort) ++ criterion = desc(criterion) + criteria.append(criterion) + + # Sort on primary key as subqueryload with limit need deterministic order +",c2cgeoform/views/abstract_views.py,"ReplaceText(target='criterion' @(227,37)->(227,41))","class AbstractViews(): + if field.id() == sort: + criterion = field.sort_column() + if order == 'desc': + criterion = desc(sort) + criteria.append(criterion) + + # Sort on primary key as subqueryload with limit need deterministic order","class AbstractViews(): + if field.id() == sort: + criterion = field.sort_column() + if order == 'desc': + criterion = desc(criterion) + criteria.append(criterion) + + # Sort on primary key as subqueryload with limit need deterministic order" +179,https://:@github.com/HumanCellAtlas/data-store.git,a28a6a38433fa3ead01ba5bd7e9289caf9c905b0,"@@ -114,7 +114,7 @@ def _verify_checkout( + ) -> typing.Tuple[str, bool]: + decoded_token: dict + if token is None: +- execution_id = start_file_checkout(blob_path, replica) ++ execution_id = start_file_checkout(replica, blob_path) + start_time = time.time() + attempts = 0 + +",dss/api/files.py,"ArgSwap(idxs=0<->1 @(117,23)->(117,42))","def _verify_checkout( + ) -> typing.Tuple[str, bool]: + decoded_token: dict + if token is None: + execution_id = start_file_checkout(blob_path, replica) + start_time = time.time() + attempts = 0 + ","def _verify_checkout( + ) -> typing.Tuple[str, bool]: + decoded_token: dict + if token is None: + execution_id = start_file_checkout(replica, blob_path) + start_time = time.time() + attempts = 0 + " +180,https://:@github.com/HumanCellAtlas/data-store.git,6ab718c4aef36abe12b10556e27d5943176f7314,"@@ -53,7 +53,7 @@ class ElasticsearchIndexBackend(IndexBackend): + tombstone_doc = BundleTombstoneDocument.from_tombstone(tombstone) + modified, index_name = doc.entomb(tombstone_doc, dryrun=self.dryrun) + if self.notify or modified and self.notify is None: +- self._notify(doc, index_name) ++ self._notify(tombstone_doc, index_name) + + def _notify(self, bundle, index_name): + subscription_ids = self._find_matching_subscriptions(bundle, index_name) +",dss/index/es/backend.py,"ReplaceText(target='tombstone_doc' @(56,25)->(56,28))","class ElasticsearchIndexBackend(IndexBackend): + tombstone_doc = BundleTombstoneDocument.from_tombstone(tombstone) + modified, index_name = doc.entomb(tombstone_doc, dryrun=self.dryrun) + if self.notify or modified and self.notify is None: + self._notify(doc, index_name) + + def _notify(self, bundle, index_name): + subscription_ids = self._find_matching_subscriptions(bundle, index_name)","class ElasticsearchIndexBackend(IndexBackend): + tombstone_doc = BundleTombstoneDocument.from_tombstone(tombstone) + modified, index_name = doc.entomb(tombstone_doc, dryrun=self.dryrun) + if self.notify or modified and self.notify is None: + self._notify(tombstone_doc, index_name) + + def _notify(self, bundle, index_name): + subscription_ids = self._find_matching_subscriptions(bundle, index_name)" +181,https://:@github.com/oemof/tespy.git,b6c36317886f435ae4dda9a8459788fabbfe85a8,"@@ -330,7 +330,7 @@ class bus: + 'This bus accepts components of type ' + + str(type(c).__bases__[0]) + '.') + raise TypeError(msg) +- return False ++ return True + return True + + +",tespy/connections.py,"ReplaceText(target='True' @(333,23)->(333,28))","class bus: + 'This bus accepts components of type ' + + str(type(c).__bases__[0]) + '.') + raise TypeError(msg) + return False + return True + + ","class bus: + 'This bus accepts components of type ' + + str(type(c).__bases__[0]) + '.') + raise TypeError(msg) + return True + return True + + " +182,https://:@github.com/oemof/tespy.git,d69bd568bde4209be5aff37328ca422171ce3467,"@@ -1318,7 +1318,7 @@ class separator(node): + res = x * self.inl[0].m.val_SI + for o in self.outl: + res -= o.fluid.val[fluid] * o.m.val_SI +- self.vec_res[k] += res ++ self.vec_res[k] = res + k += 1 + + ###################################################################### +",tespy/components/nodes.py,"ReplaceText(target='=' @(1321,28)->(1321,30))","class separator(node): + res = x * self.inl[0].m.val_SI + for o in self.outl: + res -= o.fluid.val[fluid] * o.m.val_SI + self.vec_res[k] += res + k += 1 + + ######################################################################","class separator(node): + res = x * self.inl[0].m.val_SI + for o in self.outl: + res -= o.fluid.val[fluid] * o.m.val_SI + self.vec_res[k] = res + k += 1 + + ######################################################################" +183,https://:@github.com/uber/tchannel-python.git,867364eea67d8da34f5f84a2d9fa02203f02aa95,"@@ -222,7 +222,7 @@ class TChannelClientOperation(object): + + message = CallRequestMessage( + service=self.service, +- args=[safebytes(arg_1), arg_3, arg_3], ++ args=[safebytes(arg_1), arg_2, arg_3], + ) + + response_future = peer_connection.send(message, message_id) +",tchannel/tornado/tchannel.py,"ReplaceText(target='arg_2' @(225,36)->(225,41))","class TChannelClientOperation(object): + + message = CallRequestMessage( + service=self.service, + args=[safebytes(arg_1), arg_3, arg_3], + ) + + response_future = peer_connection.send(message, message_id)","class TChannelClientOperation(object): + + message = CallRequestMessage( + service=self.service, + args=[safebytes(arg_1), arg_2, arg_3], + ) + + response_future = peer_connection.send(message, message_id)" +184,https://:@github.com/arrrlo/Google-Images-Search.git,26df6441928bc8d69224fe7bf5fc52741a3404a7,"@@ -109,7 +109,7 @@ class FetchResizeSave(object): + for i, page in enumerate(range(start, end, IMAGES_NUM_LIMIT)): + start = page+1 + +- if self._number_of_images > IMAGES_NUM_LIMIT*(i+1): ++ if self._number_of_images >= IMAGES_NUM_LIMIT*(i+1): + num = IMAGES_NUM_LIMIT + else: + num = (self._number_of_images % IMAGES_NUM_LIMIT) or \ +",google_images_search/fetch_resize_save.py,"ReplaceText(target='>=' @(112,38)->(112,39))","class FetchResizeSave(object): + for i, page in enumerate(range(start, end, IMAGES_NUM_LIMIT)): + start = page+1 + + if self._number_of_images > IMAGES_NUM_LIMIT*(i+1): + num = IMAGES_NUM_LIMIT + else: + num = (self._number_of_images % IMAGES_NUM_LIMIT) or \","class FetchResizeSave(object): + for i, page in enumerate(range(start, end, IMAGES_NUM_LIMIT)): + start = page+1 + + if self._number_of_images >= IMAGES_NUM_LIMIT*(i+1): + num = IMAGES_NUM_LIMIT + else: + num = (self._number_of_images % IMAGES_NUM_LIMIT) or \" +185,https://:@github.com/Parsl/parsl.git,794ea182f61a9626a84aa58be11952c8bb148ccd,"@@ -278,7 +278,7 @@ class EC2Provider(ExecutionProvider): + + try: + with open(credfile, 'r') as f: +- creds = json.load(credfile) ++ creds = json.load(f) + except json.JSONDecodeError as e: + logger.error( + ""Site[{0}]: Json decode error in credential file {1}"".format(self, credfile) +",libsubmit/providers/aws/aws.py,"ReplaceText(target='f' @(281,38)->(281,46))","class EC2Provider(ExecutionProvider): + + try: + with open(credfile, 'r') as f: + creds = json.load(credfile) + except json.JSONDecodeError as e: + logger.error( + ""Site[{0}]: Json decode error in credential file {1}"".format(self, credfile)","class EC2Provider(ExecutionProvider): + + try: + with open(credfile, 'r') as f: + creds = json.load(f) + except json.JSONDecodeError as e: + logger.error( + ""Site[{0}]: Json decode error in credential file {1}"".format(self, credfile)" +186,https://:@github.com/Parsl/parsl.git,547ef33559003eddb8206bb01d9bbc22bc07aba7,"@@ -83,7 +83,7 @@ def update_config(config, rundir): + ""maxThreads"": 8 + } + } +- config[""sites""].append(data_manager_site) ++ config_base[""sites""].append(data_manager_site) + + # Update the config datastructure + _config = copy.deepcopy(config) +",parsl/dataflow/config_defaults.py,"ReplaceText(target='config_base' @(86,4)->(86,10))","def update_config(config, rundir): + ""maxThreads"": 8 + } + } + config[""sites""].append(data_manager_site) + + # Update the config datastructure + _config = copy.deepcopy(config)","def update_config(config, rundir): + ""maxThreads"": 8 + } + } + config_base[""sites""].append(data_manager_site) + + # Update the config datastructure + _config = copy.deepcopy(config)" +187,https://:@github.com/Parsl/parsl.git,be25fe238b3269947cd6c882dfba88a147304937,"@@ -76,6 +76,6 @@ class PythonApp(AppBase): + fn_hash=self.func_hash, + cache=self.cache, + ignore_for_cache=self.ignore_for_cache, +- app_kwargs=kwargs) ++ app_kwargs=invocation_kwargs) + + return app_fut +",parsl/app/python.py,"ReplaceText(target='invocation_kwargs' @(79,40)->(79,46))","class PythonApp(AppBase): + fn_hash=self.func_hash, + cache=self.cache, + ignore_for_cache=self.ignore_for_cache, + app_kwargs=kwargs) + + return app_fut","class PythonApp(AppBase): + fn_hash=self.func_hash, + cache=self.cache, + ignore_for_cache=self.ignore_for_cache, + app_kwargs=invocation_kwargs) + + return app_fut" +188,https://:@github.com/qutang/padar.git,afb839dec2306e76355a03bc5b5602838e1a9201,"@@ -63,7 +63,7 @@ class OrientationFeatureComputer(SensorProcessor): + ] + + windows = mw.get_sliding_window_boundaries(start_time=st, stop_time=et, window_duration=ws, step_size=ss) +- chunk_windows_mask = (windows[:,0] >= data_start_indicator) & (windows[:,0] <= data_stop_indicator) ++ chunk_windows_mask = (windows[:,0] >= data_start_indicator) & (windows[:,0] < data_stop_indicator) + chunk_windows = windows[chunk_windows_mask,:] + if len(chunk_windows) == 0: + return pd.DataFrame() +",mhealth/scripts/OrientationFeatureComputer.py,"ReplaceText(target='<' @(66,84)->(66,86))","class OrientationFeatureComputer(SensorProcessor): + ] + + windows = mw.get_sliding_window_boundaries(start_time=st, stop_time=et, window_duration=ws, step_size=ss) + chunk_windows_mask = (windows[:,0] >= data_start_indicator) & (windows[:,0] <= data_stop_indicator) + chunk_windows = windows[chunk_windows_mask,:] + if len(chunk_windows) == 0: + return pd.DataFrame()","class OrientationFeatureComputer(SensorProcessor): + ] + + windows = mw.get_sliding_window_boundaries(start_time=st, stop_time=et, window_duration=ws, step_size=ss) + chunk_windows_mask = (windows[:,0] >= data_start_indicator) & (windows[:,0] < data_stop_indicator) + chunk_windows = windows[chunk_windows_mask,:] + if len(chunk_windows) == 0: + return pd.DataFrame()" +189,https://:@github.com/mozman/ezdxf.git,a4c290a333b51772ecb0b9184506596d49183690,"@@ -22,7 +22,7 @@ class Drawing: + self.encoding = 'cp1252' # read/write + self.filename = None # read/write + self.entitydb = EntityDB() +- self.sections = Sections(self, tagreader) ++ self.sections = Sections(tagreader, self) + self._dxfversion = self.header['$ACADVER'] + self.encoding = self._get_encoding() + nexthandle = int(self.header.get('$HANDSEED', '500'), 16) +",ezdxf/drawing.py,"ArgSwap(idxs=0<->1 @(25,24)->(25,32))","class Drawing: + self.encoding = 'cp1252' # read/write + self.filename = None # read/write + self.entitydb = EntityDB() + self.sections = Sections(self, tagreader) + self._dxfversion = self.header['$ACADVER'] + self.encoding = self._get_encoding() + nexthandle = int(self.header.get('$HANDSEED', '500'), 16)","class Drawing: + self.encoding = 'cp1252' # read/write + self.filename = None # read/write + self.entitydb = EntityDB() + self.sections = Sections(tagreader, self) + self._dxfversion = self.header['$ACADVER'] + self.encoding = self._get_encoding() + nexthandle = int(self.header.get('$HANDSEED', '500'), 16)" +190,https://:@github.com/mozman/ezdxf.git,d2bcbe493b5300e97913a1a13772a19547436239,"@@ -212,7 +212,7 @@ class GroupCollection(ObjectCollection): + raise DXFTypeError(group.dxftype()) + + if name in self: +- super().delete(group) ++ super().delete(name) + else: + raise DXFValueError(""GROUP not in group table registered."") + +",ezdxf/entities/dxfgroups.py,"ReplaceText(target='name' @(215,27)->(215,32))","class GroupCollection(ObjectCollection): + raise DXFTypeError(group.dxftype()) + + if name in self: + super().delete(group) + else: + raise DXFValueError(""GROUP not in group table registered."") + ","class GroupCollection(ObjectCollection): + raise DXFTypeError(group.dxftype()) + + if name in self: + super().delete(name) + else: + raise DXFValueError(""GROUP not in group table registered."") + " +191,https://:@github.com/mozman/ezdxf.git,f6517755bbaeb24096de1f6fb8294b36c21cb769,"@@ -116,7 +116,7 @@ class Face3d(_Base): + + def set_edge_visibilty(self, num, status=False): + """""" Set visibility of edge `num`, status `True` for visible, status `False` for invisible. """""" +- if status: ++ if not status: + self.dxf.invisible = self.dxf.invisible | (1 << num) + else: + self.dxf.invisible = self.dxf.invisible & ~(1 << num) +",src/ezdxf/entities/solid.py,"ReplaceText(target='not ' @(119,11)->(119,11))","class Face3d(_Base): + + def set_edge_visibilty(self, num, status=False): + """""" Set visibility of edge `num`, status `True` for visible, status `False` for invisible. """""" + if status: + self.dxf.invisible = self.dxf.invisible | (1 << num) + else: + self.dxf.invisible = self.dxf.invisible & ~(1 << num)","class Face3d(_Base): + + def set_edge_visibilty(self, num, status=False): + """""" Set visibility of edge `num`, status `True` for visible, status `False` for invisible. """""" + if not status: + self.dxf.invisible = self.dxf.invisible | (1 << num) + else: + self.dxf.invisible = self.dxf.invisible & ~(1 << num)" +192,https://:@github.com/mozman/ezdxf.git,516fbb01d55b9dc86b20b3d2263496560ad74415,"@@ -195,7 +195,7 @@ def virtual_block_reference_entities(block_ref: 'Insert', + + if block_ref.has_uniform_scaling and xscale < 0: + # handle reflection about all three axis -x, -y, -z explicit as non uniform scaling +- has_non_uniform_scaling = True ++ has_non_uniform_scaling = False + + if uniform_scaling_factor is not None: + uniform_scaling_factor = float(uniform_scaling_factor) +",src/ezdxf/explode.py,"ReplaceText(target='False' @(198,38)->(198,42))","def virtual_block_reference_entities(block_ref: 'Insert', + + if block_ref.has_uniform_scaling and xscale < 0: + # handle reflection about all three axis -x, -y, -z explicit as non uniform scaling + has_non_uniform_scaling = True + + if uniform_scaling_factor is not None: + uniform_scaling_factor = float(uniform_scaling_factor)","def virtual_block_reference_entities(block_ref: 'Insert', + + if block_ref.has_uniform_scaling and xscale < 0: + # handle reflection about all three axis -x, -y, -z explicit as non uniform scaling + has_non_uniform_scaling = False + + if uniform_scaling_factor is not None: + uniform_scaling_factor = float(uniform_scaling_factor)" +193,https://:@github.com/mozman/ezdxf.git,ba0c909bdfc0c64d4909b15c9e12a54b9a36d7a4,"@@ -264,7 +264,7 @@ class Frontend: + last_vertex = end + + if vertices: +- if last_vertex.isclose(vertices[0]): ++ if not last_vertex.isclose(vertices[0]): + vertices.append(last_vertex) + self.out.draw_filled_polygon(vertices, properties) + +",src/ezdxf/addons/drawing/frontend.py,"ReplaceText(target='not ' @(267,19)->(267,19))","class Frontend: + last_vertex = end + + if vertices: + if last_vertex.isclose(vertices[0]): + vertices.append(last_vertex) + self.out.draw_filled_polygon(vertices, properties) + ","class Frontend: + last_vertex = end + + if vertices: + if not last_vertex.isclose(vertices[0]): + vertices.append(last_vertex) + self.out.draw_filled_polygon(vertices, properties) + " +194,https://:@github.com/mozman/ezdxf.git,637cf54b973fb9bda6e4b0612b439ee69f04cf15,"@@ -184,7 +184,7 @@ def has_clockwise_orientation(vertices: Iterable['Vertex']) -> bool: + return sum( + (p2.x - p1.x) * (p2.y + p1.y) + for p1, p2 in zip(vertices, vertices[1:]) +- ) < 0 ++ ) > 0 + + + def enclosing_angles(angle, start_angle, end_angle, ccw=True, +",src/ezdxf/math/construct2d.py,"ReplaceText(target='>' @(187,6)->(187,7))","def has_clockwise_orientation(vertices: Iterable['Vertex']) -> bool: + return sum( + (p2.x - p1.x) * (p2.y + p1.y) + for p1, p2 in zip(vertices, vertices[1:]) + ) < 0 + + + def enclosing_angles(angle, start_angle, end_angle, ccw=True,","def has_clockwise_orientation(vertices: Iterable['Vertex']) -> bool: + return sum( + (p2.x - p1.x) * (p2.y + p1.y) + for p1, p2 in zip(vertices, vertices[1:]) + ) > 0 + + + def enclosing_angles(angle, start_angle, end_angle, ccw=True," +195,https://:@github.com/Parsely/pykafka.git,676b3119ff9f4cd2a5bebf1ee0e3e52071cd65af,"@@ -198,7 +198,7 @@ class Producer(): + else: + key, value = message + value = str(value) +- yield (key, value), self._partitioner(partitions, message).id ++ yield (key, value), self._partitioner(partitions, key).id + + def _produce(self, message_partition_tups, attempt): + """"""Publish a set of messages to relevant brokers. +",pykafka/producer.py,"ReplaceText(target='key' @(201,62)->(201,69))","class Producer(): + else: + key, value = message + value = str(value) + yield (key, value), self._partitioner(partitions, message).id + + def _produce(self, message_partition_tups, attempt): + """"""Publish a set of messages to relevant brokers.","class Producer(): + else: + key, value = message + value = str(value) + yield (key, value), self._partitioner(partitions, key).id + + def _produce(self, message_partition_tups, attempt): + """"""Publish a set of messages to relevant brokers." +196,https://:@github.com/Parsely/pykafka.git,559679443462fa62b4378453c5dfff14df85654f,"@@ -816,7 +816,7 @@ class OwnedPartition(object): + :type messages: Iterable of :class:`pykafka.common.Message` + """""" + for message in messages: +- if message.offset < self.last_offset_consumed: ++ if message.offset <= self.last_offset_consumed: + log.debug(""Skipping enqueue for offset (%s) "" + ""less than last_offset_consumed (%s)"", + message.offset, self.last_offset_consumed) +",pykafka/simpleconsumer.py,"ReplaceText(target='<=' @(819,30)->(819,31))","class OwnedPartition(object): + :type messages: Iterable of :class:`pykafka.common.Message` + """""" + for message in messages: + if message.offset < self.last_offset_consumed: + log.debug(""Skipping enqueue for offset (%s) "" + ""less than last_offset_consumed (%s)"", + message.offset, self.last_offset_consumed)","class OwnedPartition(object): + :type messages: Iterable of :class:`pykafka.common.Message` + """""" + for message in messages: + if message.offset <= self.last_offset_consumed: + log.debug(""Skipping enqueue for offset (%s) "" + ""less than last_offset_consumed (%s)"", + message.offset, self.last_offset_consumed)" +197,https://:@github.com/Parsely/pykafka.git,e515296f6b130acb930ddc9f97e84a7997aedb2f,"@@ -137,7 +137,7 @@ class ProducerIntegrationTests(unittest2.TestCase): + start = time.time() + producer.produce(uuid4().bytes) + producer.produce(uuid4().bytes) +- self.assertTrue(int(time.time() - start) > int(linger)) ++ self.assertTrue(int(time.time() - start) >= int(linger)) + self.consumer.consume() + self.consumer.consume() + +",tests/pykafka/test_producer.py,"ReplaceText(target='>=' @(140,49)->(140,50))","class ProducerIntegrationTests(unittest2.TestCase): + start = time.time() + producer.produce(uuid4().bytes) + producer.produce(uuid4().bytes) + self.assertTrue(int(time.time() - start) > int(linger)) + self.consumer.consume() + self.consumer.consume() + ","class ProducerIntegrationTests(unittest2.TestCase): + start = time.time() + producer.produce(uuid4().bytes) + producer.produce(uuid4().bytes) + self.assertTrue(int(time.time() - start) >= int(linger)) + self.consumer.consume() + self.consumer.consume() + " +198,https://:@github.com/Parsely/pykafka.git,ad8f2d457b8ca3b7dc7a75360f00becd7f0484a4,"@@ -595,7 +595,7 @@ class OwnedBroker(object): + # bind the MessageSizeTooLarge error the delivery + # report and remove it from the producer queue + message = self.queue.pop() +- self._delivery_reports.put(peeked_message, exc=exc) ++ self._delivery_reports.put(message, exc=exc) + # remove from pending message count + self.increment_messages_pending(-1) + continue +",pykafka/producer.py,"ReplaceText(target='message' @(598,51)->(598,65))","class OwnedBroker(object): + # bind the MessageSizeTooLarge error the delivery + # report and remove it from the producer queue + message = self.queue.pop() + self._delivery_reports.put(peeked_message, exc=exc) + # remove from pending message count + self.increment_messages_pending(-1) + continue","class OwnedBroker(object): + # bind the MessageSizeTooLarge error the delivery + # report and remove it from the producer queue + message = self.queue.pop() + self._delivery_reports.put(message, exc=exc) + # remove from pending message count + self.increment_messages_pending(-1) + continue" +199,https://:@github.com/Parsely/pykafka.git,217865b12c58addc95c419f159b477bc5636c6a9,"@@ -594,7 +594,7 @@ class SimpleConsumer(object): + to_retry = [pair for err in itervalues(parts_by_error) for pair in err] + reqs = [p.build_offset_fetch_request() for p, _ in to_retry] + +- if len(parts_by_error) > 1: ++ if len(parts_by_error) > 0: + raise KafkaException(parts_by_error) + + def reset_offsets(self, partition_offsets=None): +",pykafka/simpleconsumer.py,"ReplaceText(target='0' @(597,33)->(597,34))","class SimpleConsumer(object): + to_retry = [pair for err in itervalues(parts_by_error) for pair in err] + reqs = [p.build_offset_fetch_request() for p, _ in to_retry] + + if len(parts_by_error) > 1: + raise KafkaException(parts_by_error) + + def reset_offsets(self, partition_offsets=None):","class SimpleConsumer(object): + to_retry = [pair for err in itervalues(parts_by_error) for pair in err] + reqs = [p.build_offset_fetch_request() for p, _ in to_retry] + + if len(parts_by_error) > 0: + raise KafkaException(parts_by_error) + + def reset_offsets(self, partition_offsets=None):" +200,https://:@github.com/Timidger/Wikia.git,ff74a5711925274af13738f4b588a46356a1fa98,"@@ -395,7 +395,7 @@ class WikiaPage(object): + # Remove the /revision/ fluff after the image url + image = image.partition(""/revision/"")[0] + image_type = mimetypes.guess_type(image)[0] +- if image_type is None: ++ if image_type is not None: + image_type = ""."" + image_type.split(""/"")[-1] + else: + image_type = "".png"" # in case mimetypes.guess cant find it it will return None +",wikia/wikia.py,"ReplaceText(target=' is not ' @(398,23)->(398,27))","class WikiaPage(object): + # Remove the /revision/ fluff after the image url + image = image.partition(""/revision/"")[0] + image_type = mimetypes.guess_type(image)[0] + if image_type is None: + image_type = ""."" + image_type.split(""/"")[-1] + else: + image_type = "".png"" # in case mimetypes.guess cant find it it will return None","class WikiaPage(object): + # Remove the /revision/ fluff after the image url + image = image.partition(""/revision/"")[0] + image_type = mimetypes.guess_type(image)[0] + if image_type is not None: + image_type = ""."" + image_type.split(""/"")[-1] + else: + image_type = "".png"" # in case mimetypes.guess cant find it it will return None" +201,https://:@github.com/meetshah1995/pytorch-semseg.git,81997cd5af36759773a67b11cf148d3876b13a69,"@@ -156,7 +156,7 @@ def train(cfg, writer, logger): + labels_val = labels_val.to(device) + + outputs = model(images_val) +- val_loss = loss_fn(input=outputs, target=labels) ++ val_loss = loss_fn(input=outputs, target=labels_val) + + pred = outputs.data.max(1)[1].cpu().numpy() + gt = labels_val.data.cpu().numpy() +",train.py,"ReplaceText(target='labels_val' @(159,65)->(159,71))","def train(cfg, writer, logger): + labels_val = labels_val.to(device) + + outputs = model(images_val) + val_loss = loss_fn(input=outputs, target=labels) + + pred = outputs.data.max(1)[1].cpu().numpy() + gt = labels_val.data.cpu().numpy()","def train(cfg, writer, logger): + labels_val = labels_val.to(device) + + outputs = model(images_val) + val_loss = loss_fn(input=outputs, target=labels_val) + + pred = outputs.data.max(1)[1].cpu().numpy() + gt = labels_val.data.cpu().numpy()" +202,https://:@github.com/meetshah1995/pytorch-semseg.git,801fb200547caa5b0d91b8dde56b837da029f746,"@@ -27,7 +27,7 @@ def multi_scale_cross_entropy2d(input, target, weight=None, size_average=True, s + n_inp = len(input) + scale = 0.4 + scale_weight = torch.pow(scale * torch.ones(n_inp), torch.arange(n_inp).float()).to( +- input.device ++ target.device + ) + + loss = 0.0 +",ptsemseg/loss/loss.py,"ReplaceText(target='target' @(30,12)->(30,17))","def multi_scale_cross_entropy2d(input, target, weight=None, size_average=True, s + n_inp = len(input) + scale = 0.4 + scale_weight = torch.pow(scale * torch.ones(n_inp), torch.arange(n_inp).float()).to( + input.device + ) + + loss = 0.0","def multi_scale_cross_entropy2d(input, target, weight=None, size_average=True, s + n_inp = len(input) + scale = 0.4 + scale_weight = torch.pow(scale * torch.ones(n_inp), torch.arange(n_inp).float()).to( + target.device + ) + + loss = 0.0" +203,https://:@github.com/bhmm/bhmm.git,34f1e00dc49a99094b5c492381d9f711e96fc4d9,"@@ -192,7 +192,7 @@ def estimate_initial_hmm(observations, nstates, reversible=True, eps_A=None, eps + # does the count matrix too few closed sets to give nstates metastable states? Then we need a prior + if len(_tmatrix_disconnected.closed_sets(C)) < nstates: + msm_prior = 0.001 +- B = msm_prior * np.eye(C_full.shape[0]) # diagonal prior ++ B = msm_prior * np.eye(C.shape[0]) # diagonal prior + B += msmtools.estimation.prior_neighbor(C, alpha=msm_prior) # neighbor prior + C_post = C + B # posterior + P_for_pcca = _tmatrix_disconnected.estimate_P(C_post, reversible=True) +",bhmm/init/discrete.py,"ReplaceText(target='C' @(195,31)->(195,37))","def estimate_initial_hmm(observations, nstates, reversible=True, eps_A=None, eps + # does the count matrix too few closed sets to give nstates metastable states? Then we need a prior + if len(_tmatrix_disconnected.closed_sets(C)) < nstates: + msm_prior = 0.001 + B = msm_prior * np.eye(C_full.shape[0]) # diagonal prior + B += msmtools.estimation.prior_neighbor(C, alpha=msm_prior) # neighbor prior + C_post = C + B # posterior + P_for_pcca = _tmatrix_disconnected.estimate_P(C_post, reversible=True)","def estimate_initial_hmm(observations, nstates, reversible=True, eps_A=None, eps + # does the count matrix too few closed sets to give nstates metastable states? Then we need a prior + if len(_tmatrix_disconnected.closed_sets(C)) < nstates: + msm_prior = 0.001 + B = msm_prior * np.eye(C.shape[0]) # diagonal prior + B += msmtools.estimation.prior_neighbor(C, alpha=msm_prior) # neighbor prior + C_post = C + B # posterior + P_for_pcca = _tmatrix_disconnected.estimate_P(C_post, reversible=True)" +204,https://:@github.com/rackspace/pyrax.git,71a7f1924e2c53a4caac54e2b8eb985c207869c7,"@@ -220,7 +220,7 @@ class ManagerTest(unittest.TestCase): + ret = mgr.findall(some_att=""ok"") + self.assertTrue(o1 in ret) + self.assertFalse(o2 in ret) +- self.assertTrue(o1 in ret) ++ self.assertTrue(o3 in ret) + mgr.list = sav + + def test_findall_bad_att(self): +",tests/unit/test_manager.py,"ReplaceText(target='o3' @(223,24)->(223,26))","class ManagerTest(unittest.TestCase): + ret = mgr.findall(some_att=""ok"") + self.assertTrue(o1 in ret) + self.assertFalse(o2 in ret) + self.assertTrue(o1 in ret) + mgr.list = sav + + def test_findall_bad_att(self):","class ManagerTest(unittest.TestCase): + ret = mgr.findall(some_att=""ok"") + self.assertTrue(o1 in ret) + self.assertFalse(o2 in ret) + self.assertTrue(o3 in ret) + mgr.list = sav + + def test_findall_bad_att(self):" +205,https://:@github.com/deckbsd/glouton-satnogs-data-downloader.git,7b3982a3ac4c7ecb086cf6ce504aa766a54f1211,"@@ -25,7 +25,7 @@ class ObservationRepo: + + self.__read_page(r.json(), self.__cmd.start_date, self.__cmd.end_date) + page += 1 +- params['page'] += str(page) ++ params['page'] = str(page) + + print('\ndownloading started (Ctrl + F5 to stop)...\t~( ^o^)~') + self.__create_workers_and_wait() +",repositories/observation/observationsRepo.py,"ReplaceText(target='=' @(28,27)->(28,29))","class ObservationRepo: + + self.__read_page(r.json(), self.__cmd.start_date, self.__cmd.end_date) + page += 1 + params['page'] += str(page) + + print('\ndownloading started (Ctrl + F5 to stop)...\t~( ^o^)~') + self.__create_workers_and_wait()","class ObservationRepo: + + self.__read_page(r.json(), self.__cmd.start_date, self.__cmd.end_date) + page += 1 + params['page'] = str(page) + + print('\ndownloading started (Ctrl + F5 to stop)...\t~( ^o^)~') + self.__create_workers_and_wait()" +206,https://:@github.com/vmware/pyvcloud.git,e250911c7ba7666c42c2fa197f32744424d647ff,"@@ -121,7 +121,7 @@ class VCA(object): + #todo: check if vcloud session can be cached as well... + vCloudSession = self.create_vCloudSession(vdcReference[1]) + if vCloudSession: +- vcd = VCD(vCloudSession, serviceId, serviceId) ++ vcd = VCD(vCloudSession, serviceId, vdcId) + return vcd + return None + +",pyvcloud/vcloudair.py,"ReplaceText(target='vdcId' @(124,52)->(124,61))","class VCA(object): + #todo: check if vcloud session can be cached as well... + vCloudSession = self.create_vCloudSession(vdcReference[1]) + if vCloudSession: + vcd = VCD(vCloudSession, serviceId, serviceId) + return vcd + return None + ","class VCA(object): + #todo: check if vcloud session can be cached as well... + vCloudSession = self.create_vCloudSession(vdcReference[1]) + if vCloudSession: + vcd = VCD(vCloudSession, serviceId, vdcId) + return vcd + return None + " +207,https://:@github.com/vmware/pyvcloud.git,0b7926b141b58afbf94168ac95f1ab3f00f14e71,"@@ -2129,7 +2129,7 @@ class VDC(object): + policy_list = [] + for policy_reference in policy_references.VdcComputePolicyReference: + policy_list.append(policy_reference) +- return policy_reference ++ return policy_list + + def add_compute_policy(self, href): + """"""Add a VdcComputePolicy. +",pyvcloud/vcd/vdc.py,"ReplaceText(target='policy_list' @(2132,15)->(2132,31))","class VDC(object): + policy_list = [] + for policy_reference in policy_references.VdcComputePolicyReference: + policy_list.append(policy_reference) + return policy_reference + + def add_compute_policy(self, href): + """"""Add a VdcComputePolicy.","class VDC(object): + policy_list = [] + for policy_reference in policy_references.VdcComputePolicyReference: + policy_list.append(policy_reference) + return policy_list + + def add_compute_policy(self, href): + """"""Add a VdcComputePolicy." +208,https://:@github.com/springer-math/Mathematics-of-Epidemics-on-Networks.git,1f069443a464955c87cfa926c0ad8c8ce66bc424,"@@ -851,7 +851,7 @@ def get_infected_nodes(G, tau, gamma, initial_infecteds=None): + elif G.has_node(initial_infecteds): + initial_infecteds=[initial_infecteds] + H = directed_percolate_network(G, tau, gamma) +- infected_nodes = _out_component_(G, initial_infecteds) ++ infected_nodes = _out_component_(H, initial_infecteds) + return infected_nodes + + +",EoN/simulation.py,"ReplaceText(target='H' @(854,37)->(854,38))","def get_infected_nodes(G, tau, gamma, initial_infecteds=None): + elif G.has_node(initial_infecteds): + initial_infecteds=[initial_infecteds] + H = directed_percolate_network(G, tau, gamma) + infected_nodes = _out_component_(G, initial_infecteds) + return infected_nodes + + ","def get_infected_nodes(G, tau, gamma, initial_infecteds=None): + elif G.has_node(initial_infecteds): + initial_infecteds=[initial_infecteds] + H = directed_percolate_network(G, tau, gamma) + infected_nodes = _out_component_(H, initial_infecteds) + return infected_nodes + + " +209,https://:@github.com/waipbmtd/python-client.git,3d95fa3fb3d85c14d1b92da348b4f2f0b007424b,"@@ -135,7 +135,7 @@ def show(path): + def validate_params(ctx, param, value): + if any(['=' not in item for item in value]): + raise click.BadParameter('Parameters need to be in format =') +- return dict([tuple(item.split('=', 1)) for item in param]) ++ return dict([tuple(item.split('=', 1)) for item in value]) + + + def validate_inplace(ctx, param, value): +",coreapi/commandline.py,"ReplaceText(target='value' @(138,55)->(138,60))","def show(path): + def validate_params(ctx, param, value): + if any(['=' not in item for item in value]): + raise click.BadParameter('Parameters need to be in format =') + return dict([tuple(item.split('=', 1)) for item in param]) + + + def validate_inplace(ctx, param, value):","def show(path): + def validate_params(ctx, param, value): + if any(['=' not in item for item in value]): + raise click.BadParameter('Parameters need to be in format =') + return dict([tuple(item.split('=', 1)) for item in value]) + + + def validate_inplace(ctx, param, value):" +210,https://:@github.com/waipbmtd/python-client.git,e630971368e28989484272ca7774af385ce3ddd6,"@@ -436,7 +436,7 @@ def credentials_show(): + @click.option('--auth', metavar=""AUTH_SCHEME"", help='Auth scheme to apply to the credentials string. Options: ""none"", ""basic"". Default is ""none"".', default='none', type=click.Choice(['none', 'basic'])) + def credentials_add(domain, credentials_string, auth): + if auth == 'none': +- header = auth ++ header = credentials_string + elif auth == 'basic': + header = 'Basic ' + b64encode(credentials_string) + credentials = get_credentials() +",coreapi/commandline.py,"ReplaceText(target='credentials_string' @(439,17)->(439,21))","def credentials_show(): + @click.option('--auth', metavar=""AUTH_SCHEME"", help='Auth scheme to apply to the credentials string. Options: ""none"", ""basic"". Default is ""none"".', default='none', type=click.Choice(['none', 'basic'])) + def credentials_add(domain, credentials_string, auth): + if auth == 'none': + header = auth + elif auth == 'basic': + header = 'Basic ' + b64encode(credentials_string) + credentials = get_credentials()","def credentials_show(): + @click.option('--auth', metavar=""AUTH_SCHEME"", help='Auth scheme to apply to the credentials string. Options: ""none"", ""basic"". Default is ""none"".', default='none', type=click.Choice(['none', 'basic'])) + def credentials_add(domain, credentials_string, auth): + if auth == 'none': + header = credentials_string + elif auth == 'basic': + header = 'Basic ' + b64encode(credentials_string) + credentials = get_credentials()" +211,https://:@github.com/openfisca/openfisca-survey-manager.git,b1c6e08ca7ddd546171b5623ce0ae04ed9f597fd,"@@ -24,7 +24,7 @@ def temporary_store_decorator(config_files_directory = default_config_files_dire + 'tmp_directory is not set: {!r} in {}'.format(tmp_directory, read_config_file_name) + assert os.path.isabs(tmp_directory), \ + 'tmp_directory should be an absolut path: {!r} in {}'.format(tmp_directory, read_config_file_name) +- if os.path.isdir(tmp_directory): ++ if not os.path.isdir(tmp_directory): + 'tmp_directory does not exist: {!r} in {}. Creating it.'.format(tmp_directory, read_config_file_name) + os.makedirs(tmp_directory) + +",openfisca_survey_manager/temporary.py,"ReplaceText(target='not ' @(27,7)->(27,7))","def temporary_store_decorator(config_files_directory = default_config_files_dire + 'tmp_directory is not set: {!r} in {}'.format(tmp_directory, read_config_file_name) + assert os.path.isabs(tmp_directory), \ + 'tmp_directory should be an absolut path: {!r} in {}'.format(tmp_directory, read_config_file_name) + if os.path.isdir(tmp_directory): + 'tmp_directory does not exist: {!r} in {}. Creating it.'.format(tmp_directory, read_config_file_name) + os.makedirs(tmp_directory) + ","def temporary_store_decorator(config_files_directory = default_config_files_dire + 'tmp_directory is not set: {!r} in {}'.format(tmp_directory, read_config_file_name) + assert os.path.isabs(tmp_directory), \ + 'tmp_directory should be an absolut path: {!r} in {}'.format(tmp_directory, read_config_file_name) + if not os.path.isdir(tmp_directory): + 'tmp_directory does not exist: {!r} in {}. Creating it.'.format(tmp_directory, read_config_file_name) + os.makedirs(tmp_directory) + " +212,https://:@github.com/ARMmbed/yotta.git,e948620774774810165b28968ce0324b1f5bb953,"@@ -329,7 +329,7 @@ def satisfyTarget(name, version_required, working_directory, update_installed=No + # must rm the old target before continuing + fsutils.rmRf(target_path) + +- if not v and update_installed is None: ++ if not v and update_installed is not None: + v = latestSuitableVersion(name, version_required, registry='target') + + if not v: +",yotta/lib/access.py,"ReplaceText(target=' is not ' @(332,33)->(332,37))","def satisfyTarget(name, version_required, working_directory, update_installed=No + # must rm the old target before continuing + fsutils.rmRf(target_path) + + if not v and update_installed is None: + v = latestSuitableVersion(name, version_required, registry='target') + + if not v:","def satisfyTarget(name, version_required, working_directory, update_installed=No + # must rm the old target before continuing + fsutils.rmRf(target_path) + + if not v and update_installed is not None: + v = latestSuitableVersion(name, version_required, registry='target') + + if not v:" +213,https://:@github.com/ARMmbed/yotta.git,06a9d7e69861044818b5a5de490336f6be65d6f1,"@@ -371,7 +371,7 @@ def generateTest(**kwargs): + test_method.__name__ = test_name + setattr(TestCLITestGenerated, test_name, test_method) + +-if not util.canBuildNatively(): ++if util.canBuildNatively(): + forAllReporterTests(generateTest) + else: + print('WARNING: skipping test reporter tests (cannot build natively on this platform)') +",yotta/test/cli/test_test.py,"ReplaceText(target='' @(374,3)->(374,7))","def generateTest(**kwargs): + test_method.__name__ = test_name + setattr(TestCLITestGenerated, test_name, test_method) + + if not util.canBuildNatively(): + forAllReporterTests(generateTest) + else: + print('WARNING: skipping test reporter tests (cannot build natively on this platform)')","def generateTest(**kwargs): + test_method.__name__ = test_name + setattr(TestCLITestGenerated, test_name, test_method) + + if util.canBuildNatively(): + forAllReporterTests(generateTest) + else: + print('WARNING: skipping test reporter tests (cannot build natively on this platform)')" +214,https://:@github.com/b1naryth1ef/disco.git,bd75deb29adcc42f8de451d51e7dbc02eb360b1e,"@@ -112,7 +112,7 @@ class Plugin(LoggingClass, PluginDeco): + + def register_command(self, func, *args, **kwargs): + wrapped = functools.partial(self._dispatch, 'command', func) +- self.commands[func.__name__] = Command(self, func, *args, **kwargs) ++ self.commands[func.__name__] = Command(self, wrapped, *args, **kwargs) + + def destroy(self): + map(lambda k: k.remove(), self._events) +",disco/bot/plugin.py,"ReplaceText(target='wrapped' @(115,53)->(115,57))","class Plugin(LoggingClass, PluginDeco): + + def register_command(self, func, *args, **kwargs): + wrapped = functools.partial(self._dispatch, 'command', func) + self.commands[func.__name__] = Command(self, func, *args, **kwargs) + + def destroy(self): + map(lambda k: k.remove(), self._events)","class Plugin(LoggingClass, PluginDeco): + + def register_command(self, func, *args, **kwargs): + wrapped = functools.partial(self._dispatch, 'command', func) + self.commands[func.__name__] = Command(self, wrapped, *args, **kwargs) + + def destroy(self): + map(lambda k: k.remove(), self._events)" +215,https://:@github.com/b1naryth1ef/disco.git,c5848dbe8b66295598b4e6cad1c5ec8f5cc3a5fb,"@@ -305,7 +305,7 @@ class Channel(SlottedModel, Permissible): + return + + if self.can(self.client.state.me, Permissions.MANAGE_MESSAGES) and len(messages) > 2: +- for chunk in chunks(messages, 100): ++ for chunk in chunks(message_ids, 100): + self.client.api.channels_messages_delete_bulk(self.id, chunk) + else: + for msg in messages: +",disco/types/channel.py,"ReplaceText(target='message_ids' @(308,32)->(308,40))","class Channel(SlottedModel, Permissible): + return + + if self.can(self.client.state.me, Permissions.MANAGE_MESSAGES) and len(messages) > 2: + for chunk in chunks(messages, 100): + self.client.api.channels_messages_delete_bulk(self.id, chunk) + else: + for msg in messages:","class Channel(SlottedModel, Permissible): + return + + if self.can(self.client.state.me, Permissions.MANAGE_MESSAGES) and len(messages) > 2: + for chunk in chunks(message_ids, 100): + self.client.api.channels_messages_delete_bulk(self.id, chunk) + else: + for msg in messages:" +216,https://:@github.com/yuru-yuri/manga-dl.git,5cbcbd37c4f904720d08074241a890851b94a7dd,"@@ -26,7 +26,7 @@ if __name__ == '__main__': + if parse_args.cli: + cli = Cli(args) + # cli +- exit(0 if cli.status else 0) ++ exit(0 if cli.status else 1) + + # else run GUI + app = QApplication(argv) +",manga.py,"ReplaceText(target='1' @(29,34)->(29,35))","if __name__ == '__main__': + if parse_args.cli: + cli = Cli(args) + # cli + exit(0 if cli.status else 0) + + # else run GUI + app = QApplication(argv)","if __name__ == '__main__': + if parse_args.cli: + cli = Cli(args) + # cli + exit(0 if cli.status else 1) + + # else run GUI + app = QApplication(argv)" +217,https://:@github.com/yuru-yuri/manga-dl.git,f10777831c4c128a6f6a9bb1d9903889a43ad1df,"@@ -44,7 +44,7 @@ class WebDriver: + driver_path = self._driver_path() + if not is_file(driver_path): + self.download_drivder() +- self.is_win() and chmod(driver_path, 0o755) ++ self.is_win() or chmod(driver_path, 0o755) + driver = webdriver.Chrome(executable_path=driver_path) + driver.set_window_size(500, 600) + return driver +",src/base_classes/web_driver.py,"ReplaceText(target='or' @(47,22)->(47,25))","class WebDriver: + driver_path = self._driver_path() + if not is_file(driver_path): + self.download_drivder() + self.is_win() and chmod(driver_path, 0o755) + driver = webdriver.Chrome(executable_path=driver_path) + driver.set_window_size(500, 600) + return driver","class WebDriver: + driver_path = self._driver_path() + if not is_file(driver_path): + self.download_drivder() + self.is_win() or chmod(driver_path, 0o755) + driver = webdriver.Chrome(executable_path=driver_path) + driver.set_window_size(500, 600) + return driver" +218,https://:@github.com/veg/bioext.git,5fbb2b3fb52d1e59b787713f9d9521124cb2f24b,"@@ -217,7 +217,7 @@ def _translate_gapped(seq, *args, **kwds): + elif gaps: + protein += '-' * gaps + gaps = 0 +- lwr = j ++ lwr = i + if gaps: + protein += '-' * gaps + else: +",lib/BioExt/_util.py,"ReplaceText(target='i' @(220,18)->(220,19))","def _translate_gapped(seq, *args, **kwds): + elif gaps: + protein += '-' * gaps + gaps = 0 + lwr = j + if gaps: + protein += '-' * gaps + else:","def _translate_gapped(seq, *args, **kwds): + elif gaps: + protein += '-' * gaps + gaps = 0 + lwr = i + if gaps: + protein += '-' * gaps + else:" +219,https://:@github.com/python-trio/trio.git,82253caa8bd59b5b3bbb0ba61d196289c967f838,"@@ -371,7 +371,7 @@ def test_waitid_eintr(): + sync_wait_reapable(sleeper.pid) + assert sleeper.wait(timeout=1) == -9 + finally: +- if sleeper.returncode is not None: ++ if sleeper.returncode is None: + sleeper.kill() + sleeper.wait() + signal.signal(signal.SIGALRM, old_sigalrm) +",trio/tests/test_subprocess.py,"ReplaceText(target=' is ' @(374,29)->(374,37))","def test_waitid_eintr(): + sync_wait_reapable(sleeper.pid) + assert sleeper.wait(timeout=1) == -9 + finally: + if sleeper.returncode is not None: + sleeper.kill() + sleeper.wait() + signal.signal(signal.SIGALRM, old_sigalrm)","def test_waitid_eintr(): + sync_wait_reapable(sleeper.pid) + assert sleeper.wait(timeout=1) == -9 + finally: + if sleeper.returncode is None: + sleeper.kill() + sleeper.wait() + signal.signal(signal.SIGALRM, old_sigalrm)" +220,https://:@github.com/python-trio/trio.git,94a587f758f0597cd790505ca7bfbec17a247fb1,"@@ -37,7 +37,7 @@ def test_warn_deprecated(recwarn_always): + assert ""water instead"" in got.message.args[0] + assert ""/issues/1"" in got.message.args[0] + assert got.filename == filename +- assert got.lineno == lineno + 1 ++ assert got.lineno == lineno - 1 + + + def test_warn_deprecated_no_instead_or_issue(recwarn_always): +",trio/tests/test_deprecate.py,"ReplaceText(target='-' @(40,32)->(40,33))","def test_warn_deprecated(recwarn_always): + assert ""water instead"" in got.message.args[0] + assert ""/issues/1"" in got.message.args[0] + assert got.filename == filename + assert got.lineno == lineno + 1 + + + def test_warn_deprecated_no_instead_or_issue(recwarn_always):","def test_warn_deprecated(recwarn_always): + assert ""water instead"" in got.message.args[0] + assert ""/issues/1"" in got.message.args[0] + assert got.filename == filename + assert got.lineno == lineno - 1 + + + def test_warn_deprecated_no_instead_or_issue(recwarn_always):" +221,https://:@github.com/python-trio/trio.git,8d9effc1d32b8ef2f7a7a02c1b02a4de3f5f8e3d,"@@ -90,7 +90,7 @@ def ki_protection_enabled(frame): + if frame.f_code.co_name == ""__del__"": + return True + frame = frame.f_back +- return False ++ return True + + + def currently_ki_protected(): +",trio/_core/_ki.py,"ReplaceText(target='True' @(93,11)->(93,16))","def ki_protection_enabled(frame): + if frame.f_code.co_name == ""__del__"": + return True + frame = frame.f_back + return False + + + def currently_ki_protected():","def ki_protection_enabled(frame): + if frame.f_code.co_name == ""__del__"": + return True + frame = frame.f_back + return True + + + def currently_ki_protected():" +222,https://:@github.com/tkrajina/srtm.py.git,b1e1c673b613780c6a7151ab3db53461e2b668c7,"@@ -187,7 +187,7 @@ class GeoElevationData: + for row in range(height): + for column in range(width): + latitude = latitude_from + float(row) / height * (latitude_to - latitude_from) +- longitude = longitude_from + float(column) / height * (longitude_to - longitude_from) ++ longitude = longitude_from + float(column) / width * (longitude_to - longitude_from) + elevation = self.get_elevation(latitude, longitude) + array[row,column] = elevation + +",srtm/data.py,"ReplaceText(target='width' @(190,65)->(190,71))","class GeoElevationData: + for row in range(height): + for column in range(width): + latitude = latitude_from + float(row) / height * (latitude_to - latitude_from) + longitude = longitude_from + float(column) / height * (longitude_to - longitude_from) + elevation = self.get_elevation(latitude, longitude) + array[row,column] = elevation + ","class GeoElevationData: + for row in range(height): + for column in range(width): + latitude = latitude_from + float(row) / height * (latitude_to - latitude_from) + longitude = longitude_from + float(column) / width * (longitude_to - longitude_from) + elevation = self.get_elevation(latitude, longitude) + array[row,column] = elevation + " +223,https://:@github.com/tkrajina/srtm.py.git,771bb0e73e7b478603f73644a8c8f441b0e02e9f,"@@ -208,7 +208,7 @@ class GeoElevationData: + for row in range(height): + for column in range(width): + latitude = latitude_from + float(row) / height * (latitude_to - latitude_from) +- longitude = longitude_from + float(column) / height * (longitude_to - longitude_from) ++ longitude = longitude_from + float(column) / width * (longitude_to - longitude_from) + elevation = self.get_elevation(latitude, longitude) + if elevation == None: + color = unknown_color +",srtm/data.py,"ReplaceText(target='width' @(211,65)->(211,71))","class GeoElevationData: + for row in range(height): + for column in range(width): + latitude = latitude_from + float(row) / height * (latitude_to - latitude_from) + longitude = longitude_from + float(column) / height * (longitude_to - longitude_from) + elevation = self.get_elevation(latitude, longitude) + if elevation == None: + color = unknown_color","class GeoElevationData: + for row in range(height): + for column in range(width): + latitude = latitude_from + float(row) / height * (latitude_to - latitude_from) + longitude = longitude_from + float(column) / width * (longitude_to - longitude_from) + elevation = self.get_elevation(latitude, longitude) + if elevation == None: + color = unknown_color" +224,https://:@github.com/mwouts/nbrmd.git,628e3f952bb786220efc1e14b976809bf8ea96be,"@@ -218,7 +218,7 @@ def readf(nb_file): + 'Expected extensions are {}'.format(nb_file, + notebook_extensions)) + with io.open(nb_file, encoding='utf-8') as fp: +- return read(nb_file, as_version=4, ext=ext) ++ return read(fp, as_version=4, ext=ext) + + + def writef(nb, nb_file): +",nbrmd/nbrmd.py,"ReplaceText(target='fp' @(221,20)->(221,27))","def readf(nb_file): + 'Expected extensions are {}'.format(nb_file, + notebook_extensions)) + with io.open(nb_file, encoding='utf-8') as fp: + return read(nb_file, as_version=4, ext=ext) + + + def writef(nb, nb_file):","def readf(nb_file): + 'Expected extensions are {}'.format(nb_file, + notebook_extensions)) + with io.open(nb_file, encoding='utf-8') as fp: + return read(fp, as_version=4, ext=ext) + + + def writef(nb, nb_file):" +225,https://:@github.com/mwouts/nbrmd.git,366614bce3dc65c6e88bcf37c4e2cd31ea36de92,"@@ -63,7 +63,7 @@ def test_load_save_rename_nbpy(nb_file, tmpdir): + cm.save(model=dict(type='notebook', content=nb), path=tmp_ipynb) + + # rename nbpy +- cm.rename(tmp_ipynb, 'new.nb.py') ++ cm.rename(tmp_nbpy, 'new.nb.py') + assert not os.path.isfile(str(tmpdir.join(tmp_ipynb))) + assert not os.path.isfile(str(tmpdir.join(tmp_nbpy))) + +",tests/test_contentsmanager.py,"ReplaceText(target='tmp_nbpy' @(66,14)->(66,23))","def test_load_save_rename_nbpy(nb_file, tmpdir): + cm.save(model=dict(type='notebook', content=nb), path=tmp_ipynb) + + # rename nbpy + cm.rename(tmp_ipynb, 'new.nb.py') + assert not os.path.isfile(str(tmpdir.join(tmp_ipynb))) + assert not os.path.isfile(str(tmpdir.join(tmp_nbpy))) + ","def test_load_save_rename_nbpy(nb_file, tmpdir): + cm.save(model=dict(type='notebook', content=nb), path=tmp_ipynb) + + # rename nbpy + cm.rename(tmp_nbpy, 'new.nb.py') + assert not os.path.isfile(str(tmpdir.join(tmp_ipynb))) + assert not os.path.isfile(str(tmpdir.join(tmp_nbpy))) + " +226,https://:@github.com/mwouts/nbrmd.git,171256b67818ab86f43e35065fc828234e9abf98,"@@ -163,7 +163,7 @@ class CellExporter(): + return True + if all([line.startswith('#') for line in self.source]): + return True +- if CellReader(self.ext).read(source)[1] != len(source): ++ if CellReader(self.ext).read(source)[1] < len(source): + return True + + return False +",jupytext/cell_to_text.py,"ReplaceText(target='<' @(166,48)->(166,50))","class CellExporter(): + return True + if all([line.startswith('#') for line in self.source]): + return True + if CellReader(self.ext).read(source)[1] != len(source): + return True + + return False","class CellExporter(): + return True + if all([line.startswith('#') for line in self.source]): + return True + if CellReader(self.ext).read(source)[1] < len(source): + return True + + return False" +227,https://:@github.com/mwouts/nbrmd.git,8048c8d0a09eab875376c7a4d1efb3cd886b8d3c,"@@ -122,7 +122,7 @@ def metadata_and_cell_to_header(notebook, text_format, ext): + if lines_to_next_cell is None and notebook.cells: + lines_to_next_cell = pep8_lines_between_cells(header, notebook.cells[0], ext) + else: +- lines_to_next_cell = 0 ++ lines_to_next_cell = 1 + + header.extend([''] * lines_to_next_cell) + +",jupytext/header.py,"ReplaceText(target='1' @(125,29)->(125,30))","def metadata_and_cell_to_header(notebook, text_format, ext): + if lines_to_next_cell is None and notebook.cells: + lines_to_next_cell = pep8_lines_between_cells(header, notebook.cells[0], ext) + else: + lines_to_next_cell = 0 + + header.extend([''] * lines_to_next_cell) + ","def metadata_and_cell_to_header(notebook, text_format, ext): + if lines_to_next_cell is None and notebook.cells: + lines_to_next_cell = pep8_lines_between_cells(header, notebook.cells[0], ext) + else: + lines_to_next_cell = 1 + + header.extend([''] * lines_to_next_cell) + " +228,https://:@github.com/mwouts/nbrmd.git,120bebc0d37792cfa1418476d5f26809b996dca8,"@@ -615,7 +615,7 @@ def test_sync(nb_file, tmpdir): + compare_notebooks(nb, nb2) + + # ipynb must be older than py file, otherwise our Contents Manager will complain +- assert os.path.getmtime(tmp_ipynb) < os.path.getmtime(tmp_py) ++ assert os.path.getmtime(tmp_ipynb) <= os.path.getmtime(tmp_py) + + + @pytest.mark.parametrize('nb_file,ext', +",tests/test_cli.py,"ReplaceText(target='<=' @(618,39)->(618,40))","def test_sync(nb_file, tmpdir): + compare_notebooks(nb, nb2) + + # ipynb must be older than py file, otherwise our Contents Manager will complain + assert os.path.getmtime(tmp_ipynb) < os.path.getmtime(tmp_py) + + + @pytest.mark.parametrize('nb_file,ext',","def test_sync(nb_file, tmpdir): + compare_notebooks(nb, nb2) + + # ipynb must be older than py file, otherwise our Contents Manager will complain + assert os.path.getmtime(tmp_ipynb) <= os.path.getmtime(tmp_py) + + + @pytest.mark.parametrize('nb_file,ext'," +229,https://:@github.com/mwouts/nbrmd.git,dfa96996445cbc7514b93337dbf94d592ba06bad,"@@ -19,4 +19,4 @@ def test_identity_source_write_read(nb_file, ext): + R = jupytext.writes(nb1, ext) + nb2 = jupytext.reads(R, ext) + +- compare_notebooks(nb1, nb2) ++ compare_notebooks(nb2, nb1) +",tests/test_ipynb_to_R.py,"ArgSwap(idxs=0<->1 @(22,4)->(22,21))","def test_identity_source_write_read(nb_file, ext): + R = jupytext.writes(nb1, ext) + nb2 = jupytext.reads(R, ext) + + compare_notebooks(nb1, nb2)","def test_identity_source_write_read(nb_file, ext): + R = jupytext.writes(nb1, ext) + nb2 = jupytext.reads(R, ext) + + compare_notebooks(nb2, nb1)" +230,https://:@github.com/mwouts/nbrmd.git,dfa96996445cbc7514b93337dbf94d592ba06bad,"@@ -16,4 +16,4 @@ def test_identity_source_write_read(nb_file): + py = jupytext.writes(nb1, 'py') + nb2 = jupytext.reads(py, 'py') + +- compare_notebooks(nb1, nb2) ++ compare_notebooks(nb2, nb1) +",tests/test_ipynb_to_py.py,"ArgSwap(idxs=0<->1 @(19,4)->(19,21))","def test_identity_source_write_read(nb_file): + py = jupytext.writes(nb1, 'py') + nb2 = jupytext.reads(py, 'py') + + compare_notebooks(nb1, nb2)","def test_identity_source_write_read(nb_file): + py = jupytext.writes(nb1, 'py') + nb2 = jupytext.reads(py, 'py') + + compare_notebooks(nb2, nb1)" +231,https://:@github.com/mwouts/nbrmd.git,dfa96996445cbc7514b93337dbf94d592ba06bad,"@@ -16,4 +16,4 @@ def test_identity_source_write_read(nb_file): + rmd = jupytext.writes(nb1, 'Rmd') + nb2 = jupytext.reads(rmd, 'Rmd') + +- compare_notebooks(nb1, nb2, 'Rmd') ++ compare_notebooks(nb2, nb1, 'Rmd') +",tests/test_ipynb_to_rmd.py,"ArgSwap(idxs=0<->1 @(19,4)->(19,21))","def test_identity_source_write_read(nb_file): + rmd = jupytext.writes(nb1, 'Rmd') + nb2 = jupytext.reads(rmd, 'Rmd') + + compare_notebooks(nb1, nb2, 'Rmd')","def test_identity_source_write_read(nb_file): + rmd = jupytext.writes(nb1, 'Rmd') + nb2 = jupytext.reads(rmd, 'Rmd') + + compare_notebooks(nb2, nb1, 'Rmd')" +232,https://:@github.com/splunk/splunk-sdk-python.git,68f87378d5bac7efc97cf118f6754b5a6de73fa3,"@@ -48,7 +48,7 @@ class EventWriter(object): + else: + self._out = TextIOWrapper(output) + +- if isinstance(output, TextIOBase): ++ if isinstance(error, TextIOBase): + self._err = error + else: + self._err = TextIOWrapper(error) +",splunklib/modularinput/event_writer.py,"ReplaceText(target='error' @(51,22)->(51,28))","class EventWriter(object): + else: + self._out = TextIOWrapper(output) + + if isinstance(output, TextIOBase): + self._err = error + else: + self._err = TextIOWrapper(error)","class EventWriter(object): + else: + self._out = TextIOWrapper(output) + + if isinstance(error, TextIOBase): + self._err = error + else: + self._err = TextIOWrapper(error)" +233,https://:@github.com/tgbugs/pyontutils.git,78db71bb8b163794ef9bafb5a0ee50453d29971a,"@@ -56,7 +56,7 @@ def sysidpath(ignore_options=False): + ) + for option in options: + if (option.exists() and +- os.access(options, os.R_OK) and ++ os.access(option, os.R_OK) and + option.stat().st_size > 0): + return option + +",pyontutils/utils.py,"ReplaceText(target='option' @(59,26)->(59,33))","def sysidpath(ignore_options=False): + ) + for option in options: + if (option.exists() and + os.access(options, os.R_OK) and + option.stat().st_size > 0): + return option + ","def sysidpath(ignore_options=False): + ) + for option in options: + if (option.exists() and + os.access(option, os.R_OK) and + option.stat().st_size > 0): + return option + " +234,https://:@github.com/holgern/beem.git,45ae6dc0380434d3544f5588fa24b379f5a62541,"@@ -224,7 +224,7 @@ class Blockchain(object): + else: + self.steem.rpc.get_block(blocknum, add_to_queue=True) + latest_block = blocknum +- if batches > 1: ++ if batches >= 1: + latest_block += 1 + if latest_block <= head_block: + if self.steem.rpc.get_use_appbase(): +",beem/blockchain.py,"ReplaceText(target='>=' @(227,31)->(227,32))","class Blockchain(object): + else: + self.steem.rpc.get_block(blocknum, add_to_queue=True) + latest_block = blocknum + if batches > 1: + latest_block += 1 + if latest_block <= head_block: + if self.steem.rpc.get_use_appbase():","class Blockchain(object): + else: + self.steem.rpc.get_block(blocknum, add_to_queue=True) + latest_block = blocknum + if batches >= 1: + latest_block += 1 + if latest_block <= head_block: + if self.steem.rpc.get_use_appbase():" +235,https://:@github.com/holgern/beem.git,9eb381d23d582979934e0d3256447aef7d67de55,"@@ -509,7 +509,7 @@ class Testcases(unittest.TestCase): + op_num = account.estimate_virtual_op_num(block_num, stop_diff=0.1, max_count=100) + if op_num > 0: + op_num -= 1 +- self.assertTrue(op_num < i) ++ self.assertTrue(op_num <= i) + i += 1 + last_block = new_block + +",tests/beem/test_account.py,"ReplaceText(target='<=' @(512,35)->(512,36))","class Testcases(unittest.TestCase): + op_num = account.estimate_virtual_op_num(block_num, stop_diff=0.1, max_count=100) + if op_num > 0: + op_num -= 1 + self.assertTrue(op_num < i) + i += 1 + last_block = new_block + ","class Testcases(unittest.TestCase): + op_num = account.estimate_virtual_op_num(block_num, stop_diff=0.1, max_count=100) + if op_num > 0: + op_num -= 1 + self.assertTrue(op_num <= i) + i += 1 + last_block = new_block + " +236,https://:@github.com/holgern/beem.git,5f156fdf5a75367c32d85efb02e456abfa2719f6,"@@ -714,6 +714,6 @@ class RecentByPath(list): + comments = [] + for reply in replies: + post = state[""content""][reply] +- if category is None or (category is not None and post[""category""] != category): ++ if category is None or (category is not None and post[""category""] == category): + comments.append(Comment(post, lazy=True, steem_instance=self.steem)) + super(RecentByPath, self).__init__(comments) +",beem/comment.py,"ReplaceText(target='==' @(717,78)->(717,80))","class RecentByPath(list): + comments = [] + for reply in replies: + post = state[""content""][reply] + if category is None or (category is not None and post[""category""] != category): + comments.append(Comment(post, lazy=True, steem_instance=self.steem)) + super(RecentByPath, self).__init__(comments)","class RecentByPath(list): + comments = [] + for reply in replies: + post = state[""content""][reply] + if category is None or (category is not None and post[""category""] == category): + comments.append(Comment(post, lazy=True, steem_instance=self.steem)) + super(RecentByPath, self).__init__(comments)" +237,https://:@github.com/holgern/beem.git,7b9ee9c75cbf285d18c1b4913cffe3798444ac30,"@@ -50,7 +50,7 @@ class RC(object): + resource_count[""resource_state_bytes""] += state_bytes_count + resource_count[""resource_new_accounts""] = new_account_op_count + if market_op_count > 0: +- resource_count[""resource_market_bytes""] = market_op_count ++ resource_count[""resource_market_bytes""] = tx_size + return resource_count + + def comment_dict(self, comment_dict): +",beem/rc.py,"ReplaceText(target='tx_size' @(53,54)->(53,69))","class RC(object): + resource_count[""resource_state_bytes""] += state_bytes_count + resource_count[""resource_new_accounts""] = new_account_op_count + if market_op_count > 0: + resource_count[""resource_market_bytes""] = market_op_count + return resource_count + + def comment_dict(self, comment_dict):","class RC(object): + resource_count[""resource_state_bytes""] += state_bytes_count + resource_count[""resource_new_accounts""] = new_account_op_count + if market_op_count > 0: + resource_count[""resource_market_bytes""] = tx_size + return resource_count + + def comment_dict(self, comment_dict):" +238,https://:@github.com/holgern/beem.git,9e96dc84f9965b25b6b2a56a1bca7b7652b93be8,"@@ -1456,7 +1456,7 @@ class Steem(object): + 'key_auths': active_key_authority, + ""address_auths"": [], + 'weight_threshold': 1}, +- 'posting': {'account_auths': active_accounts_authority, ++ 'posting': {'account_auths': posting_accounts_authority, + 'key_auths': posting_key_authority, + ""address_auths"": [], + 'weight_threshold': 1}, +",beem/steem.py,"ReplaceText(target='posting_accounts_authority' @(1459,41)->(1459,66))","class Steem(object): + 'key_auths': active_key_authority, + ""address_auths"": [], + 'weight_threshold': 1}, + 'posting': {'account_auths': active_accounts_authority, + 'key_auths': posting_key_authority, + ""address_auths"": [], + 'weight_threshold': 1},","class Steem(object): + 'key_auths': active_key_authority, + ""address_auths"": [], + 'weight_threshold': 1}, + 'posting': {'account_auths': posting_accounts_authority, + 'key_auths': posting_key_authority, + ""address_auths"": [], + 'weight_threshold': 1}," +239,https://:@github.com/holgern/beem.git,8e4214f27e746be7ed01c5d644911c830bfe988a,"@@ -135,7 +135,7 @@ class Block(BlockchainObject): + if ops_ops is None: + ops = None + else: +- ops = ops[""ops""] ++ ops = ops_ops[""ops""] + except ApiNotSupported: + ops = self.steem.rpc.get_ops_in_block(self.identifier, self.only_virtual_ops, api=""condenser"") + else: +",beem/block.py,"ReplaceText(target='ops_ops' @(138,30)->(138,33))","class Block(BlockchainObject): + if ops_ops is None: + ops = None + else: + ops = ops[""ops""] + except ApiNotSupported: + ops = self.steem.rpc.get_ops_in_block(self.identifier, self.only_virtual_ops, api=""condenser"") + else:","class Block(BlockchainObject): + if ops_ops is None: + ops = None + else: + ops = ops_ops[""ops""] + except ApiNotSupported: + ops = self.steem.rpc.get_ops_in_block(self.identifier, self.only_virtual_ops, api=""condenser"") + else:" +240,https://:@github.com/holgern/beem.git,d19894c85464f2bc5221e15f858326c4e8efdaf3,"@@ -367,7 +367,7 @@ class ActiveVotes(VotesObject): + elif isinstance(authorperm, string_types): + [author, permlink] = resolve_authorperm(authorperm) + if self.steem.rpc.get_use_appbase(): +- self.steem.rpc.set_next_node_on_empty_reply(True) ++ self.steem.rpc.set_next_node_on_empty_reply(False) + try: + votes = self.steem.rpc.get_active_votes(author, permlink, api=""condenser"") + except: +",beem/vote.py,"ReplaceText(target='False' @(370,60)->(370,64))","class ActiveVotes(VotesObject): + elif isinstance(authorperm, string_types): + [author, permlink] = resolve_authorperm(authorperm) + if self.steem.rpc.get_use_appbase(): + self.steem.rpc.set_next_node_on_empty_reply(True) + try: + votes = self.steem.rpc.get_active_votes(author, permlink, api=""condenser"") + except:","class ActiveVotes(VotesObject): + elif isinstance(authorperm, string_types): + [author, permlink] = resolve_authorperm(authorperm) + if self.steem.rpc.get_use_appbase(): + self.steem.rpc.set_next_node_on_empty_reply(False) + try: + votes = self.steem.rpc.get_active_votes(author, permlink, api=""condenser"") + except:" +241,https://:@github.com/holgern/beem.git,8f173f0ab272a57a5c036589dcc19b8543026b3e,"@@ -780,7 +780,7 @@ def keygen(import_word_list, strength, passphrase, path, network, role, account_ + t.add_row([""Key role"", role]) + t.add_row([""path"", path]) + pubkey = ledgertx.ledgertx.get_pubkey(path, request_screen_approval=False) +- aprove_key = PrettyTable([""Approve %s Key"" % r]) ++ aprove_key = PrettyTable([""Approve %s Key"" % role]) + aprove_key.align = ""l"" + aprove_key.add_row([format(pubkey, ""STM"")]) + print(aprove_key) +",beem/cli.py,"ReplaceText(target='role' @(783,57)->(783,58))","def keygen(import_word_list, strength, passphrase, path, network, role, account_ + t.add_row([""Key role"", role]) + t.add_row([""path"", path]) + pubkey = ledgertx.ledgertx.get_pubkey(path, request_screen_approval=False) + aprove_key = PrettyTable([""Approve %s Key"" % r]) + aprove_key.align = ""l"" + aprove_key.add_row([format(pubkey, ""STM"")]) + print(aprove_key)","def keygen(import_word_list, strength, passphrase, path, network, role, account_ + t.add_row([""Key role"", role]) + t.add_row([""path"", path]) + pubkey = ledgertx.ledgertx.get_pubkey(path, request_screen_approval=False) + aprove_key = PrettyTable([""Approve %s Key"" % role]) + aprove_key.align = ""l"" + aprove_key.add_row([format(pubkey, ""STM"")]) + print(aprove_key)" +242,https://:@github.com/BlackLight/platypush.git,56b87f343693e89131b3b30930acfeeaec4915fe,"@@ -101,7 +101,7 @@ class MqttBackend(Backend): + format(response_topic, response)) + + client = get_plugin('mqtt') +- client.send_message(topic=self.topic, msg=msg, host=self.host, ++ client.send_message(topic=self.topic, msg=response, host=self.host, + port=self.port, username=self.username, + password=self.password, tls_cafile=self.tls_cafile, + tls_certfile=self.tls_certfile, +",platypush/backend/mqtt.py,"ReplaceText(target='response' @(104,58)->(104,61))","class MqttBackend(Backend): + format(response_topic, response)) + + client = get_plugin('mqtt') + client.send_message(topic=self.topic, msg=msg, host=self.host, + port=self.port, username=self.username, + password=self.password, tls_cafile=self.tls_cafile, + tls_certfile=self.tls_certfile,","class MqttBackend(Backend): + format(response_topic, response)) + + client = get_plugin('mqtt') + client.send_message(topic=self.topic, msg=response, host=self.host, + port=self.port, username=self.username, + password=self.password, tls_cafile=self.tls_cafile, + tls_certfile=self.tls_certfile," +243,https://:@github.com/BlackLight/platypush.git,c9dc1aac44ec4df76071092f4a17601d97955a38,"@@ -47,7 +47,7 @@ class SensorEnvirophatBackend(SensorBackend): + if enabled and sensor in sensors and sensors[sensor] != self._last_read.get(sensor) + } + +- self._last_read = ret ++ self._last_read = sensors + return ret + + +",platypush/backend/sensor/envirophat.py,"ReplaceText(target='sensors' @(50,26)->(50,29))","class SensorEnvirophatBackend(SensorBackend): + if enabled and sensor in sensors and sensors[sensor] != self._last_read.get(sensor) + } + + self._last_read = ret + return ret + + ","class SensorEnvirophatBackend(SensorBackend): + if enabled and sensor in sensors and sensors[sensor] != self._last_read.get(sensor) + } + + self._last_read = sensors + return ret + + " +244,https://:@github.com/BlackLight/platypush.git,7f440a9160619c699f7e8e58b3c0fad3c80ceaf3,"@@ -46,7 +46,7 @@ class GpioPlugin(Plugin): + import RPi.GPIO as GPIO + + with self._init_lock: +- if self._initialized or GPIO.getmode(): ++ if self._initialized and GPIO.getmode(): + return + + GPIO.setmode(self.mode) +",platypush/plugins/gpio/__init__.py,"ReplaceText(target='and' @(49,33)->(49,35))","class GpioPlugin(Plugin): + import RPi.GPIO as GPIO + + with self._init_lock: + if self._initialized or GPIO.getmode(): + return + + GPIO.setmode(self.mode)","class GpioPlugin(Plugin): + import RPi.GPIO as GPIO + + with self._init_lock: + if self._initialized and GPIO.getmode(): + return + + GPIO.setmode(self.mode)" +245,https://:@github.com/BlackLight/platypush.git,c26d456109fea166f8fb5da25aed1d4fb7fc94ab,"@@ -175,7 +175,7 @@ class SensorBackend(Backend): + + def process_data(self, data, new_data): + if new_data: +- self.bus.post(SensorDataChangeEvent(data=data, source=self.plugin or self.__class__.__name__)) ++ self.bus.post(SensorDataChangeEvent(data=new_data, source=self.plugin or self.__class__.__name__)) + + def run(self): + super().run() +",platypush/backend/sensor/__init__.py,"ReplaceText(target='new_data' @(178,53)->(178,57))","class SensorBackend(Backend): + + def process_data(self, data, new_data): + if new_data: + self.bus.post(SensorDataChangeEvent(data=data, source=self.plugin or self.__class__.__name__)) + + def run(self): + super().run()","class SensorBackend(Backend): + + def process_data(self, data, new_data): + if new_data: + self.bus.post(SensorDataChangeEvent(data=new_data, source=self.plugin or self.__class__.__name__)) + + def run(self): + super().run()" +246,https://:@github.com/chrisjsewell/ipypublish.git,cfb66fb74d48cbcc99c695b64fe6336213877e04,"@@ -52,7 +52,7 @@ class LatexDocLinks(Preprocessor): + ': {}'.format(bib)) + else: + external_files.append(bib) +- resources['bibliopath'] = external_files ++ resources['bibliopath'] = bib + + nb.metadata.latex_doc.bibliography = os.path.join(self.filesfolder, + os.path.basename(bib)) +",ipypublish/preprocessors/latex_doc.py,"ReplaceText(target='bib' @(55,46)->(55,60))","class LatexDocLinks(Preprocessor): + ': {}'.format(bib)) + else: + external_files.append(bib) + resources['bibliopath'] = external_files + + nb.metadata.latex_doc.bibliography = os.path.join(self.filesfolder, + os.path.basename(bib))","class LatexDocLinks(Preprocessor): + ': {}'.format(bib)) + else: + external_files.append(bib) + resources['bibliopath'] = bib + + nb.metadata.latex_doc.bibliography = os.path.join(self.filesfolder, + os.path.basename(bib))" +247,https://:@github.com/pazz/alot.git,dd7b2a15495ce5fddcac0d34c14e5ef9f1032482,"@@ -64,7 +64,7 @@ class ThreadlineWidget(urwid.AttrMap): + mailcountstring = ""(%d)"" % self.thread.get_total_messages() + else: + mailcountstring = ""(?)"" +- datestring = pad(mailcountstring) ++ mailcountstring = pad(mailcountstring) + width = len(mailcountstring) + mailcount_w = AttrFlipWidget(urwid.Text(mailcountstring), + struct['mailcount']) +",alot/widgets/search.py,"ReplaceText(target='mailcountstring' @(67,12)->(67,22))","class ThreadlineWidget(urwid.AttrMap): + mailcountstring = ""(%d)"" % self.thread.get_total_messages() + else: + mailcountstring = ""(?)"" + datestring = pad(mailcountstring) + width = len(mailcountstring) + mailcount_w = AttrFlipWidget(urwid.Text(mailcountstring), + struct['mailcount'])","class ThreadlineWidget(urwid.AttrMap): + mailcountstring = ""(%d)"" % self.thread.get_total_messages() + else: + mailcountstring = ""(?)"" + mailcountstring = pad(mailcountstring) + width = len(mailcountstring) + mailcount_w = AttrFlipWidget(urwid.Text(mailcountstring), + struct['mailcount'])" +248,https://:@github.com/luozhouyang/python-string-similarity.git,5f6717fe6d7cae48a664eaa76a47e3388ffd0cf2,"@@ -33,7 +33,7 @@ class Levenshtein(MetricStringDistance): + if len(s0) == 0: + return len(s1) + if len(s1) == 0: +- return len(s1) ++ return len(s0) + + v0 = [0] * (len(s1) + 1) + v1 = [0] * (len(s1) + 1) +",strsimpy/levenshtein.py,"ReplaceText(target='s0' @(36,23)->(36,25))","class Levenshtein(MetricStringDistance): + if len(s0) == 0: + return len(s1) + if len(s1) == 0: + return len(s1) + + v0 = [0] * (len(s1) + 1) + v1 = [0] * (len(s1) + 1)","class Levenshtein(MetricStringDistance): + if len(s0) == 0: + return len(s1) + if len(s1) == 0: + return len(s0) + + v0 = [0] * (len(s1) + 1) + v1 = [0] * (len(s1) + 1)" +249,https://:@github.com/ElementsProject/lightning.git,84b9e3e72b2bf8590603072d709a3ea294dd5483,"@@ -943,7 +943,7 @@ def test_logging(node_factory): + + def check_new_log(): + log2 = open(logpath).readlines() +- return len(log2) > 1 and log2[0].endswith(""Started log due to SIGHUP\n"") ++ return len(log2) > 0 and log2[0].endswith(""Started log due to SIGHUP\n"") + wait_for(check_new_log) + + +",tests/test_misc.py,"ReplaceText(target='0' @(946,27)->(946,28))","def test_logging(node_factory): + + def check_new_log(): + log2 = open(logpath).readlines() + return len(log2) > 1 and log2[0].endswith(""Started log due to SIGHUP\n"") + wait_for(check_new_log) + + ","def test_logging(node_factory): + + def check_new_log(): + log2 = open(logpath).readlines() + return len(log2) > 0 and log2[0].endswith(""Started log due to SIGHUP\n"") + wait_for(check_new_log) + + " +250,https://:@github.com/ElementsProject/lightning.git,c8579b99d01d8b738feadd2d9f541daba5230a63,"@@ -305,7 +305,7 @@ other types. Since 'msgtype' is almost identical, it inherits from this too. + def read(self, io_in: BufferedIOBase, otherfields: Dict[str, Any]) -> Optional[Dict[str, Any]]: + vals = {} + for field in self.fields: +- val = field.fieldtype.read(io_in, otherfields) ++ val = field.fieldtype.read(io_in, vals) + if val is None: + # If first field fails to read, we return None. + if field == self.fields[0]: +",contrib/pyln-proto/pyln/proto/message/message.py,"ReplaceText(target='vals' @(308,46)->(308,57))","other types. Since 'msgtype' is almost identical, it inherits from this too. + def read(self, io_in: BufferedIOBase, otherfields: Dict[str, Any]) -> Optional[Dict[str, Any]]: + vals = {} + for field in self.fields: + val = field.fieldtype.read(io_in, otherfields) + if val is None: + # If first field fails to read, we return None. + if field == self.fields[0]:","other types. Since 'msgtype' is almost identical, it inherits from this too. + def read(self, io_in: BufferedIOBase, otherfields: Dict[str, Any]) -> Optional[Dict[str, Any]]: + vals = {} + for field in self.fields: + val = field.fieldtype.read(io_in, vals) + if val is None: + # If first field fails to read, we return None. + if field == self.fields[0]:" +251,https://:@github.com/funilrys/PyFunceble.git,c766732abdf31c0c1ce283ee9aa2ec32f0ac7829,"@@ -301,7 +301,7 @@ class Generate(object): # pragma: no cover + regex_blogger = [""create-blog.g?"", ""87065"", ""doesn’t exist""] + + if self.tested == PyFunceble.CONFIGURATION[""domain""]: +- url_to_get = ""http://%s"" & self.tested ++ url_to_get = ""http://%s"" % self.tested + else: + url_to_get = self.tested + +",PyFunceble/generate.py,"ReplaceText(target='%' @(304,37)->(304,38))","class Generate(object): # pragma: no cover + regex_blogger = [""create-blog.g?"", ""87065"", ""doesn’t exist""] + + if self.tested == PyFunceble.CONFIGURATION[""domain""]: + url_to_get = ""http://%s"" & self.tested + else: + url_to_get = self.tested + ","class Generate(object): # pragma: no cover + regex_blogger = [""create-blog.g?"", ""87065"", ""doesn’t exist""] + + if self.tested == PyFunceble.CONFIGURATION[""domain""]: + url_to_get = ""http://%s"" % self.tested + else: + url_to_get = self.tested + " +252,https://:@github.com/funilrys/PyFunceble.git,08400b05f5f3e20c24c9222a9cb9216d1a76aea5,"@@ -80,7 +80,7 @@ class Load(object): # pylint: disable=too-few-public-methods + def __init__(self, path_to_config): + self.path_to_config = path_to_config + +- if path_to_config.endswith(directory_separator): ++ if not path_to_config.endswith(directory_separator): + self.path_to_config += directory_separator + + self.path_to_config += PyFunceble.CONFIGURATION_FILENAME +",PyFunceble/config.py,"ReplaceText(target='not ' @(83,11)->(83,11))","class Load(object): # pylint: disable=too-few-public-methods + def __init__(self, path_to_config): + self.path_to_config = path_to_config + + if path_to_config.endswith(directory_separator): + self.path_to_config += directory_separator + + self.path_to_config += PyFunceble.CONFIGURATION_FILENAME","class Load(object): # pylint: disable=too-few-public-methods + def __init__(self, path_to_config): + self.path_to_config = path_to_config + + if not path_to_config.endswith(directory_separator): + self.path_to_config += directory_separator + + self.path_to_config += PyFunceble.CONFIGURATION_FILENAME" +253,https://:@github.com/funilrys/PyFunceble.git,fb9465acb6a7124aa84b8c419c9709243e001f94,"@@ -96,7 +96,7 @@ class Clean: + if ( + number_of_tested == 0 + or list_to_test[number_of_tested - 1] == list_to_test[-1] +- or number_of_tested == len(list_to_test) ++ or number_of_tested >= len(list_to_test) + ): + # * If the number of tested is null, + # or +",PyFunceble/clean.py,"ReplaceText(target='>=' @(99,40)->(99,42))","class Clean: + if ( + number_of_tested == 0 + or list_to_test[number_of_tested - 1] == list_to_test[-1] + or number_of_tested == len(list_to_test) + ): + # * If the number of tested is null, + # or","class Clean: + if ( + number_of_tested == 0 + or list_to_test[number_of_tested - 1] == list_to_test[-1] + or number_of_tested >= len(list_to_test) + ): + # * If the number of tested is null, + # or" +254,https://:@github.com/funilrys/PyFunceble.git,a9e45c83e13eca92389d0be56634cc45ef601bc1,"@@ -92,7 +92,7 @@ class DBTypeDownloader(DownloaderBase): + f""{PyFunceble.OUTPUTS.db_type.files[PyFunceble.CONFIGURATION.db_type]}"" + ) + +- if is_cloned_version and ( ++ if not is_cloned_version and ( + PyFunceble.CONFIGURATION.db_type not in not_supported_db_types + ): + destination_dir_instance.delete() +",PyFunceble/downloader/db_type.py,"ReplaceText(target='not ' @(95,11)->(95,11))","class DBTypeDownloader(DownloaderBase): + f""{PyFunceble.OUTPUTS.db_type.files[PyFunceble.CONFIGURATION.db_type]}"" + ) + + if is_cloned_version and ( + PyFunceble.CONFIGURATION.db_type not in not_supported_db_types + ): + destination_dir_instance.delete()","class DBTypeDownloader(DownloaderBase): + f""{PyFunceble.OUTPUTS.db_type.files[PyFunceble.CONFIGURATION.db_type]}"" + ) + + if not is_cloned_version and ( + PyFunceble.CONFIGURATION.db_type not in not_supported_db_types + ): + destination_dir_instance.delete()" +255,https://:@github.com/funilrys/PyFunceble.git,76bc73c57f4ac2865fc89d70ad330be2aa501c08,"@@ -154,7 +154,7 @@ class Credential: + regex = f""{name}=.*"" + + if not content: +- content += f""{to_write}\n"" ++ content = f""{to_write}\n"" + continue + + if PyFunceble.helpers.Regex(f""^{regex}"").get_matching_list( +",PyFunceble/engine/database/loader/credential.py,"ReplaceText(target='=' @(157,28)->(157,30))","class Credential: + regex = f""{name}=.*"" + + if not content: + content += f""{to_write}\n"" + continue + + if PyFunceble.helpers.Regex(f""^{regex}"").get_matching_list(","class Credential: + regex = f""{name}=.*"" + + if not content: + content = f""{to_write}\n"" + continue + + if PyFunceble.helpers.Regex(f""^{regex}"").get_matching_list(" +256,https://:@github.com/valassis-digital-media/conda-mirror.git,e0b34555d779f9b440512f850da39aa5a0e29ece,"@@ -85,5 +85,5 @@ def test_handling_bad_package(tmpdir, repodata): + with bz2.BZ2File(bad_pkg_path, 'wb') as f: + f.write(""This is a fake package"".encode()) + assert bad_pkg_name in os.listdir(bad_pkg_root) +- conda_mirror._validate_packages(repodata, local_repo_root) ++ conda_mirror._validate_packages(repodata, bad_pkg_root) + assert bad_pkg_name not in os.listdir(bad_pkg_root) +\ No newline at end of file +",test/test_conda_mirror.py,"ReplaceText(target='bad_pkg_root' @(88,46)->(88,61))","def test_handling_bad_package(tmpdir, repodata): + with bz2.BZ2File(bad_pkg_path, 'wb') as f: + f.write(""This is a fake package"".encode()) + assert bad_pkg_name in os.listdir(bad_pkg_root) + conda_mirror._validate_packages(repodata, local_repo_root) + assert bad_pkg_name not in os.listdir(bad_pkg_root) +\ No newline at end of file","def test_handling_bad_package(tmpdir, repodata): + with bz2.BZ2File(bad_pkg_path, 'wb') as f: + f.write(""This is a fake package"".encode()) + assert bad_pkg_name in os.listdir(bad_pkg_root) + conda_mirror._validate_packages(repodata, bad_pkg_root) + assert bad_pkg_name not in os.listdir(bad_pkg_root) +\ No newline at end of file" +257,https://:@github.com/fact-project/pycustos.git,e2432cee5bba6dc97b30d0b640c0c92f3bdd6961,"@@ -8,7 +8,7 @@ class Notifier(metaclass=ABCMeta): + self.categories = set(categories) + + def handle_message(self, msg): +- if self.categories.intersection(msg.categories) and msg.level > self.level: ++ if self.categories.intersection(msg.categories) and msg.level >= self.level: + self.notify(msg) + + @abstractmethod +",custos/notify/base.py,"ReplaceText(target='>=' @(11,70)->(11,71))","class Notifier(metaclass=ABCMeta): + self.categories = set(categories) + + def handle_message(self, msg): + if self.categories.intersection(msg.categories) and msg.level > self.level: + self.notify(msg) + + @abstractmethod","class Notifier(metaclass=ABCMeta): + self.categories = set(categories) + + def handle_message(self, msg): + if self.categories.intersection(msg.categories) and msg.level >= self.level: + self.notify(msg) + + @abstractmethod" +258,https://:@github.com/danilobellini/audiolazy.git,3119b12f8f0b175b3f55aecf3053ed6a0d1a477a,"@@ -249,4 +249,4 @@ def gammatone(freq, bandwidth): + freqs = tee(freq, 4) + resons = [resonator.z_exp, resonator.poles_exp] * 2 + return CascadeFilter(reson(f, bw) +- for reson, f, bw in zip(bws, freqs, resons)) ++ for reson, f, bw in zip(resons, freqs, bws)) +",audiolazy/lazy_auditory.py,"ArgSwap(idxs=0<->2 @(252,43)->(252,46))","def gammatone(freq, bandwidth): + freqs = tee(freq, 4) + resons = [resonator.z_exp, resonator.poles_exp] * 2 + return CascadeFilter(reson(f, bw) + for reson, f, bw in zip(bws, freqs, resons))","def gammatone(freq, bandwidth): + freqs = tee(freq, 4) + resons = [resonator.z_exp, resonator.poles_exp] * 2 + return CascadeFilter(reson(f, bw) + for reson, f, bw in zip(resons, freqs, bws))" +259,https://:@github.com/ojii/django-sekizai.git,b0b50e0713a90e84acabe1ab39e951421fd4aa7a,"@@ -91,6 +91,6 @@ class CSSSingleFileFilter(BaseMinifierFilter): + mtime = os.path.getmtime(master) + for f in files: + fpath = media_url_to_filepath(f) +- if os.path.getmtime(fpath) > mtime: ++ if os.path.getmtime(fpath) >= mtime: + return True + return False +\ No newline at end of file +",sekizai/filters/css.py,"ReplaceText(target='>=' @(94,39)->(94,40))","class CSSSingleFileFilter(BaseMinifierFilter): + mtime = os.path.getmtime(master) + for f in files: + fpath = media_url_to_filepath(f) + if os.path.getmtime(fpath) > mtime: + return True + return False +\ No newline at end of file","class CSSSingleFileFilter(BaseMinifierFilter): + mtime = os.path.getmtime(master) + for f in files: + fpath = media_url_to_filepath(f) + if os.path.getmtime(fpath) >= mtime: + return True + return False +\ No newline at end of file" +260,https://:@github.com/websocket-client/websocket-client.git,6410340fca47f258d50a34646138ba03b2b2783b,"@@ -183,7 +183,7 @@ def _tunnel(sock, host, port, auth): + + if status != 200: + raise WebSocketProxyException( +- ""failed CONNECT via proxy status: %r"" + status) ++ ""failed CONNECT via proxy status: %r"" % status) + + return sock + +",websocket/_http.py,"ReplaceText(target='%' @(186,50)->(186,51))","def _tunnel(sock, host, port, auth): + + if status != 200: + raise WebSocketProxyException( + ""failed CONNECT via proxy status: %r"" + status) + + return sock + ","def _tunnel(sock, host, port, auth): + + if status != 200: + raise WebSocketProxyException( + ""failed CONNECT via proxy status: %r"" % status) + + return sock + " +261,https://:@github.com/getsentry/raven-python.git,dedca8e5c98124f6a43a18986e142e8cb7ecc3cf,"@@ -59,7 +59,7 @@ def setup_logging(handler, exclude=['raven', 'sentry.errors']): + Returns a boolean based on if logging was configured or not. + """""" + logger = logging.getLogger() +- if handler.__class__ not in map(type, logger.handlers): ++ if handler.__class__ in map(type, logger.handlers): + return False + + logger.addHandler(handler) +",raven/conf/__init__.py,"ReplaceText(target=' in ' @(62,24)->(62,32))","def setup_logging(handler, exclude=['raven', 'sentry.errors']): + Returns a boolean based on if logging was configured or not. + """""" + logger = logging.getLogger() + if handler.__class__ not in map(type, logger.handlers): + return False + + logger.addHandler(handler)","def setup_logging(handler, exclude=['raven', 'sentry.errors']): + Returns a boolean based on if logging was configured or not. + """""" + logger = logging.getLogger() + if handler.__class__ in map(type, logger.handlers): + return False + + logger.addHandler(handler)" +262,https://:@github.com/getsentry/raven-python.git,f0ad0ca6a9de44128982de50c30157b779b69d71,"@@ -16,7 +16,7 @@ class TransportRegistry(object): + self.register_transport(transport) + + def register_transport(self, transport): +- if not hasattr(transport, 'scheme') and not hasattr(transport.scheme, '__iter__'): ++ if not hasattr(transport, 'scheme') or not hasattr(transport.scheme, '__iter__'): + raise AttributeError('Transport %s must have a scheme list', transport.__class__.__name__) + + for scheme in transport.scheme: +",raven/transport/registry.py,"ReplaceText(target='or' @(19,44)->(19,47))","class TransportRegistry(object): + self.register_transport(transport) + + def register_transport(self, transport): + if not hasattr(transport, 'scheme') and not hasattr(transport.scheme, '__iter__'): + raise AttributeError('Transport %s must have a scheme list', transport.__class__.__name__) + + for scheme in transport.scheme:","class TransportRegistry(object): + self.register_transport(transport) + + def register_transport(self, transport): + if not hasattr(transport, 'scheme') or not hasattr(transport.scheme, '__iter__'): + raise AttributeError('Transport %s must have a scheme list', transport.__class__.__name__) + + for scheme in transport.scheme:" +263,https://:@github.com/ilius/pyglossary.git,8ad925bbb4ce19207322471c4c758d1a66f0db9d,"@@ -186,7 +186,7 @@ def write( + with open(filePathBase + "".xml"", ""w"", encoding=""utf8"") as toFile: + write_header(glos, toFile, frontBackMatter) + for entryI, entry in enumerate(glos): +- if glos.isData(): ++ if entry.isData(): + entry.save(myResDir) + continue + +",pyglossary/plugins/appledict/__init__.py,"ReplaceText(target='entry' @(189,6)->(189,10))","def write( + with open(filePathBase + "".xml"", ""w"", encoding=""utf8"") as toFile: + write_header(glos, toFile, frontBackMatter) + for entryI, entry in enumerate(glos): + if glos.isData(): + entry.save(myResDir) + continue + ","def write( + with open(filePathBase + "".xml"", ""w"", encoding=""utf8"") as toFile: + write_header(glos, toFile, frontBackMatter) + for entryI, entry in enumerate(glos): + if entry.isData(): + entry.save(myResDir) + continue + " +264,https://:@github.com/ilius/pyglossary.git,194fea3e176f5c9caf090a58bee3c5b04fd483ef,"@@ -450,7 +450,7 @@ class Glossary(GlossaryType): + wordCount = len(reader) + except Exception: + log.exception("""") +- if wordCount > 0: ++ if wordCount >= 0: + progressbar = True + if progressbar: + self.progressInit(""Converting"") +",pyglossary/glossary.py,"ReplaceText(target='>=' @(453,17)->(453,18))","class Glossary(GlossaryType): + wordCount = len(reader) + except Exception: + log.exception("""") + if wordCount > 0: + progressbar = True + if progressbar: + self.progressInit(""Converting"")","class Glossary(GlossaryType): + wordCount = len(reader) + except Exception: + log.exception("""") + if wordCount >= 0: + progressbar = True + if progressbar: + self.progressInit(""Converting"")" +265,https://:@github.com/ilius/pyglossary.git,a7237c6749dcd2f2cf34b5f8ec385b6ba0b5565a,"@@ -99,7 +99,7 @@ class TextGlossaryReader(object): + try: + wordDefi = self.nextPair() + except StopIteration as e: +- if self._fileIndex < self._fileCount + 1: ++ if self._fileIndex < self._fileCount - 1: + if self.openNextFile(): + return self.__next__() + self._wordCount = self._pos +",pyglossary/text_reader.py,"ReplaceText(target='-' @(102,40)->(102,41))","class TextGlossaryReader(object): + try: + wordDefi = self.nextPair() + except StopIteration as e: + if self._fileIndex < self._fileCount + 1: + if self.openNextFile(): + return self.__next__() + self._wordCount = self._pos","class TextGlossaryReader(object): + try: + wordDefi = self.nextPair() + except StopIteration as e: + if self._fileIndex < self._fileCount - 1: + if self.openNextFile(): + return self.__next__() + self._wordCount = self._pos" +266,https://:@github.com/GOVCERT-LU/eml_parser.git,5a129fd37081de0c3483a317e4eefced52fed44d,"@@ -636,7 +636,7 @@ def parse_email(msg, include_raw_body=False, include_attachment_data=False): + if list_observed_dom: + bodie['domain'] = list(set(list_observed_dom)) + +- if list_observed_dom: ++ if list_observed_ip: + bodie['ip'] = list(set(list_observed_ip)) + + else: +",eml_parser/eml_parser.py,"ReplaceText(target='list_observed_ip' @(639,15)->(639,32))","def parse_email(msg, include_raw_body=False, include_attachment_data=False): + if list_observed_dom: + bodie['domain'] = list(set(list_observed_dom)) + + if list_observed_dom: + bodie['ip'] = list(set(list_observed_ip)) + + else:","def parse_email(msg, include_raw_body=False, include_attachment_data=False): + if list_observed_dom: + bodie['domain'] = list(set(list_observed_dom)) + + if list_observed_ip: + bodie['ip'] = list(set(list_observed_ip)) + + else:" +267,https://:@github.com/noripyt/wagtail-react-streamfield.git,fcd366318ffd0f20f93efcc58e00658f1334899c,"@@ -75,4 +75,4 @@ class NewListBlock(ListBlock): + _('The maximum number of items is %d') % self.meta.max_num + ) + +- return value ++ return result +",wagtail_react_streamfield/blocks/list_block.py,"ReplaceText(target='result' @(78,15)->(78,20))","class NewListBlock(ListBlock): + _('The maximum number of items is %d') % self.meta.max_num + ) + + return value","class NewListBlock(ListBlock): + _('The maximum number of items is %d') % self.meta.max_num + ) + + return result" +268,https://:@github.com/noripyt/wagtail-react-streamfield.git,4a33dab16bc9665349e6aaa011df3a47eea25277,"@@ -43,7 +43,7 @@ class NewBlock(Block): + else errors.as_data()[0].params.get(NON_FIELD_ERRORS, ())) + else: + non_block_errors = errors +- if help_text and non_block_errors: ++ if help_text or non_block_errors: + return render_to_string( + 'wagtailadmin/block_forms/blocks_container.html', + { +",wagtail_react_streamfield/blocks/block.py,"ReplaceText(target='or' @(46,21)->(46,24))","class NewBlock(Block): + else errors.as_data()[0].params.get(NON_FIELD_ERRORS, ())) + else: + non_block_errors = errors + if help_text and non_block_errors: + return render_to_string( + 'wagtailadmin/block_forms/blocks_container.html', + {","class NewBlock(Block): + else errors.as_data()[0].params.get(NON_FIELD_ERRORS, ())) + else: + non_block_errors = errors + if help_text or non_block_errors: + return render_to_string( + 'wagtailadmin/block_forms/blocks_container.html', + {" +269,https://:@github.com/PMBio/MOFA.git,f7cd442f209ce679001b67e2ed439016bdef6991,"@@ -82,7 +82,7 @@ class initModel(object): + + elif qmean == ""pca"": # Latent variables are initialised from PCA in the concatenated matrix + pca = sklearn.decomposition.PCA(n_components=self.K, copy=True, whiten=True) +- pca.fit(s.concatenate(self.data,axis=0).T) ++ pca.fit(s.concatenate(self.data,axis=1).T) + qmean = pca.components_.T + + elif isinstance(qmean,s.ndarray): +",mofa/core/init_nodes.py,"ReplaceText(target='1' @(85,57)->(85,58))","class initModel(object): + + elif qmean == ""pca"": # Latent variables are initialised from PCA in the concatenated matrix + pca = sklearn.decomposition.PCA(n_components=self.K, copy=True, whiten=True) + pca.fit(s.concatenate(self.data,axis=0).T) + qmean = pca.components_.T + + elif isinstance(qmean,s.ndarray):","class initModel(object): + + elif qmean == ""pca"": # Latent variables are initialised from PCA in the concatenated matrix + pca = sklearn.decomposition.PCA(n_components=self.K, copy=True, whiten=True) + pca.fit(s.concatenate(self.data,axis=1).T) + qmean = pca.components_.T + + elif isinstance(qmean,s.ndarray):" +270,https://:@github.com/twisted/tubes.git,836d6021f14ad923bb595dffb0a6ca39f0b884b5,"@@ -168,7 +168,7 @@ class _SiphonFount(_SiphonPiece): + def _actuallyPause(): + fount = self._siphon._tdrain.fount + self._siphon._pending.suspend() +- if fount is None: ++ if fount is not None: + pbpc = fount.pauseFlow() + else: + pbpc = NoPause() +",tubes/_siphon.py,"ReplaceText(target=' is not ' @(171,20)->(171,24))","class _SiphonFount(_SiphonPiece): + def _actuallyPause(): + fount = self._siphon._tdrain.fount + self._siphon._pending.suspend() + if fount is None: + pbpc = fount.pauseFlow() + else: + pbpc = NoPause()","class _SiphonFount(_SiphonPiece): + def _actuallyPause(): + fount = self._siphon._tdrain.fount + self._siphon._pending.suspend() + if fount is not None: + pbpc = fount.pauseFlow() + else: + pbpc = NoPause()" +271,https://:@github.com/deschler/django-modeltranslation.git,656dca3e4031d8f030a0aae833fc43c0c09cb51c,"@@ -57,7 +57,7 @@ class TranslationBaseModelAdmin(BaseModelAdmin): + else: + orig_formfield = self.formfield_for_dbfield(orig_field, **kwargs) + field.widget = deepcopy(orig_formfield.widget) +- if orig_field.null and isinstance(field.widget, (forms.TextInput, forms.Textarea)): ++ if db_field.null and isinstance(field.widget, (forms.TextInput, forms.Textarea)): + field.widget = ClearableWidgetWrapper(field.widget) + css_classes = field.widget.attrs.get('class', '').split(' ') + css_classes.append('mt') +",modeltranslation/admin.py,"ReplaceText(target='db_field' @(60,15)->(60,25))","class TranslationBaseModelAdmin(BaseModelAdmin): + else: + orig_formfield = self.formfield_for_dbfield(orig_field, **kwargs) + field.widget = deepcopy(orig_formfield.widget) + if orig_field.null and isinstance(field.widget, (forms.TextInput, forms.Textarea)): + field.widget = ClearableWidgetWrapper(field.widget) + css_classes = field.widget.attrs.get('class', '').split(' ') + css_classes.append('mt')","class TranslationBaseModelAdmin(BaseModelAdmin): + else: + orig_formfield = self.formfield_for_dbfield(orig_field, **kwargs) + field.widget = deepcopy(orig_formfield.widget) + if db_field.null and isinstance(field.widget, (forms.TextInput, forms.Textarea)): + field.widget = ClearableWidgetWrapper(field.widget) + css_classes = field.widget.attrs.get('class', '').split(' ') + css_classes.append('mt')" +272,https://:@github.com/xcgspring/AXUI.git,82f7d6f7f2565d28553fda3c12bb1a2aafb5bab9,"@@ -123,7 +123,7 @@ class AppMap(object): + UI_element_group.stop_func = self.get_func_by_name(xml_element.attrib[""stop_func""]) + if xml_element.attrib.has_key(""identifier""): + UI_element_group.identifier_string = xml_element.attrib[""identifier""] +- UI_element_group.identifier = identifier_parser.parse(UI_element.identifier_string, lexer=identifier_lexer) ++ UI_element_group.identifier = identifier_parser.parse(UI_element_group.identifier_string, lexer=identifier_lexer) + + return UI_element_group + +",AXUI/XML/app_map.py,"ReplaceText(target='UI_element_group' @(126,70)->(126,80))","class AppMap(object): + UI_element_group.stop_func = self.get_func_by_name(xml_element.attrib[""stop_func""]) + if xml_element.attrib.has_key(""identifier""): + UI_element_group.identifier_string = xml_element.attrib[""identifier""] + UI_element_group.identifier = identifier_parser.parse(UI_element.identifier_string, lexer=identifier_lexer) + + return UI_element_group + ","class AppMap(object): + UI_element_group.stop_func = self.get_func_by_name(xml_element.attrib[""stop_func""]) + if xml_element.attrib.has_key(""identifier""): + UI_element_group.identifier_string = xml_element.attrib[""identifier""] + UI_element_group.identifier = identifier_parser.parse(UI_element_group.identifier_string, lexer=identifier_lexer) + + return UI_element_group + " +273,https://:@github.com/docker/compose.git,0e19c92e82c75f821c231367b5cda88eefdf1427,"@@ -577,7 +577,7 @@ class VolumeConfigTest(unittest.TestCase): + + def test_volume_path_with_non_ascii_directory(self): + volume = u'/Füü/data:/data' +- container_path = config.resolve_volume_path(volume, ""."", ""test"") ++ container_path = config.resolve_volume_path(""."", volume, ""test"") + self.assertEqual(container_path, volume) + + +",tests/unit/config/config_test.py,"ArgSwap(idxs=0<->1 @(580,25)->(580,51))","class VolumeConfigTest(unittest.TestCase): + + def test_volume_path_with_non_ascii_directory(self): + volume = u'/Füü/data:/data' + container_path = config.resolve_volume_path(volume, ""."", ""test"") + self.assertEqual(container_path, volume) + + ","class VolumeConfigTest(unittest.TestCase): + + def test_volume_path_with_non_ascii_directory(self): + volume = u'/Füü/data:/data' + container_path = config.resolve_volume_path(""."", volume, ""test"") + self.assertEqual(container_path, volume) + + " +274,https://:@github.com/docker/compose.git,c4f59e731d540780a767d105bcb8d7d164ba4cd5,"@@ -577,7 +577,7 @@ class VolumeConfigTest(unittest.TestCase): + + def test_volume_path_with_non_ascii_directory(self): + volume = u'/Füü/data:/data' +- container_path = config.resolve_volume_path(volume, ""."", ""test"") ++ container_path = config.resolve_volume_path(""."", volume, ""test"") + self.assertEqual(container_path, volume) + + +",tests/unit/config/config_test.py,"ArgSwap(idxs=0<->1 @(580,25)->(580,51))","class VolumeConfigTest(unittest.TestCase): + + def test_volume_path_with_non_ascii_directory(self): + volume = u'/Füü/data:/data' + container_path = config.resolve_volume_path(volume, ""."", ""test"") + self.assertEqual(container_path, volume) + + ","class VolumeConfigTest(unittest.TestCase): + + def test_volume_path_with_non_ascii_directory(self): + volume = u'/Füü/data:/data' + container_path = config.resolve_volume_path(""."", volume, ""test"") + self.assertEqual(container_path, volume) + + " +275,https://:@github.com/ranaroussi/qtpylib.git,e5eac01b67e908823c80b1bdeac57dcb68dbb164,"@@ -65,7 +65,7 @@ def _gen_symbol_group(sym): + + def _gen_asset_class(sym): + sym_class = str(sym).split(""_"") +- if len(sym_class) > 0: ++ if len(sym_class) > 1: + return sym_class[1] + return ""STK"" + +",qtpylib/blotter.py,"ReplaceText(target='1' @(68,24)->(68,25))","def _gen_symbol_group(sym): + + def _gen_asset_class(sym): + sym_class = str(sym).split(""_"") + if len(sym_class) > 0: + return sym_class[1] + return ""STK"" + ","def _gen_symbol_group(sym): + + def _gen_asset_class(sym): + sym_class = str(sym).split(""_"") + if len(sym_class) > 1: + return sym_class[1] + return ""STK"" + " +276,https://:@github.com/lmjohns3/theanets.git,507eac0d7fe007cdc93d89ca6cb0db9521908eac,"@@ -253,7 +253,7 @@ class Network(object): + h = self.hiddens[-1] + a, b = self.weights[i].get_value(borrow=True).shape + logging.info('tied weights from layer %d: %s x %s', i, b, a) +- o = theano.shared(np.zeros((b, ), FLOAT), name='b_out{}'.format(i)) ++ o = theano.shared(np.zeros((a, ), FLOAT), name='b_out{}'.format(i)) + self.preacts.append(TT.dot(h, self.weights[i].T) + o) + func = self._output_func if i == 0 else self._hidden_func + self.hiddens.append(func(self.preacts[-1])) +",theanets/feedforward.py,"ReplaceText(target='a' @(256,44)->(256,45))","class Network(object): + h = self.hiddens[-1] + a, b = self.weights[i].get_value(borrow=True).shape + logging.info('tied weights from layer %d: %s x %s', i, b, a) + o = theano.shared(np.zeros((b, ), FLOAT), name='b_out{}'.format(i)) + self.preacts.append(TT.dot(h, self.weights[i].T) + o) + func = self._output_func if i == 0 else self._hidden_func + self.hiddens.append(func(self.preacts[-1]))","class Network(object): + h = self.hiddens[-1] + a, b = self.weights[i].get_value(borrow=True).shape + logging.info('tied weights from layer %d: %s x %s', i, b, a) + o = theano.shared(np.zeros((a, ), FLOAT), name='b_out{}'.format(i)) + self.preacts.append(TT.dot(h, self.weights[i].T) + o) + func = self._output_func if i == 0 else self._hidden_func + self.hiddens.append(func(self.preacts[-1]))" +277,https://:@github.com/lmjohns3/theanets.git,62f7125e1b179df846fdcd5d213c8bca18595648,"@@ -83,7 +83,7 @@ class SequenceDataset: + slices = [slice(None), slice(None)] + self.batches = [] + i = 0 +- while i + size < shape[axis]: ++ while i + size <= shape[axis]: + slices[axis] = slice(i, i + size) + self.batches.append([d[tuple(slices)] for d in data]) + i += size +",theanets/dataset.py,"ReplaceText(target='<=' @(86,27)->(86,28))","class SequenceDataset: + slices = [slice(None), slice(None)] + self.batches = [] + i = 0 + while i + size < shape[axis]: + slices[axis] = slice(i, i + size) + self.batches.append([d[tuple(slices)] for d in data]) + i += size","class SequenceDataset: + slices = [slice(None), slice(None)] + self.batches = [] + i = 0 + while i + size <= shape[axis]: + slices[axis] = slice(i, i + size) + self.batches.append([d[tuple(slices)] for d in data]) + i += size" +278,https://:@github.com/lmjohns3/theanets.git,8fa4792eaae89e4da7d041178fdcb341f5313914,"@@ -834,4 +834,4 @@ class Classifier(Network): + k : ndarray (num-examples, ) + A vector of class index values, one per row of input data. + ''' +- return self.predict(x).argmax(axis=1) ++ return self.predict(x).argmax(axis=-1) +",theanets/feedforward.py,"ReplaceText(target='-1' @(837,43)->(837,44))","class Classifier(Network): + k : ndarray (num-examples, ) + A vector of class index values, one per row of input data. + ''' + return self.predict(x).argmax(axis=1)","class Classifier(Network): + k : ndarray (num-examples, ) + A vector of class index values, one per row of input data. + ''' + return self.predict(x).argmax(axis=-1)" +279,https://:@github.com/lmjohns3/theanets.git,114f37976b5c00330da9c5fed75ecf7b727eff58,"@@ -338,7 +338,7 @@ class Network(object): + if i == 0: + noise = kwargs.get('input_noise', 0) + dropout = kwargs.get('input_dropouts', 0) +- elif i == len(self.layers) - 1: ++ elif i != len(self.layers) - 1: + noise = kwargs.get('hidden_noise', 0) + dropout = kwargs.get('hidden_dropouts', 0) + out, mon, upd = layer.connect(inputs, noise=noise, dropout=dropout) +",theanets/graph.py,"ReplaceText(target='!=' @(341,23)->(341,25))","class Network(object): + if i == 0: + noise = kwargs.get('input_noise', 0) + dropout = kwargs.get('input_dropouts', 0) + elif i == len(self.layers) - 1: + noise = kwargs.get('hidden_noise', 0) + dropout = kwargs.get('hidden_dropouts', 0) + out, mon, upd = layer.connect(inputs, noise=noise, dropout=dropout)","class Network(object): + if i == 0: + noise = kwargs.get('input_noise', 0) + dropout = kwargs.get('input_dropouts', 0) + elif i != len(self.layers) - 1: + noise = kwargs.get('hidden_noise', 0) + dropout = kwargs.get('hidden_dropouts', 0) + out, mon, upd = layer.connect(inputs, noise=noise, dropout=dropout)" +280,https://:@github.com/pyiron/pyiron_base.git,f9ea8a31ec8fe36704c4c8f73e127ee3e077ca3a,"@@ -98,7 +98,7 @@ class Vasprun(object): + d[""cells""] = np.array(d[""cells""]) + d[""positions""] = np.array(d[""positions""]) + # Check if the parsed coordinates are in absolute/relative coordinates. If absolute, convert to relative +- if len(np.argwhere(d[""positions""].flatten() > 1).flatten()) / len(d[""positions""].flatten()) < 0.01: ++ if len(np.argwhere(d[""positions""].flatten() > 1).flatten()) / len(d[""positions""].flatten()) > 0.01: + pos_new = d[""positions""].copy() + for i, pos in enumerate(pos_new): + d[""positions""][i] = np.dot(pos, np.linalg.inv(d[""cells""][i])) +",pyiron_vasp/vasprun.py,"ReplaceText(target='>' @(101,100)->(101,101))","class Vasprun(object): + d[""cells""] = np.array(d[""cells""]) + d[""positions""] = np.array(d[""positions""]) + # Check if the parsed coordinates are in absolute/relative coordinates. If absolute, convert to relative + if len(np.argwhere(d[""positions""].flatten() > 1).flatten()) / len(d[""positions""].flatten()) < 0.01: + pos_new = d[""positions""].copy() + for i, pos in enumerate(pos_new): + d[""positions""][i] = np.dot(pos, np.linalg.inv(d[""cells""][i]))","class Vasprun(object): + d[""cells""] = np.array(d[""cells""]) + d[""positions""] = np.array(d[""positions""]) + # Check if the parsed coordinates are in absolute/relative coordinates. If absolute, convert to relative + if len(np.argwhere(d[""positions""].flatten() > 1).flatten()) / len(d[""positions""].flatten()) > 0.01: + pos_new = d[""positions""].copy() + for i, pos in enumerate(pos_new): + d[""positions""][i] = np.dot(pos, np.linalg.inv(d[""cells""][i]))" +281,https://:@github.com/pyiron/pyiron_base.git,5d9677db9fcbca5fce348a7208830467381cd643,"@@ -487,7 +487,7 @@ class ParallelMaster(GenericMaster): + job_lst.append(ham._process) + ham = next(self._job_generator, None) + if ham is None and self.server.run_mode.modal: +- while ham is not None: ++ while ham is None: + time.sleep(10) + ham = next(self._job_generator, None) + else: +",pyiron_base/objects/job/parallel.py,"ReplaceText(target=' is ' @(490,29)->(490,37))","class ParallelMaster(GenericMaster): + job_lst.append(ham._process) + ham = next(self._job_generator, None) + if ham is None and self.server.run_mode.modal: + while ham is not None: + time.sleep(10) + ham = next(self._job_generator, None) + else:","class ParallelMaster(GenericMaster): + job_lst.append(ham._process) + ham = next(self._job_generator, None) + if ham is None and self.server.run_mode.modal: + while ham is None: + time.sleep(10) + ham = next(self._job_generator, None) + else:" +282,https://:@github.com/pyiron/pyiron_base.git,a4ed8375fa375ff740a8334f7ce5eb5bf9d7d4a2,"@@ -477,7 +477,7 @@ class Settings(with_metaclass(Singleton)): + else: + # SQLite is raising ugly error messages when the database directory does not exist. + if config[""sql_file""] is None: +- if len(config[""resource_paths""]) > 1: ++ if len(config[""resource_paths""]) >= 1: + config[""sql_file""] = ""/"".join( + [config[""resource_paths""][0], ""pyiron.db""] + ) +",pyiron_base/settings/generic.py,"ReplaceText(target='>=' @(480,49)->(480,50))","class Settings(with_metaclass(Singleton)): + else: + # SQLite is raising ugly error messages when the database directory does not exist. + if config[""sql_file""] is None: + if len(config[""resource_paths""]) > 1: + config[""sql_file""] = ""/"".join( + [config[""resource_paths""][0], ""pyiron.db""] + )","class Settings(with_metaclass(Singleton)): + else: + # SQLite is raising ugly error messages when the database directory does not exist. + if config[""sql_file""] is None: + if len(config[""resource_paths""]) >= 1: + config[""sql_file""] = ""/"".join( + [config[""resource_paths""][0], ""pyiron.db""] + )" +283,https://:@github.com/ESSolutions/django-mssql-backend.git,06578347a5e775088cfe3a2c2e9c528c5ffb7de0,"@@ -201,7 +201,7 @@ class DatabaseWrapper(BaseDatabaseWrapper): + # Only append DRIVER if DATABASE_ODBC_DSN hasn't been set + cstr_parts.append('DRIVER={%s}' % driver) + if ms_drivers.match(driver) or driver == 'FreeTDS' and \ +- conn_params.get('host_is_server', False): ++ options.get('host_is_server', False): + if port: + host += ';PORT=%s' % port + cstr_parts.append('SERVER=%s' % host) +",sql_server/pyodbc/base.py,"ReplaceText(target='options' @(204,16)->(204,27))","class DatabaseWrapper(BaseDatabaseWrapper): + # Only append DRIVER if DATABASE_ODBC_DSN hasn't been set + cstr_parts.append('DRIVER={%s}' % driver) + if ms_drivers.match(driver) or driver == 'FreeTDS' and \ + conn_params.get('host_is_server', False): + if port: + host += ';PORT=%s' % port + cstr_parts.append('SERVER=%s' % host)","class DatabaseWrapper(BaseDatabaseWrapper): + # Only append DRIVER if DATABASE_ODBC_DSN hasn't been set + cstr_parts.append('DRIVER={%s}' % driver) + if ms_drivers.match(driver) or driver == 'FreeTDS' and \ + options.get('host_is_server', False): + if port: + host += ';PORT=%s' % port + cstr_parts.append('SERVER=%s' % host)" +284,https://:@github.com/bykof/billomapy.git,29dc1fcd8f491c158a713b07680ea1305748c959,"@@ -112,7 +112,7 @@ todo_include_todos = False + # a list of builtin themes. + on_rtd = os.environ.get('READTHEDOCS', None) == 'True' + +-if not on_rtd: # only import and set the theme if we're building docs locally ++if on_rtd: # only import and set the theme if we're building docs locally + import sphinx_rtd_theme + html_theme = 'sphinx_rtd_theme' + html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] +",docs/source/conf.py,"ReplaceText(target='' @(115,3)->(115,7))","todo_include_todos = False + # a list of builtin themes. + on_rtd = os.environ.get('READTHEDOCS', None) == 'True' + + if not on_rtd: # only import and set the theme if we're building docs locally + import sphinx_rtd_theme + html_theme = 'sphinx_rtd_theme' + html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]","todo_include_todos = False + # a list of builtin themes. + on_rtd = os.environ.get('READTHEDOCS', None) == 'True' + + if on_rtd: # only import and set the theme if we're building docs locally + import sphinx_rtd_theme + html_theme = 'sphinx_rtd_theme' + html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]" +285,https://:@github.com/quva-lab/artemis.git,26ae4a7049b0f6ac2aef7daf4c2a5184748be516,"@@ -76,7 +76,7 @@ def get_new_positions(fixed_positions, layout, n_plots): + positions.append(fixed_positions[i]) + else: + while True: +- row, col = ix/n_cols, ix%n_cols ++ row, col = ix//n_cols, ix%n_cols + if (row, col) not in taken_positions: + positions.append((row, col)) + taken_positions.add((row, col)) +",artemis/plotting/expanding_subplots.py,"ReplaceText(target='//' @(79,29)->(79,30))","def get_new_positions(fixed_positions, layout, n_plots): + positions.append(fixed_positions[i]) + else: + while True: + row, col = ix/n_cols, ix%n_cols + if (row, col) not in taken_positions: + positions.append((row, col)) + taken_positions.add((row, col))","def get_new_positions(fixed_positions, layout, n_plots): + positions.append(fixed_positions[i]) + else: + while True: + row, col = ix//n_cols, ix%n_cols + if (row, col) not in taken_positions: + positions.append((row, col)) + taken_positions.add((row, col))" +286,https://:@github.com/OCR-D/core.git,e82299a48e4cf4677535819f81bb944ad4f64f8a,"@@ -312,7 +312,7 @@ def validate_consistency(node, page_textequiv_consistency, page_textequiv_strate + pass # already reported in recursive call above + elif not child_poly.within(node_poly.buffer(PARENT_SLACK)): + # TODO: automatic repair? +- report.add_error(CoordinateConsistencyError(tag, child.id, file_id, ++ report.add_error(CoordinateConsistencyError(child_tag, child.id, file_id, + parent_points, child_points)) + log.debug(""Inconsistent coords of %s %s"", child_tag, child.id) + consistent = False +",ocrd_validators/ocrd_validators/page_validator.py,"ReplaceText(target='child_tag' @(315,64)->(315,67))","def validate_consistency(node, page_textequiv_consistency, page_textequiv_strate + pass # already reported in recursive call above + elif not child_poly.within(node_poly.buffer(PARENT_SLACK)): + # TODO: automatic repair? + report.add_error(CoordinateConsistencyError(tag, child.id, file_id, + parent_points, child_points)) + log.debug(""Inconsistent coords of %s %s"", child_tag, child.id) + consistent = False","def validate_consistency(node, page_textequiv_consistency, page_textequiv_strate + pass # already reported in recursive call above + elif not child_poly.within(node_poly.buffer(PARENT_SLACK)): + # TODO: automatic repair? + report.add_error(CoordinateConsistencyError(child_tag, child.id, file_id, + parent_points, child_points)) + log.debug(""Inconsistent coords of %s %s"", child_tag, child.id) + consistent = False" +287,https://:@github.com/jhuapl-boss/heaviside.git,3adb4902a04dc3e1d9a325ab1752c4b2d856b677,"@@ -69,7 +69,7 @@ class ASTCompAndOr(ASTNode): + super(ASTCompAndOr, self).__init__(comp.token) + self.comps = [comp] + for c in comps: +- self.comps.append(comp) ++ self.comps.append(c) + + class ASTCompAnd(ASTCompAndOr): + op = 'And' +",heaviside/ast.py,"ReplaceText(target='c' @(72,30)->(72,34))","class ASTCompAndOr(ASTNode): + super(ASTCompAndOr, self).__init__(comp.token) + self.comps = [comp] + for c in comps: + self.comps.append(comp) + + class ASTCompAnd(ASTCompAndOr): + op = 'And'","class ASTCompAndOr(ASTNode): + super(ASTCompAndOr, self).__init__(comp.token) + self.comps = [comp] + for c in comps: + self.comps.append(c) + + class ASTCompAnd(ASTCompAndOr): + op = 'And'" +288,https://:@github.com/google-research/text-to-text-transfer-transformer.git,d2c010b48b702f22fb665d2e5723c7baaf4f6a1c,"@@ -98,7 +98,7 @@ def main(_): + "" "".join(str(i) for i in v) if FLAGS.tokenize + else v.decode(""utf-8"")) + else: +- v[k] = """" ++ key_to_string[k] = """" + return FLAGS.format_string.format(**key_to_string) + + for shard_path in files: +",t5/scripts/dump_task.py,"ReplaceText(target='key_to_string' @(101,8)->(101,9))","def main(_): + "" "".join(str(i) for i in v) if FLAGS.tokenize + else v.decode(""utf-8"")) + else: + v[k] = """" + return FLAGS.format_string.format(**key_to_string) + + for shard_path in files:","def main(_): + "" "".join(str(i) for i in v) if FLAGS.tokenize + else v.decode(""utf-8"")) + else: + key_to_string[k] = """" + return FLAGS.format_string.format(**key_to_string) + + for shard_path in files:" +289,https://:@github.com/lvieirajr/mongorest.git,470f17173b63b14ab60bbc99db7ca3b3f93afdac,"@@ -401,4 +401,4 @@ class CoercionError(SchemaValidationError): + + self['collection'] = collection + self['field'] = field +- self['coercion_type'] = coercion_type ++ self['coercion_type'] = coercion_type_repr +",mongorest/errors.py,"ReplaceText(target='coercion_type_repr' @(404,32)->(404,45))","class CoercionError(SchemaValidationError): + + self['collection'] = collection + self['field'] = field + self['coercion_type'] = coercion_type","class CoercionError(SchemaValidationError): + + self['collection'] = collection + self['field'] = field + self['coercion_type'] = coercion_type_repr" +290,https://:@github.com/internetarchive/fatcat.git,89b729feac30a272b557542c5c4149d3611f869a,"@@ -295,7 +295,7 @@ def container_to_elasticsearch(entity): + t['in_sherpa_romeo'] = in_sherpa_romeo + t['is_oa'] = in_doaj or in_road or is_longtail_oa or is_oa + t['is_longtail_oa'] = is_longtail_oa +- t['any_kbart'] = any_ia_sim ++ t['any_kbart'] = any_kbart + t['any_jstor'] = any_jstor + t['any_ia_sim'] = bool(any_ia_sim) + return t +",python/fatcat_tools/transforms.py,"ReplaceText(target='any_kbart' @(298,21)->(298,31))","def container_to_elasticsearch(entity): + t['in_sherpa_romeo'] = in_sherpa_romeo + t['is_oa'] = in_doaj or in_road or is_longtail_oa or is_oa + t['is_longtail_oa'] = is_longtail_oa + t['any_kbart'] = any_ia_sim + t['any_jstor'] = any_jstor + t['any_ia_sim'] = bool(any_ia_sim) + return t","def container_to_elasticsearch(entity): + t['in_sherpa_romeo'] = in_sherpa_romeo + t['is_oa'] = in_doaj or in_road or is_longtail_oa or is_oa + t['is_longtail_oa'] = is_longtail_oa + t['any_kbart'] = any_kbart + t['any_jstor'] = any_jstor + t['any_ia_sim'] = bool(any_ia_sim) + return t" +291,https://:@github.com/internetarchive/fatcat.git,11dfac5f8f9ced9b56cf277d0e3adeccc572b251,"@@ -57,7 +57,7 @@ class ArabesqueMatchImporter(EntityImporter): + eg_extra = kwargs.get('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.ArabesqueMatchImporter') + if kwargs.get('crawl_id'): +- eg_extra['crawl_id'] = eg_extra.get('crawl_id') ++ eg_extra['crawl_id'] = kwargs.get('crawl_id') + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra, +",python/fatcat_tools/importers/arabesque.py,"ReplaceText(target='kwargs' @(60,35)->(60,43))","class ArabesqueMatchImporter(EntityImporter): + eg_extra = kwargs.get('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.ArabesqueMatchImporter') + if kwargs.get('crawl_id'): + eg_extra['crawl_id'] = eg_extra.get('crawl_id') + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra,","class ArabesqueMatchImporter(EntityImporter): + eg_extra = kwargs.get('editgroup_extra', dict()) + eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.ArabesqueMatchImporter') + if kwargs.get('crawl_id'): + eg_extra['crawl_id'] = kwargs.get('crawl_id') + super().__init__(api, + editgroup_description=eg_desc, + editgroup_extra=eg_extra," +292,https://:@github.com/internetarchive/fatcat.git,7104e6dfb99717353e3819853ae61ac6387a02a1,"@@ -128,7 +128,7 @@ class EntityUpdatesWorker(FatcatWorker): + # update release when a file changes + # TODO: fetch old revision as well, and only update + # releases for which list changed +- release_ids.extend(e['release_ids']) ++ release_ids.extend(file_entity['release_ids']) + file_dict = self.api.api_client.sanitize_for_serialization(file_entity) + file_producer.produce( + message=json.dumps(file_dict).encode('utf-8'), +",python/fatcat_tools/workers/changelog.py,"ReplaceText(target='file_entity' @(131,35)->(131,36))","class EntityUpdatesWorker(FatcatWorker): + # update release when a file changes + # TODO: fetch old revision as well, and only update + # releases for which list changed + release_ids.extend(e['release_ids']) + file_dict = self.api.api_client.sanitize_for_serialization(file_entity) + file_producer.produce( + message=json.dumps(file_dict).encode('utf-8'),","class EntityUpdatesWorker(FatcatWorker): + # update release when a file changes + # TODO: fetch old revision as well, and only update + # releases for which list changed + release_ids.extend(file_entity['release_ids']) + file_dict = self.api.api_client.sanitize_for_serialization(file_entity) + file_producer.produce( + message=json.dumps(file_dict).encode('utf-8')," +293,https://:@github.com/internetarchive/fatcat.git,80b756d6feec3f66225287b9ca73c8b02d012027,"@@ -167,7 +167,7 @@ class IngestFileResultImporter(EntityImporter): + urls=urls, + ) + if request.get('edit_extra'): +- fe.edit_extra = fatcat['edit_extra'] ++ fe.edit_extra = request['edit_extra'] + else: + fe.edit_extra = dict() + if request.get('ingest_request_source'): +",python/fatcat_tools/importers/ingest.py,"ReplaceText(target='request' @(170,28)->(170,34))","class IngestFileResultImporter(EntityImporter): + urls=urls, + ) + if request.get('edit_extra'): + fe.edit_extra = fatcat['edit_extra'] + else: + fe.edit_extra = dict() + if request.get('ingest_request_source'):","class IngestFileResultImporter(EntityImporter): + urls=urls, + ) + if request.get('edit_extra'): + fe.edit_extra = request['edit_extra'] + else: + fe.edit_extra = dict() + if request.get('ingest_request_source'):" +294,https://:@github.com/pallets/flask-ext-migrate.git,ea6a0666e08ce176031456dced635ca3c92c1386,"@@ -43,7 +43,7 @@ def fix_from_imports(red): + modules = node.value + + if (len(modules) < 2 or +- modules[0].value != 'flask' and modules[1].value != 'ext'): ++ modules[0].value != 'flask' or modules[1].value != 'ext'): + continue + + if len(modules) >= 3: +",flask_ext_migrate/__init__.py,"ReplaceText(target='or' @(46,44)->(46,47))","def fix_from_imports(red): + modules = node.value + + if (len(modules) < 2 or + modules[0].value != 'flask' and modules[1].value != 'ext'): + continue + + if len(modules) >= 3:","def fix_from_imports(red): + modules = node.value + + if (len(modules) < 2 or + modules[0].value != 'flask' or modules[1].value != 'ext'): + continue + + if len(modules) >= 3:" +295,https://:@github.com/SpockBotMC/SpockBot.git,6c8e63b97e3d9617ce0ca9bea9a677902b5ef2fb,"@@ -42,7 +42,7 @@ class SelectSocket: + else: + slist = [(self.sock,), (), (self.sock,)] + timeout = self.timer.get_timeout() +- if timeout>0: ++ if timeout>=0: + slist.append(timeout) + try: + rlist, wlist, xlist = select.select(*slist) +",spock/plugins/core/net.py,"ReplaceText(target='>=' @(45,12)->(45,13))","class SelectSocket: + else: + slist = [(self.sock,), (), (self.sock,)] + timeout = self.timer.get_timeout() + if timeout>0: + slist.append(timeout) + try: + rlist, wlist, xlist = select.select(*slist)","class SelectSocket: + else: + slist = [(self.sock,), (), (self.sock,)] + timeout = self.timer.get_timeout() + if timeout>=0: + slist.append(timeout) + try: + rlist, wlist, xlist = select.select(*slist)" +296,https://:@github.com/SpockBotMC/SpockBot.git,bebe1187dd6432ec3b4b6dddb8246baef83c2203,"@@ -15,7 +15,7 @@ class PloaderFetch: + @pl_announce('PloaderFetch') + class SettingsPlugin: + def __init__(self, ploader, kwargs): +- settings = get_settings(kwargs, kwargs.get('settings', {})) ++ settings = get_settings(kwargs.get('settings', {}), kwargs) + plugin_list = settings.get('plugins', DefaultPlugins) + plugins = [] + plugin_settings = {} +",spock/plugins/core/settings.py,"ArgSwap(idxs=0<->1 @(18,13)->(18,25))","class PloaderFetch: + @pl_announce('PloaderFetch') + class SettingsPlugin: + def __init__(self, ploader, kwargs): + settings = get_settings(kwargs, kwargs.get('settings', {})) + plugin_list = settings.get('plugins', DefaultPlugins) + plugins = [] + plugin_settings = {}","class PloaderFetch: + @pl_announce('PloaderFetch') + class SettingsPlugin: + def __init__(self, ploader, kwargs): + settings = get_settings(kwargs.get('settings', {}), kwargs) + plugin_list = settings.get('plugins', DefaultPlugins) + plugins = [] + plugin_settings = {}" +297,https://:@github.com/SpockBotMC/SpockBot.git,bebe1187dd6432ec3b4b6dddb8246baef83c2203,"@@ -19,7 +19,7 @@ default_settings = { + + class StartPlugin: + def __init__(self, ploader, settings): +- self.settings = utils.get_settings(settings, default_settings) ++ self.settings = utils.get_settings(default_settings, settings) + self.event = ploader.requires('Event') + self.net = ploader.requires('Net') + self.auth = ploader.requires('Auth') +",spock/plugins/helpers/start.py,"ArgSwap(idxs=0<->1 @(22,18)->(22,36))","default_settings = { + + class StartPlugin: + def __init__(self, ploader, settings): + self.settings = utils.get_settings(settings, default_settings) + self.event = ploader.requires('Event') + self.net = ploader.requires('Net') + self.auth = ploader.requires('Auth')","default_settings = { + + class StartPlugin: + def __init__(self, ploader, settings): + self.settings = utils.get_settings(default_settings, settings) + self.event = ploader.requires('Event') + self.net = ploader.requires('Net') + self.auth = ploader.requires('Auth')" +298,https://:@github.com/hungpham2511/toppra.git,fefd8430ad55fb09414a1d4c6d8be41e81977842,"@@ -19,7 +19,7 @@ def _find_left_index(ss_waypoints, s): + for i in range(1, len(ss_waypoints)): + if ss_waypoints[i - 1] <= s and s < ss_waypoints[i]: + return i - 1 +- return len(ss_waypoints) - 1 ++ return len(ss_waypoints) - 2 + + + class Interpolator(object): +",toppra/interpolator.py,"ReplaceText(target='2' @(22,31)->(22,32))","def _find_left_index(ss_waypoints, s): + for i in range(1, len(ss_waypoints)): + if ss_waypoints[i - 1] <= s and s < ss_waypoints[i]: + return i - 1 + return len(ss_waypoints) - 1 + + + class Interpolator(object):","def _find_left_index(ss_waypoints, s): + for i in range(1, len(ss_waypoints)): + if ss_waypoints[i - 1] <= s and s < ss_waypoints[i]: + return i - 1 + return len(ss_waypoints) - 2 + + + class Interpolator(object):" +299,https://:@github.com/cmrivers/epipy.git,c541e6f7f559c92279623aa3c2cb7f644247280e,"@@ -34,7 +34,7 @@ def generate_example_data(cluster_size, outbreak_len, clusters, gen_time, attrib + for i in range(clusters): + cluster_letter = np.random.choice([i for i in string.ascii_uppercase if i not in used])[0] + cluster_name = 'Cluster' + cluster_letter +- used.append(cluster_name) ++ used.append(cluster_letter) + + ix_rng = pd.date_range('1/1/2014', periods=outbreak_len, freq='D') + ix_date = np.random.choice(ix_rng, size=1) +",epipy/data_generator.py,"ReplaceText(target='cluster_letter' @(37,20)->(37,32))","def generate_example_data(cluster_size, outbreak_len, clusters, gen_time, attrib + for i in range(clusters): + cluster_letter = np.random.choice([i for i in string.ascii_uppercase if i not in used])[0] + cluster_name = 'Cluster' + cluster_letter + used.append(cluster_name) + + ix_rng = pd.date_range('1/1/2014', periods=outbreak_len, freq='D') + ix_date = np.random.choice(ix_rng, size=1)","def generate_example_data(cluster_size, outbreak_len, clusters, gen_time, attrib + for i in range(clusters): + cluster_letter = np.random.choice([i for i in string.ascii_uppercase if i not in used])[0] + cluster_name = 'Cluster' + cluster_letter + used.append(cluster_letter) + + ix_rng = pd.date_range('1/1/2014', periods=outbreak_len, freq='D') + ix_date = np.random.choice(ix_rng, size=1)" +300,https://:@github.com/parmed/ParmEd.git,9eda010f0342ace7a3ccc6452a8c8014c73bd130,"@@ -282,7 +282,7 @@ class AmberFormat(object): + rawdata = self.parm_data[flag] + self.parm_data[flag] = [] + for line in rawdata: +- self.parm_data[flag].extend(self.formats[key].read(line)) ++ self.parm_data[flag].extend(self.formats[flag].read(line)) + + try: + for i, chg in enumerate(self.parm_data[self.charge_flag]): +",chemistry/amber/amberformat.py,"ReplaceText(target='flag' @(285,61)->(285,64))","class AmberFormat(object): + rawdata = self.parm_data[flag] + self.parm_data[flag] = [] + for line in rawdata: + self.parm_data[flag].extend(self.formats[key].read(line)) + + try: + for i, chg in enumerate(self.parm_data[self.charge_flag]):","class AmberFormat(object): + rawdata = self.parm_data[flag] + self.parm_data[flag] = [] + for line in rawdata: + self.parm_data[flag].extend(self.formats[flag].read(line)) + + try: + for i, chg in enumerate(self.parm_data[self.charge_flag]):" +301,https://:@github.com/parmed/ParmEd.git,9167bf221e4fe5d71ccaa6bf310fce60f09dc873,"@@ -192,7 +192,7 @@ def diff_files(file1, file2, ignore_whitespace=True, + i = 1 + same = True + if ignore_whitespace: +- while l1 and l2: ++ while l1 or l2: + if l1.strip() != l2.strip(): + if l1.startswith('%VERSION') and l2.startswith('%VERSION'): + l1 = f1.readline() +",test/utils.py,"ReplaceText(target='or' @(195,21)->(195,24))","def diff_files(file1, file2, ignore_whitespace=True, + i = 1 + same = True + if ignore_whitespace: + while l1 and l2: + if l1.strip() != l2.strip(): + if l1.startswith('%VERSION') and l2.startswith('%VERSION'): + l1 = f1.readline()","def diff_files(file1, file2, ignore_whitespace=True, + i = 1 + same = True + if ignore_whitespace: + while l1 or l2: + if l1.strip() != l2.strip(): + if l1.startswith('%VERSION') and l2.startswith('%VERSION'): + l1 = f1.readline()" +302,https://:@github.com/parmed/ParmEd.git,b5fdf3d9b7095b96bcb8ac0bdbdfb3694d1d5220,"@@ -334,7 +334,7 @@ class ChamberParm(AmberParm): + for i, j, k, l, m, n in zip(it, it, it, it, it, it): + self.cmaps.append( + Cmap(self.atoms[i-1], self.atoms[j-1], self.atoms[k-1], +- self.atoms[k-1], self.atoms[m-1], self.cmap_types[n-1]) ++ self.atoms[l-1], self.atoms[m-1], self.cmap_types[n-1]) + ) + + #=================================================== +",chemistry/amber/_chamberparm.py,"ReplaceText(target='l' @(337,36)->(337,37))","class ChamberParm(AmberParm): + for i, j, k, l, m, n in zip(it, it, it, it, it, it): + self.cmaps.append( + Cmap(self.atoms[i-1], self.atoms[j-1], self.atoms[k-1], + self.atoms[k-1], self.atoms[m-1], self.cmap_types[n-1]) + ) + + #===================================================","class ChamberParm(AmberParm): + for i, j, k, l, m, n in zip(it, it, it, it, it, it): + self.cmaps.append( + Cmap(self.atoms[i-1], self.atoms[j-1], self.atoms[k-1], + self.atoms[l-1], self.atoms[m-1], self.cmap_types[n-1]) + ) + + #===================================================" +303,https://:@github.com/parmed/ParmEd.git,820a80ccad22ee881042f03b83a0f07b5f1b537d,"@@ -1272,7 +1272,7 @@ class Structure(object): + break + elif a2.residue is None: + break +- elif a1.residue.name != a1.residue.name: ++ elif a1.residue.name != a2.residue.name: + break + if not a1.type and not a2.type: + if a1.name != a2.name: break +",chemistry/structure.py,"ReplaceText(target='a2' @(1275,48)->(1275,50))","class Structure(object): + break + elif a2.residue is None: + break + elif a1.residue.name != a1.residue.name: + break + if not a1.type and not a2.type: + if a1.name != a2.name: break","class Structure(object): + break + elif a2.residue is None: + break + elif a1.residue.name != a2.residue.name: + break + if not a1.type and not a2.type: + if a1.name != a2.name: break" +304,https://:@github.com/parmed/ParmEd.git,4cba8197ae90a1af4abe0dee3f19e1c8c61c959f,"@@ -313,7 +313,7 @@ class Mol2File(object): + if a == '0': continue + for atom in res: + if atom.name == a: +- atom.connections.append(atom) ++ res.connections.append(atom) + break + else: + raise Mol2Error('Residue connection atom %s not ' +",parmed/formats/mol2.py,"ReplaceText(target='res' @(316,32)->(316,36))","class Mol2File(object): + if a == '0': continue + for atom in res: + if atom.name == a: + atom.connections.append(atom) + break + else: + raise Mol2Error('Residue connection atom %s not '","class Mol2File(object): + if a == '0': continue + for atom in res: + if atom.name == a: + res.connections.append(atom) + break + else: + raise Mol2Error('Residue connection atom %s not '" +305,https://:@github.com/parmed/ParmEd.git,9be43ac3521aca71f84de9b2b11740b00dfdb1b6,"@@ -696,6 +696,6 @@ def _set_owner(atoms, owner_array, atm, mol_id): + if not partner.marked: + owner_array.append(partner.idx) + _set_owner(atoms, owner_array, partner.idx, mol_id) +- assert partner.marked != mol_id, 'Atom in multiple molecules!' ++ assert partner.marked == mol_id, 'Atom in multiple molecules!' + + # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +",parmed/charmm/psf.py,"ReplaceText(target='==' @(699,30)->(699,32))","def _set_owner(atoms, owner_array, atm, mol_id): + if not partner.marked: + owner_array.append(partner.idx) + _set_owner(atoms, owner_array, partner.idx, mol_id) + assert partner.marked != mol_id, 'Atom in multiple molecules!' + + # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++","def _set_owner(atoms, owner_array, atm, mol_id): + if not partner.marked: + owner_array.append(partner.idx) + _set_owner(atoms, owner_array, partner.idx, mol_id) + assert partner.marked == mol_id, 'Atom in multiple molecules!' + + # ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" +306,https://:@github.com/parmed/ParmEd.git,8f1dc98d485ea57e4046494ad1e6f84cfbd17f4f,"@@ -449,7 +449,7 @@ class ParameterSet(object): + for name, residue in iteritems(self.residues): + if isinstance(residue, ResidueTemplateContainer): + for res in residue: +- for atom in residue: ++ for atom in res: + atom.atom_type = self.atom_types[atom.type] + else: + assert isinstance(residue, ResidueTemplate), 'Wrong type!' +",parmed/parameters.py,"ReplaceText(target='res' @(452,32)->(452,39))","class ParameterSet(object): + for name, residue in iteritems(self.residues): + if isinstance(residue, ResidueTemplateContainer): + for res in residue: + for atom in residue: + atom.atom_type = self.atom_types[atom.type] + else: + assert isinstance(residue, ResidueTemplate), 'Wrong type!'","class ParameterSet(object): + for name, residue in iteritems(self.residues): + if isinstance(residue, ResidueTemplateContainer): + for res in residue: + for atom in res: + atom.atom_type = self.atom_types[atom.type] + else: + assert isinstance(residue, ResidueTemplate), 'Wrong type!'" +307,https://:@github.com/parmed/ParmEd.git,403c2874c1826cbe182386959a23118b33d1e27c,"@@ -219,7 +219,7 @@ class OpenMMParameterSet(ParameterSet): + if tag not in sub_content: + raise KeyError('Content of an attribute-containing element ' + 'specified incorrectly.') +- attributes = [key for key in content if key != tag] ++ attributes = [key for key in sub_content if key != tag] + element_content = sub_content[tag] + dest.write(' <%s' % tag) + for attribute in attributes: +",parmed/openmm/parameters.py,"ReplaceText(target='sub_content' @(222,49)->(222,56))","class OpenMMParameterSet(ParameterSet): + if tag not in sub_content: + raise KeyError('Content of an attribute-containing element ' + 'specified incorrectly.') + attributes = [key for key in content if key != tag] + element_content = sub_content[tag] + dest.write(' <%s' % tag) + for attribute in attributes:","class OpenMMParameterSet(ParameterSet): + if tag not in sub_content: + raise KeyError('Content of an attribute-containing element ' + 'specified incorrectly.') + attributes = [key for key in sub_content if key != tag] + element_content = sub_content[tag] + dest.write(' <%s' % tag) + for attribute in attributes:" +308,https://:@github.com/parmed/ParmEd.git,657ba99e2338df75ef118155d95d144c7b33ab32,"@@ -281,7 +281,7 @@ T = RNAResidue('Thymine', 'T', ['THY', 'T3', 'T5', 'TN', + + WATER_NAMES = set(['WAT', 'HOH', 'TIP3', 'TIP4', + 'TIP5', 'SPCE', 'SPC']) +-SOLVENT_NAMES = WATER_NAMES ^ set({'SOL'}) ++SOLVENT_NAMES = WATER_NAMES | set({'SOL'}) + EXTRA_POINT_NAMES = set(['EP', 'LP']) + CATION_NAMES = set(['Na+', 'Li+', 'Mg+', 'Rb+', 'MG', 'Cs+', 'POT', 'SOD', + 'MG2', 'CAL', 'RUB', 'LIT', 'ZN2', 'CD2', 'NA', 'K+', 'K', +",parmed/residue.py,"ReplaceText(target='|' @(284,28)->(284,29))","T = RNAResidue('Thymine', 'T', ['THY', 'T3', 'T5', 'TN', + + WATER_NAMES = set(['WAT', 'HOH', 'TIP3', 'TIP4', + 'TIP5', 'SPCE', 'SPC']) + SOLVENT_NAMES = WATER_NAMES ^ set({'SOL'}) + EXTRA_POINT_NAMES = set(['EP', 'LP']) + CATION_NAMES = set(['Na+', 'Li+', 'Mg+', 'Rb+', 'MG', 'Cs+', 'POT', 'SOD', + 'MG2', 'CAL', 'RUB', 'LIT', 'ZN2', 'CD2', 'NA', 'K+', 'K',","T = RNAResidue('Thymine', 'T', ['THY', 'T3', 'T5', 'TN', + + WATER_NAMES = set(['WAT', 'HOH', 'TIP3', 'TIP4', + 'TIP5', 'SPCE', 'SPC']) + SOLVENT_NAMES = WATER_NAMES | set({'SOL'}) + EXTRA_POINT_NAMES = set(['EP', 'LP']) + CATION_NAMES = set(['Na+', 'Li+', 'Mg+', 'Rb+', 'MG', 'Cs+', 'POT', 'SOD', + 'MG2', 'CAL', 'RUB', 'LIT', 'ZN2', 'CD2', 'NA', 'K+', 'K'," +309,https://:@github.com/parmed/ParmEd.git,bd2a1120adf53ab364dda802a272c19c7d335fdd,"@@ -374,7 +374,7 @@ class OpenMMParameterSet(ParameterSet): + for attribute in attributes: + dest.write(' %s=""%s""' % (attribute, sub_content[attribute])) + escaped_element_content = escape(element_content, XML_ESCAPES) +- dest.write('>%s\n' % (element_content, tag)) ++ dest.write('>%s\n' % (escaped_element_content, tag)) + else: + raise TypeError('Incorrect type of the %s element content' % tag) + dest.write(' \n') +",parmed/openmm/parameters.py,"ReplaceText(target='escaped_element_content' @(377,47)->(377,62))","class OpenMMParameterSet(ParameterSet): + for attribute in attributes: + dest.write(' %s=""%s""' % (attribute, sub_content[attribute])) + escaped_element_content = escape(element_content, XML_ESCAPES) + dest.write('>%s\n' % (element_content, tag)) + else: + raise TypeError('Incorrect type of the %s element content' % tag) + dest.write(' \n')","class OpenMMParameterSet(ParameterSet): + for attribute in attributes: + dest.write(' %s=""%s""' % (attribute, sub_content[attribute])) + escaped_element_content = escape(element_content, XML_ESCAPES) + dest.write('>%s\n' % (escaped_element_content, tag)) + else: + raise TypeError('Incorrect type of the %s element content' % tag) + dest.write(' \n')" +310,https://:@github.com/parmed/ParmEd.git,62e0c8aa4561628d005e84bbe97b1ef37f32dee5,"@@ -502,7 +502,7 @@ class OpenMMParameterSet(ParameterSet): + patched_residue = residue.apply_patch(patch) + + for atom in patch.atoms: +- if atom.name not in patched_residue: ++ if atom.name not in residue: + dest.write(' \n' % + (atom.name, atom.type, atom.charge)) + else: +",parmed/openmm/parameters.py,"ReplaceText(target='residue' @(505,36)->(505,51))","class OpenMMParameterSet(ParameterSet): + patched_residue = residue.apply_patch(patch) + + for atom in patch.atoms: + if atom.name not in patched_residue: + dest.write(' \n' % + (atom.name, atom.type, atom.charge)) + else:","class OpenMMParameterSet(ParameterSet): + patched_residue = residue.apply_patch(patch) + + for atom in patch.atoms: + if atom.name not in residue: + dest.write(' \n' % + (atom.name, atom.type, atom.charge)) + else:" +311,https://:@github.com/parmed/ParmEd.git,90fa4626c3db158047991044f4dd4619a7cc2599,"@@ -502,7 +502,7 @@ class AmberFormat(object): + own_handle = True + elif hasattr(fname, 'read'): + prm = fname +- own_handle = True ++ own_handle = False + else: + raise TypeError('%s must be a file name or file-like object' % fname) + +",parmed/amber/amberformat.py,"ReplaceText(target='False' @(505,25)->(505,29))","class AmberFormat(object): + own_handle = True + elif hasattr(fname, 'read'): + prm = fname + own_handle = True + else: + raise TypeError('%s must be a file name or file-like object' % fname) + ","class AmberFormat(object): + own_handle = True + elif hasattr(fname, 'read'): + prm = fname + own_handle = False + else: + raise TypeError('%s must be a file name or file-like object' % fname) + " +312,https://:@github.com/xmunoz/sodapy.git,76bdcfd9670e94c833b66b8894ea4153c27004ee,"@@ -71,7 +71,7 @@ class Socrata(object): + else: + self.uri_prefix = ""https://"" + +- if isinstance(timeout, (int, long, float)): ++ if not isinstance(timeout, (int, long, float)): + raise TypeError(""Timeout must be numeric."") + self.timeout = timeout + +",sodapy/__init__.py,"ReplaceText(target='not ' @(74,11)->(74,11))","class Socrata(object): + else: + self.uri_prefix = ""https://"" + + if isinstance(timeout, (int, long, float)): + raise TypeError(""Timeout must be numeric."") + self.timeout = timeout + ","class Socrata(object): + else: + self.uri_prefix = ""https://"" + + if not isinstance(timeout, (int, long, float)): + raise TypeError(""Timeout must be numeric."") + self.timeout = timeout + " +313,https://:@github.com/xmunoz/sodapy.git,be6804a7f566eda08af7bb5d67f9c75512581189,"@@ -129,7 +129,7 @@ class Socrata(object): + next(iter(kwargs))) + + if order: +- kwargs.append(('order', order)) ++ params.append(('order', order)) + + results = self._perform_request(""get"", DATASETS_PATH, + params=params + [('offset', offset)]) +",sodapy/__init__.py,"ReplaceText(target='params' @(132,12)->(132,18))","class Socrata(object): + next(iter(kwargs))) + + if order: + kwargs.append(('order', order)) + + results = self._perform_request(""get"", DATASETS_PATH, + params=params + [('offset', offset)])","class Socrata(object): + next(iter(kwargs))) + + if order: + params.append(('order', order)) + + results = self._perform_request(""get"", DATASETS_PATH, + params=params + [('offset', offset)])" +314,https://:@github.com/visgence/teleceptor.git,4a8db10b79207b4bf8b48bbcaafdd03cc1166a2f,"@@ -397,7 +397,7 @@ def _updateCalibration(sensor, coefficients, timestamp, session): + logging.debug(""Comparing coefficients."") + + # check if coefficients are different +- if ""{}"".format(Cal.coefficients) == ""{}"".format(coefficients): ++ if ""{}"".format(Cal.coefficients) != ""{}"".format(coefficients): + logging.debug(""Coefficients are different, updating..."") + + assert isinstance(coefficients, list) +",teleceptor/api/sensors.py,"ReplaceText(target='!=' @(400,49)->(400,51))","def _updateCalibration(sensor, coefficients, timestamp, session): + logging.debug(""Comparing coefficients."") + + # check if coefficients are different + if ""{}"".format(Cal.coefficients) == ""{}"".format(coefficients): + logging.debug(""Coefficients are different, updating..."") + + assert isinstance(coefficients, list)","def _updateCalibration(sensor, coefficients, timestamp, session): + logging.debug(""Comparing coefficients."") + + # check if coefficients are different + if ""{}"".format(Cal.coefficients) != ""{}"".format(coefficients): + logging.debug(""Coefficients are different, updating..."") + + assert isinstance(coefficients, list)" +315,https://:@github.com/projectmesa/mesa.git,0893a8f03d7f22f1b064e66c97da3dddd987b7ea,"@@ -50,7 +50,7 @@ class Schelling(Model): + self.homophily = homophily + + self.schedule = RandomActivation(self) +- self.grid = SingleGrid(height, width, torus=True) ++ self.grid = SingleGrid(width, height, torus=True) + + self.happy = 0 + self.datacollector = DataCollector( +",examples/schelling/model.py,"ArgSwap(idxs=0<->1 @(53,20)->(53,30))","class Schelling(Model): + self.homophily = homophily + + self.schedule = RandomActivation(self) + self.grid = SingleGrid(height, width, torus=True) + + self.happy = 0 + self.datacollector = DataCollector(","class Schelling(Model): + self.homophily = homophily + + self.schedule = RandomActivation(self) + self.grid = SingleGrid(width, height, torus=True) + + self.happy = 0 + self.datacollector = DataCollector(" +316,https://:@github.com/projectmesa/mesa.git,9277b0f55ed63d3b8a32c7f3e52e3df1e7de6579,"@@ -31,7 +31,7 @@ class PdGrid(Model): + Determines the agent activation regime. + payoffs: (optional) Dictionary of (move, neighbor_move) payoffs. + ''' +- self.grid = SingleGrid(height, width, torus=True) ++ self.grid = SingleGrid(width, height, torus=True) + self.schedule_type = schedule_type + self.schedule = self.schedule_types[self.schedule_type](self) + +",examples/pd_grid/pd_grid/model.py,"ArgSwap(idxs=0<->1 @(34,20)->(34,30))","class PdGrid(Model): + Determines the agent activation regime. + payoffs: (optional) Dictionary of (move, neighbor_move) payoffs. + ''' + self.grid = SingleGrid(height, width, torus=True) + self.schedule_type = schedule_type + self.schedule = self.schedule_types[self.schedule_type](self) + ","class PdGrid(Model): + Determines the agent activation regime. + payoffs: (optional) Dictionary of (move, neighbor_move) payoffs. + ''' + self.grid = SingleGrid(width, height, torus=True) + self.schedule_type = schedule_type + self.schedule = self.schedule_types[self.schedule_type](self) + " +317,https://:@github.com/iCHEF/queryfilter.git,96c25a4e5e750ae3415712d6812eee04d2187e64,"@@ -70,7 +70,7 @@ class DictFilterMixin(object): + if not dictobj: + # Point to which level doesn't exist exactly + return handle_missing_field( +- ""__"".join(level_field_names[:index+1]) ++ ""__"".join(parent_field_names[:index+1]) + ) + if final_field_name not in dictobj: + return handle_missing_field(field_name) +",queryfilter/base.py,"ReplaceText(target='parent_field_names' @(73,30)->(73,47))","class DictFilterMixin(object): + if not dictobj: + # Point to which level doesn't exist exactly + return handle_missing_field( + ""__"".join(level_field_names[:index+1]) + ) + if final_field_name not in dictobj: + return handle_missing_field(field_name)","class DictFilterMixin(object): + if not dictobj: + # Point to which level doesn't exist exactly + return handle_missing_field( + ""__"".join(parent_field_names[:index+1]) + ) + if final_field_name not in dictobj: + return handle_missing_field(field_name)" +318,https://:@github.com/slaclab/paws.git,953037e723903e2213495189c9a99eb5445ecc9a,"@@ -293,7 +293,7 @@ class XRSDFitGUI(Operation): + ubnd = xrsdkit.param_bound_defaults[param_nm][1] + if xrsdkit.contains_param(self.inputs['param_bounds'],pop_nm,param_nm): + lbnd = self.inputs['param_bounds'][pop_nm]['parameters'][param_nm][0] +- lbnd = self.inputs['param_bounds'][pop_nm]['parameters'][param_nm][1] ++ ubnd = self.inputs['param_bounds'][pop_nm]['parameters'][param_nm][1] + # TODO: the bounds entries need to be connected to DoubleVars. + pbnde1.insert(0,str(lbnd)) + pbnde2.insert(0,str(ubnd)) +",paws/core/operations/PROCESSING/FITTING/XRSDFitGUI.py,"ReplaceText(target='ubnd' @(296,16)->(296,20))","class XRSDFitGUI(Operation): + ubnd = xrsdkit.param_bound_defaults[param_nm][1] + if xrsdkit.contains_param(self.inputs['param_bounds'],pop_nm,param_nm): + lbnd = self.inputs['param_bounds'][pop_nm]['parameters'][param_nm][0] + lbnd = self.inputs['param_bounds'][pop_nm]['parameters'][param_nm][1] + # TODO: the bounds entries need to be connected to DoubleVars. + pbnde1.insert(0,str(lbnd)) + pbnde2.insert(0,str(ubnd))","class XRSDFitGUI(Operation): + ubnd = xrsdkit.param_bound_defaults[param_nm][1] + if xrsdkit.contains_param(self.inputs['param_bounds'],pop_nm,param_nm): + lbnd = self.inputs['param_bounds'][pop_nm]['parameters'][param_nm][0] + ubnd = self.inputs['param_bounds'][pop_nm]['parameters'][param_nm][1] + # TODO: the bounds entries need to be connected to DoubleVars. + pbnde1.insert(0,str(lbnd)) + pbnde2.insert(0,str(ubnd))" +319,https://:@github.com/PyFilesystem/pyfilesystem2.git,cd1a973dd80e4083502db51844981f3457d13760,"@@ -258,7 +258,7 @@ class OSFS(FS): + with convert_os_errors(""getinfo"", path): + _stat = os.stat(fsencode(sys_path)) + if ""lstat"" in namespaces: +- _stat = os.lstat(fsencode(sys_path)) ++ _lstat = os.lstat(fsencode(sys_path)) + + info = { + ""basic"": {""name"": basename(_path), ""is_dir"": stat.S_ISDIR(_stat.st_mode)} +",fs/osfs.py,"ReplaceText(target='_lstat' @(261,16)->(261,21))","class OSFS(FS): + with convert_os_errors(""getinfo"", path): + _stat = os.stat(fsencode(sys_path)) + if ""lstat"" in namespaces: + _stat = os.lstat(fsencode(sys_path)) + + info = { + ""basic"": {""name"": basename(_path), ""is_dir"": stat.S_ISDIR(_stat.st_mode)}","class OSFS(FS): + with convert_os_errors(""getinfo"", path): + _stat = os.stat(fsencode(sys_path)) + if ""lstat"" in namespaces: + _lstat = os.lstat(fsencode(sys_path)) + + info = { + ""basic"": {""name"": basename(_path), ""is_dir"": stat.S_ISDIR(_stat.st_mode)}" +320,https://:@github.com/kevinzg/facebook-scraper.git,c11dffbc1beef25271fb5bc6d2aa3aeb5b2079aa,"@@ -83,7 +83,7 @@ def _get_posts(path, pages=10, timeout=5, sleep=0, credentials=None, extra_info= + yield post + + pages -= 1 +- if pages == 0: ++ if pages <= 0: + return + + cursor = _find_cursor(cursor_blob) +",facebook_scraper.py,"ReplaceText(target='<=' @(86,17)->(86,19))","def _get_posts(path, pages=10, timeout=5, sleep=0, credentials=None, extra_info= + yield post + + pages -= 1 + if pages == 0: + return + + cursor = _find_cursor(cursor_blob)","def _get_posts(path, pages=10, timeout=5, sleep=0, credentials=None, extra_info= + yield post + + pages -= 1 + if pages <= 0: + return + + cursor = _find_cursor(cursor_blob)" +321,https://:@github.com/linkedin/naarad.git,897858ba0d80fb74bbad40bfc8f96b0f59b0900e,"@@ -75,10 +75,10 @@ class Report(object): + for metric in self.metric_list: + metric_stats = [] + metric_stats_file, summary_stats, metric_plots, correlated_plots = self.discover_metric_data(self.output_directory, metric) +- if metric_stats_file != '' and len(metric_plots) > 0: ++ if metric_stats_file != '' or len(metric_plots) > 0: + metric_stats = self.get_summary_table(metric_stats_file) + metric_html = template_environment.get_template(self.report_templates['header']).render(custom_javascript_includes=[""http://www.kryogenix.org/code/browser/sorttable/sorttable.js""]) + metric_html += template_environment.get_template(self.report_templates['metric']).render(metric_stats=metric_stats, metric_plots=metric_plots, correlated_plots=correlated_plots, metric=metric) + metric_html += template_environment.get_template(self.report_templates['footer']).render() +- with open(os.path.join(self.output_directory, metric + '_report.html'),'w') as metric_report: ++ with open(os.path.join(self.output_directory, metric + '_report.html'), 'w') as metric_report: + metric_report.write(metric_html) +",src/naarad/reporting/report.py,"ReplaceText(target='or' @(78,33)->(78,36))","class Report(object): + for metric in self.metric_list: + metric_stats = [] + metric_stats_file, summary_stats, metric_plots, correlated_plots = self.discover_metric_data(self.output_directory, metric) + if metric_stats_file != '' and len(metric_plots) > 0: + metric_stats = self.get_summary_table(metric_stats_file) + metric_html = template_environment.get_template(self.report_templates['header']).render(custom_javascript_includes=[""http://www.kryogenix.org/code/browser/sorttable/sorttable.js""]) + metric_html += template_environment.get_template(self.report_templates['metric']).render(metric_stats=metric_stats, metric_plots=metric_plots, correlated_plots=correlated_plots, metric=metric) + metric_html += template_environment.get_template(self.report_templates['footer']).render() + with open(os.path.join(self.output_directory, metric + '_report.html'),'w') as metric_report: + metric_report.write(metric_html)","class Report(object): + for metric in self.metric_list: + metric_stats = [] + metric_stats_file, summary_stats, metric_plots, correlated_plots = self.discover_metric_data(self.output_directory, metric) + if metric_stats_file != '' or len(metric_plots) > 0: + metric_stats = self.get_summary_table(metric_stats_file) + metric_html = template_environment.get_template(self.report_templates['header']).render(custom_javascript_includes=[""http://www.kryogenix.org/code/browser/sorttable/sorttable.js""]) + metric_html += template_environment.get_template(self.report_templates['metric']).render(metric_stats=metric_stats, metric_plots=metric_plots, correlated_plots=correlated_plots, metric=metric) + metric_html += template_environment.get_template(self.report_templates['footer']).render() + with open(os.path.join(self.output_directory, metric + '_report.html'), 'w') as metric_report: + metric_report.write(metric_html)" +322,https://:@github.com/linkedin/naarad.git,74c5928b9c26fb7bd708fb9480dd2014b4305b89,"@@ -67,7 +67,7 @@ def graph_data(list_of_plots, output_directory, output_filename): + plot_count = len(plots) + + if plot_count == 0: +- return True, None ++ return False, None + + graph_height, graph_width, graph_title = get_graph_metadata(list_of_plots) + +",src/naarad/graphing/matplotlib_naarad.py,"ReplaceText(target='False' @(70,11)->(70,15))","def graph_data(list_of_plots, output_directory, output_filename): + plot_count = len(plots) + + if plot_count == 0: + return True, None + + graph_height, graph_width, graph_title = get_graph_metadata(list_of_plots) + ","def graph_data(list_of_plots, output_directory, output_filename): + plot_count = len(plots) + + if plot_count == 0: + return False, None + + graph_height, graph_width, graph_title = get_graph_metadata(list_of_plots) + " +323,https://:@github.com/linkedin/naarad.git,fa8753e74e301602fd50281ef36bc13cde421ac2,"@@ -204,7 +204,7 @@ class Metric(object): + if i+1 in groupby_idxes: + continue + else: +- out_csv = self.get_csv(groupby_names, self.columns[i]) ++ out_csv = self.get_csv(self.columns[i], groupby_names) + if out_csv in data: + data[out_csv].append(ts + ',' + words[i+1]) + else: +",src/naarad/metrics/metric.py,"ArgSwap(idxs=0<->1 @(207,26)->(207,38))","class Metric(object): + if i+1 in groupby_idxes: + continue + else: + out_csv = self.get_csv(groupby_names, self.columns[i]) + if out_csv in data: + data[out_csv].append(ts + ',' + words[i+1]) + else:","class Metric(object): + if i+1 in groupby_idxes: + continue + else: + out_csv = self.get_csv(self.columns[i], groupby_names) + if out_csv in data: + data[out_csv].append(ts + ',' + words[i+1]) + else:" +324,https://:@gitlab.com/mailman/postorius.git,308434aa505637da8275150484943b2442bc4b3c,"@@ -232,6 +232,6 @@ class ListMembersTest(ViewTestCase): + {'q': 'not_a_member'}) + self.assertEqual(response.status_code, 200) + self.assertEqual(len(response.context['members']), 0) +- self.assertNotContains(response, member_2.email) ++ self.assertNotContains(response, member_1.email) + self.assertNotContains(response, member_2.email) + +",src/postorius/tests/mailman_api_tests/test_list_members.py,"ReplaceText(target='member_1' @(235,41)->(235,49))","class ListMembersTest(ViewTestCase): + {'q': 'not_a_member'}) + self.assertEqual(response.status_code, 200) + self.assertEqual(len(response.context['members']), 0) + self.assertNotContains(response, member_2.email) + self.assertNotContains(response, member_2.email) + ","class ListMembersTest(ViewTestCase): + {'q': 'not_a_member'}) + self.assertEqual(response.status_code, 200) + self.assertEqual(len(response.context['members']), 0) + self.assertNotContains(response, member_1.email) + self.assertNotContains(response, member_2.email) + " +325,https://:@github.com/crsmithdev/arrow.git,fa5bce04765198071c17fa2ee889c16b5dbe6377,"@@ -94,7 +94,7 @@ class DateTimeFormatter(object): + tz = dateutil_tz.tzutc() if dt.tzinfo is None else dt.tzinfo + total_minutes = int(util.total_seconds(tz.utcoffset(dt)) / 60) + +- sign = '+' if total_minutes > 0 else '-' ++ sign = '+' if total_minutes >= 0 else '-' + total_minutes = abs(total_minutes) + hour, minute = divmod(total_minutes, 60) + +",arrow/formatter.py,"ReplaceText(target='>=' @(97,40)->(97,41))","class DateTimeFormatter(object): + tz = dateutil_tz.tzutc() if dt.tzinfo is None else dt.tzinfo + total_minutes = int(util.total_seconds(tz.utcoffset(dt)) / 60) + + sign = '+' if total_minutes > 0 else '-' + total_minutes = abs(total_minutes) + hour, minute = divmod(total_minutes, 60) + ","class DateTimeFormatter(object): + tz = dateutil_tz.tzutc() if dt.tzinfo is None else dt.tzinfo + total_minutes = int(util.total_seconds(tz.utcoffset(dt)) / 60) + + sign = '+' if total_minutes >= 0 else '-' + total_minutes = abs(total_minutes) + hour, minute = divmod(total_minutes, 60) + " +326,https://:@github.com/AICoE/log-anomaly-detector.git,cd462c169c77152ae10cf3b0b99adfa51d53c043,"@@ -37,4 +37,4 @@ class SOMPYModel(BaseModel): + dist = np.linalg.norm(self.model[x][y] - log) + if dist < dist_smallest: + dist_smallest = dist +- return dist ++ return dist_smallest +",anomaly_detector/model/sompy_model.py,"ReplaceText(target='dist_smallest' @(40,15)->(40,19))","class SOMPYModel(BaseModel): + dist = np.linalg.norm(self.model[x][y] - log) + if dist < dist_smallest: + dist_smallest = dist + return dist","class SOMPYModel(BaseModel): + dist = np.linalg.norm(self.model[x][y] - log) + if dist < dist_smallest: + dist_smallest = dist + return dist_smallest" +327,https://:@github.com/ksmet1977/luxpy.git,6b6e6f7dd1dd257c8394dcd439f2bbb39be46fef,"@@ -896,7 +896,7 @@ def plot_spectrum_colors(spd = None, spdmax = None,\ + cmfs = _CMF[cieobs]['bar'] + else: + cmfs = cieobs +- cmfs = cmfs[:,cmfs[1:].sum(axis=1)>0] # avoid div by zero in xyz-to-Yxy conversion ++ cmfs = cmfs[:,cmfs[1:].sum(axis=0)>0] # avoid div by zero in xyz-to-Yxy conversion + + wavs = cmfs[0:1].T + SL = cmfs[1:4].T +",luxpy/color/utils/plotters.py,"ReplaceText(target='0' @(899,36)->(899,37))","def plot_spectrum_colors(spd = None, spdmax = None,\ + cmfs = _CMF[cieobs]['bar'] + else: + cmfs = cieobs + cmfs = cmfs[:,cmfs[1:].sum(axis=1)>0] # avoid div by zero in xyz-to-Yxy conversion + + wavs = cmfs[0:1].T + SL = cmfs[1:4].T ","def plot_spectrum_colors(spd = None, spdmax = None,\ + cmfs = _CMF[cieobs]['bar'] + else: + cmfs = cieobs + cmfs = cmfs[:,cmfs[1:].sum(axis=0)>0] # avoid div by zero in xyz-to-Yxy conversion + + wavs = cmfs[0:1].T + SL = cmfs[1:4].T " +328,https://:@github.com/melexis/sphinx-traceability-extension.git,64a00adbbbec4088a6e0bb88b1ed43e26c2776bd,"@@ -760,7 +760,7 @@ def process_item_nodes(app, doctree, fromdocname): + for source in node['sources']: + for target in node['targets']: + try: +- env.traceability_collection.add_relation(target, node['type'], source) ++ env.traceability_collection.add_relation(source, node['type'], target) + except TraceabilityException as err: + report_warning(env, err, env.docname, self.lineno) + # The ItemLink node has no final representation, so is removed from the tree +",mlx/traceability.py,"ArgSwap(idxs=0<->2 @(763,20)->(763,60))","def process_item_nodes(app, doctree, fromdocname): + for source in node['sources']: + for target in node['targets']: + try: + env.traceability_collection.add_relation(target, node['type'], source) + except TraceabilityException as err: + report_warning(env, err, env.docname, self.lineno) + # The ItemLink node has no final representation, so is removed from the tree","def process_item_nodes(app, doctree, fromdocname): + for source in node['sources']: + for target in node['targets']: + try: + env.traceability_collection.add_relation(source, node['type'], target) + except TraceabilityException as err: + report_warning(env, err, env.docname, self.lineno) + # The ItemLink node has no final representation, so is removed from the tree" +329,https://:@github.com/rocky/python3-trepan.git,2ff3e8439122926251ef9e7e4b7b89018feb9892,"@@ -47,7 +47,7 @@ and recolor all source code output."""""" + pass + + def run(self, args): +- if len(args) >= 1 and 'reset' == args[0]: ++ if len(args) > 1 and 'reset' == args[0]: + highlight_type = self.get_highlight_type(args[1]) + if not highlight_type: return + clear_file_format_cache() +",trepan/processor/command/set_subcmd/highlight.py,"ReplaceText(target='>' @(50,21)->(50,23))","and recolor all source code output."""""" + pass + + def run(self, args): + if len(args) >= 1 and 'reset' == args[0]: + highlight_type = self.get_highlight_type(args[1]) + if not highlight_type: return + clear_file_format_cache()","and recolor all source code output."""""" + pass + + def run(self, args): + if len(args) > 1 and 'reset' == args[0]: + highlight_type = self.get_highlight_type(args[1]) + if not highlight_type: return + clear_file_format_cache()" +330,https://:@github.com/rocky/python3-trepan.git,7fe5f2be86cf60c41b67ea4a6d24990b06dd536a,"@@ -4,7 +4,7 @@ from fn_helper import strarray_setup, compare_output + + + class TestSkip(unittest.TestCase): +- @unittest.skipIf('TRAVIS' not in os.environ, ++ @unittest.skipIf('TRAVIS' in os.environ, + ""FIXME: figure out why this doesn't work in travis"") + def test_skip(self): + +",test/functional/test-skip.py,"ReplaceText(target=' in ' @(7,29)->(7,37))","from fn_helper import strarray_setup, compare_output + + + class TestSkip(unittest.TestCase): + @unittest.skipIf('TRAVIS' not in os.environ, + ""FIXME: figure out why this doesn't work in travis"") + def test_skip(self): + ","from fn_helper import strarray_setup, compare_output + + + class TestSkip(unittest.TestCase): + @unittest.skipIf('TRAVIS' in os.environ, + ""FIXME: figure out why this doesn't work in travis"") + def test_skip(self): + " +331,https://:@github.com/rocky/python3-trepan.git,ce7705f666154604fb580ca56cd22ec7cc6eae69,"@@ -183,7 +183,7 @@ dictionary that gets fed to trepan.Debugger.core.start(). + Parameter ""step_ignore"" specifies how many line events to ignore after the + debug() call. 0 means don't even wait for the debug() call to finish. + """""" +- if isinstance(Mdebugger.debugger_obj, Mdebugger.Trepan): ++ if not isinstance(Mdebugger.debugger_obj, Mdebugger.Trepan): + Mdebugger.debugger_obj = Mdebugger.Trepan(dbg_opts) + Mdebugger.debugger_obj.core.add_ignore(debug, stop) + pass +",trepan/api.py,"ReplaceText(target='not ' @(186,7)->(186,7))","dictionary that gets fed to trepan.Debugger.core.start(). + Parameter ""step_ignore"" specifies how many line events to ignore after the + debug() call. 0 means don't even wait for the debug() call to finish. + """""" + if isinstance(Mdebugger.debugger_obj, Mdebugger.Trepan): + Mdebugger.debugger_obj = Mdebugger.Trepan(dbg_opts) + Mdebugger.debugger_obj.core.add_ignore(debug, stop) + pass","dictionary that gets fed to trepan.Debugger.core.start(). + Parameter ""step_ignore"" specifies how many line events to ignore after the + debug() call. 0 means don't even wait for the debug() call to finish. + """""" + if not isinstance(Mdebugger.debugger_obj, Mdebugger.Trepan): + Mdebugger.debugger_obj = Mdebugger.Trepan(dbg_opts) + Mdebugger.debugger_obj.core.add_ignore(debug, stop) + pass" +332,https://:@github.com/rocky/python3-trepan.git,342c05260ac86fcc4e6d711a3f579c71d1d53d64,"@@ -116,7 +116,7 @@ See also: + pass + + sys_version = version_info.major + (version_info.minor / 10.0) +- if len(args) >= 1 and args[1] == '.': ++ if len(args) >= 1 and args[0] == '.': + try: + if pretty: + deparsed = deparse_code(sys_version, co) +",trepan/processor/command/deparse.py,"ReplaceText(target='0' @(119,35)->(119,36))","See also: + pass + + sys_version = version_info.major + (version_info.minor / 10.0) + if len(args) >= 1 and args[1] == '.': + try: + if pretty: + deparsed = deparse_code(sys_version, co)","See also: + pass + + sys_version = version_info.major + (version_info.minor / 10.0) + if len(args) >= 1 and args[0] == '.': + try: + if pretty: + deparsed = deparse_code(sys_version, co)" +333,https://:@github.com/kanaka/websockify.git,0da91c7fdb3a49873121594e1820eef7ac078595,"@@ -225,7 +225,7 @@ Sec-WebSocket-Accept: %s\r + payload_len = len(buf) + if payload_len <= 125: + header = struct.pack('>BB', b1, payload_len) +- elif payload_len > 125 and payload_len <= 65536: ++ elif payload_len > 125 and payload_len < 65536: + header = struct.pack('>BBH', b1, 126, payload_len) + elif payload_len >= 65536: + header = struct.pack('>BBQ', b1, 127, payload_len) +",websocket.py,"ReplaceText(target='<' @(228,47)->(228,49))","Sec-WebSocket-Accept: %s\r + payload_len = len(buf) + if payload_len <= 125: + header = struct.pack('>BB', b1, payload_len) + elif payload_len > 125 and payload_len <= 65536: + header = struct.pack('>BBH', b1, 126, payload_len) + elif payload_len >= 65536: + header = struct.pack('>BBQ', b1, 127, payload_len)","Sec-WebSocket-Accept: %s\r + payload_len = len(buf) + if payload_len <= 125: + header = struct.pack('>BB', b1, payload_len) + elif payload_len > 125 and payload_len < 65536: + header = struct.pack('>BBH', b1, 126, payload_len) + elif payload_len >= 65536: + header = struct.pack('>BBQ', b1, 127, payload_len)" +334,https://:@github.com/annoviko/pyclustering.git,70597e34bed02d7c3cb4a3d2e2ed6b30cd6cb3df,"@@ -320,7 +320,7 @@ class hysteresis_network(network): + + if (collect_dynamic is False): + dyn_state.append(self._states); +- dyn_time.append(t); ++ dyn_time.append(time); + + return hysteresis_dynamic(dyn_state, dyn_time); + +",pyclustering/nnet/hysteresis.py,"ReplaceText(target='time' @(323,28)->(323,29))","class hysteresis_network(network): + + if (collect_dynamic is False): + dyn_state.append(self._states); + dyn_time.append(t); + + return hysteresis_dynamic(dyn_state, dyn_time); + ","class hysteresis_network(network): + + if (collect_dynamic is False): + dyn_state.append(self._states); + dyn_time.append(time); + + return hysteresis_dynamic(dyn_state, dyn_time); + " +335,https://:@github.com/annoviko/pyclustering.git,7e1bf5ed9cc2817c00c7e5e216adb4cc9fa8fc49,"@@ -123,7 +123,7 @@ class ttsas(bsas): + + index_cluster, distance = self._find_nearest_cluster(point); + +- if distance < self._threshold: ++ if distance <= self._threshold: + self.__append_to_cluster(index_cluster, index_point, point); + elif distance > self._threshold2: + self.__allocate_cluster(index_point, point); +",pyclustering/cluster/ttsas.py,"ReplaceText(target='<=' @(126,20)->(126,21))","class ttsas(bsas): + + index_cluster, distance = self._find_nearest_cluster(point); + + if distance < self._threshold: + self.__append_to_cluster(index_cluster, index_point, point); + elif distance > self._threshold2: + self.__allocate_cluster(index_point, point);","class ttsas(bsas): + + index_cluster, distance = self._find_nearest_cluster(point); + + if distance <= self._threshold: + self.__append_to_cluster(index_cluster, index_point, point); + elif distance > self._threshold2: + self.__allocate_cluster(index_point, point);" +336,https://:@github.com/annoviko/pyclustering.git,cdb0ca92c076282084f54816d681f7d0a1588066,"@@ -64,7 +64,7 @@ class XmeansTestTemplates: + assertion.eq(expected_wce, wce) + + if expected_cluster_length is not None: +- assertion.eq(len(centers), len(expected_cluster_length)) ++ assertion.eq(len(expected_cluster_length), len(centers)) + + obtained_cluster_sizes.sort() + expected_cluster_length.sort() +",pyclustering/cluster/tests/xmeans_templates.py,"ArgSwap(idxs=0<->1 @(67,12)->(67,24))","class XmeansTestTemplates: + assertion.eq(expected_wce, wce) + + if expected_cluster_length is not None: + assertion.eq(len(centers), len(expected_cluster_length)) + + obtained_cluster_sizes.sort() + expected_cluster_length.sort()","class XmeansTestTemplates: + assertion.eq(expected_wce, wce) + + if expected_cluster_length is not None: + assertion.eq(len(expected_cluster_length), len(centers)) + + obtained_cluster_sizes.sort() + expected_cluster_length.sort()" +337,https://:@github.com/evolbioinfo/pastml.git,06384fd264d834bff88efdc6bf70a098b06f307d,"@@ -232,7 +232,7 @@ def parsimonious_acr(tree, feature, prediction_method, states, num_nodes, num_ti + .format(feature, num_steps)) + num_scenarios, unresolved_nodes = choose_parsimonious_states(tree, feature) + logger.debug('{} node{} unresolved ({:.2f}%) for {}, leading to {:g} ancestral scenario{}.' +- .format(unresolved_nodes, 's are' if unresolved_nodes > 1 else ' is', ++ .format(unresolved_nodes, 's are' if unresolved_nodes != 1 else ' is', + unresolved_nodes * 100 / num_nodes, feature, + num_scenarios, 's' if num_scenarios > 1 else '')) + +",pastml/parsimony.py,"ReplaceText(target='!=' @(235,71)->(235,72))","def parsimonious_acr(tree, feature, prediction_method, states, num_nodes, num_ti + .format(feature, num_steps)) + num_scenarios, unresolved_nodes = choose_parsimonious_states(tree, feature) + logger.debug('{} node{} unresolved ({:.2f}%) for {}, leading to {:g} ancestral scenario{}.' + .format(unresolved_nodes, 's are' if unresolved_nodes > 1 else ' is', + unresolved_nodes * 100 / num_nodes, feature, + num_scenarios, 's' if num_scenarios > 1 else '')) + ","def parsimonious_acr(tree, feature, prediction_method, states, num_nodes, num_ti + .format(feature, num_steps)) + num_scenarios, unresolved_nodes = choose_parsimonious_states(tree, feature) + logger.debug('{} node{} unresolved ({:.2f}%) for {}, leading to {:g} ancestral scenario{}.' + .format(unresolved_nodes, 's are' if unresolved_nodes != 1 else ' is', + unresolved_nodes * 100 / num_nodes, feature, + num_scenarios, 's' if num_scenarios > 1 else '')) + " +338,https://:@github.com/jirifilip/pyARC.git,e18a6c280f30bc753192bfa83f311ce36915aca4,"@@ -42,7 +42,7 @@ class TestClassAssociationRule(unittest.TestCase): + sorted_cars = sorted([car1, car2, car3, car4], reverse=True) + + assert car1 < car2 +- assert car2 < car3 ++ assert car2 > car3 + assert car3 < car2 + assert car4 > car3 + assert car1.antecedent <= transaction1 +",cba/test/test_class_association_rule.py,"ReplaceText(target='>' @(45,20)->(45,21))","class TestClassAssociationRule(unittest.TestCase): + sorted_cars = sorted([car1, car2, car3, car4], reverse=True) + + assert car1 < car2 + assert car2 < car3 + assert car3 < car2 + assert car4 > car3 + assert car1.antecedent <= transaction1","class TestClassAssociationRule(unittest.TestCase): + sorted_cars = sorted([car1, car2, car3, car4], reverse=True) + + assert car1 < car2 + assert car2 > car3 + assert car3 < car2 + assert car4 > car3 + assert car1.antecedent <= transaction1" +339,https://:@github.com/oblalex/verboselib.git,5ec91a09ae9f0674513f4953111009b93eaad74a,"@@ -123,4 +123,4 @@ class VerboselibTranslationTestCase(unittest.TestCase): + + t1.merge(t2) + self.assertEqual(t1.ugettext(""Hello""), ""Вітаю"") +- self.assertEqual(t2.ugettext(""Good bye""), ""До зустрічі"") ++ self.assertEqual(t1.ugettext(""Good bye""), ""До зустрічі"") +",tests/test_package.py,"ReplaceText(target='t1' @(126,25)->(126,27))","class VerboselibTranslationTestCase(unittest.TestCase): + + t1.merge(t2) + self.assertEqual(t1.ugettext(""Hello""), ""Вітаю"") + self.assertEqual(t2.ugettext(""Good bye""), ""До зустрічі"")","class VerboselibTranslationTestCase(unittest.TestCase): + + t1.merge(t2) + self.assertEqual(t1.ugettext(""Hello""), ""Вітаю"") + self.assertEqual(t1.ugettext(""Good bye""), ""До зустрічі"")" +340,https://:@github.com/lexndru/hap.git,5ef18f88572400983578d8723663562329066779,"@@ -87,7 +87,7 @@ class Cache(object): + tuple: Boolean for success read and string for size or error. + """""" + +- if len(cache) == 0: ++ if len(cache_path) == 0: + return False, ""missing cache path"" + if len(cache) == 0: + return False, ""missing cache data"" +",hap/cache.py,"ReplaceText(target='cache_path' @(90,15)->(90,20))","class Cache(object): + tuple: Boolean for success read and string for size or error. + """""" + + if len(cache) == 0: + return False, ""missing cache path"" + if len(cache) == 0: + return False, ""missing cache data""","class Cache(object): + tuple: Boolean for success read and string for size or error. + """""" + + if len(cache_path) == 0: + return False, ""missing cache path"" + if len(cache) == 0: + return False, ""missing cache data""" +341,https://:@github.com/littlezz/island-backup.git,fed75aebccfa31e418e351492618a2d50c15b9cb,"@@ -103,7 +103,7 @@ class ImageManager: + print('this is {} in busying'.format(len(self.busying))) + urls = [] + for i, url in enumerate(self.busying): +- if i > 3: ++ if i >= 3: + break + urls.append(url) + +",main.py,"ReplaceText(target='>=' @(106,17)->(106,18))","class ImageManager: + print('this is {} in busying'.format(len(self.busying))) + urls = [] + for i, url in enumerate(self.busying): + if i > 3: + break + urls.append(url) + ","class ImageManager: + print('this is {} in busying'.format(len(self.busying))) + urls = [] + for i, url in enumerate(self.busying): + if i >= 3: + break + urls.append(url) + " +342,https://:@github.com/parrt/dtreeviz.git,aa5b4811af5c5a5c9620705fc44ffd9e48377664,"@@ -1121,7 +1121,7 @@ def draw_legend(shadow_tree, target_name, filename, colors=None): + boxes = [] + for i, c in enumerate(class_values): + box = patches.Rectangle((0, 0), 20, 10, linewidth=.4, edgecolor=colors['rect_edge'], +- facecolor=color_map[c], label=class_names[c]) ++ facecolor=color_map[c], label=class_names[i]) + boxes.append(box) + + fig, ax = plt.subplots(1, 1, figsize=(1,1)) +",dtreeviz/trees.py,"ReplaceText(target='i' @(1124,74)->(1124,75))","def draw_legend(shadow_tree, target_name, filename, colors=None): + boxes = [] + for i, c in enumerate(class_values): + box = patches.Rectangle((0, 0), 20, 10, linewidth=.4, edgecolor=colors['rect_edge'], + facecolor=color_map[c], label=class_names[c]) + boxes.append(box) + + fig, ax = plt.subplots(1, 1, figsize=(1,1))","def draw_legend(shadow_tree, target_name, filename, colors=None): + boxes = [] + for i, c in enumerate(class_values): + box = patches.Rectangle((0, 0), 20, 10, linewidth=.4, edgecolor=colors['rect_edge'], + facecolor=color_map[c], label=class_names[i]) + boxes.append(box) + + fig, ax = plt.subplots(1, 1, figsize=(1,1))" +343,https://:@github.com/parrt/dtreeviz.git,01cc13f495decbd6f8f716d7be586e02864f3434,"@@ -809,7 +809,7 @@ def dtreeviz(tree_model: (tree.DecisionTreeRegressor, tree.DecisionTreeClassifie + lcolor = colors['highlight'] + lpw = ""1.2"" + if node.right.id in highlight_path: +- lcolor = colors['highlight'] ++ rcolor = colors['highlight'] + rpw = ""1.2"" + edges.append( f'{nname} -> {left_node_name} [penwidth={lpw} color=""{lcolor}"" label=<{llabel}>]' ) + edges.append( f'{nname} -> {right_node_name} [penwidth={rpw} color=""{rcolor}"" label=<{rlabel}>]' ) +",dtreeviz/trees.py,"ReplaceText(target='rcolor' @(812,12)->(812,18))","def dtreeviz(tree_model: (tree.DecisionTreeRegressor, tree.DecisionTreeClassifie + lcolor = colors['highlight'] + lpw = ""1.2"" + if node.right.id in highlight_path: + lcolor = colors['highlight'] + rpw = ""1.2"" + edges.append( f'{nname} -> {left_node_name} [penwidth={lpw} color=""{lcolor}"" label=<{llabel}>]' ) + edges.append( f'{nname} -> {right_node_name} [penwidth={rpw} color=""{rcolor}"" label=<{rlabel}>]' )","def dtreeviz(tree_model: (tree.DecisionTreeRegressor, tree.DecisionTreeClassifie + lcolor = colors['highlight'] + lpw = ""1.2"" + if node.right.id in highlight_path: + rcolor = colors['highlight'] + rpw = ""1.2"" + edges.append( f'{nname} -> {left_node_name} [penwidth={lpw} color=""{lcolor}"" label=<{llabel}>]' ) + edges.append( f'{nname} -> {right_node_name} [penwidth={rpw} color=""{rcolor}"" label=<{rlabel}>]' )" +344,https://:@github.com/4teamwork/ftw.workspace.git,b12970101f5ca213e4604c2c3cf2f767f911b71e,"@@ -75,7 +75,7 @@ class AssignableUsersVocabulary(object): + if user not in groups: + groups.add(user) + +- if getattr(aq_base(workspace), '__ac_local_roles_block__', None): ++ if getattr(aq_base(context), '__ac_local_roles_block__', None): + cont = False + else: + context = aq_parent(context) +",ftw/workspace/vocabularies.py,"ReplaceText(target='context' @(78,31)->(78,40))","class AssignableUsersVocabulary(object): + if user not in groups: + groups.add(user) + + if getattr(aq_base(workspace), '__ac_local_roles_block__', None): + cont = False + else: + context = aq_parent(context)","class AssignableUsersVocabulary(object): + if user not in groups: + groups.add(user) + + if getattr(aq_base(context), '__ac_local_roles_block__', None): + cont = False + else: + context = aq_parent(context)" +345,https://:@github.com/regulusweb/wagtail-extensions.git,ea388649a0c6dc6fbc1ce018d767c8b583486523,"@@ -74,7 +74,7 @@ class ContactDetailsSetting(BaseSetting): + today = date.today() + cache_key = self.get_opening_today_cache_key(today) + times = cache.get(cache_key) +- if times is not None: ++ if times is None: + opening_times = self.primary_opening_times + if opening_times: + specific_times = utils.first_true(opening_times, lambda x: x.get('date') == today) +",wagtail_extensions/models.py,"ReplaceText(target=' is ' @(77,16)->(77,24))","class ContactDetailsSetting(BaseSetting): + today = date.today() + cache_key = self.get_opening_today_cache_key(today) + times = cache.get(cache_key) + if times is not None: + opening_times = self.primary_opening_times + if opening_times: + specific_times = utils.first_true(opening_times, lambda x: x.get('date') == today)","class ContactDetailsSetting(BaseSetting): + today = date.today() + cache_key = self.get_opening_today_cache_key(today) + times = cache.get(cache_key) + if times is None: + opening_times = self.primary_opening_times + if opening_times: + specific_times = utils.first_true(opening_times, lambda x: x.get('date') == today)" +346,https://:@github.com/tjcsl/cslbot.git,eaa1165f7ceb19b8e98828fea2894d275ffe5743,"@@ -394,7 +394,7 @@ class MyHandler(): + elif cmd[0] == ""get"": + if cmd[1] == ""disabled"" and cmd[2] == ""modules"": + send(str(self.disabled_mods)) +- if cmd[2] == ""enabled"" and cmd[2] == ""modules"": ++ if cmd[1] == ""enabled"" and cmd[2] == ""modules"": + send(str([i for i in self.modules if i not in self.disabled_mods])) + + def handle_msg(self, msgtype, c, e): +",handler.py,"ReplaceText(target='1' @(397,19)->(397,20))","class MyHandler(): + elif cmd[0] == ""get"": + if cmd[1] == ""disabled"" and cmd[2] == ""modules"": + send(str(self.disabled_mods)) + if cmd[2] == ""enabled"" and cmd[2] == ""modules"": + send(str([i for i in self.modules if i not in self.disabled_mods])) + + def handle_msg(self, msgtype, c, e):","class MyHandler(): + elif cmd[0] == ""get"": + if cmd[1] == ""disabled"" and cmd[2] == ""modules"": + send(str(self.disabled_mods)) + if cmd[1] == ""enabled"" and cmd[2] == ""modules"": + send(str([i for i in self.modules if i not in self.disabled_mods])) + + def handle_msg(self, msgtype, c, e):" +347,https://:@github.com/tjcsl/cslbot.git,6c801ad70e0a9d1a963b9b560f9c654616e64a3b,"@@ -260,7 +260,7 @@ class BotHandler(): + if self.log_to_ctrlchan: + # somewhat hacky fix + if target != CTRLCHAN: +- self.connection.send_raw((""PRIVMSG %s :(%s) <%s> %s"" % (CTRLCHAN, target, nick, log))\ ++ self.connection.send_raw((""PRIVMSG %s :(%s) <%s> %s"" % (CTRLCHAN, target, nick, msg))\ + .replace(""\n"", """").replace(""\r"", """")) + self.logs[target].append([day, log]) + self.logfiles[target].write(log) +",handler.py,"ReplaceText(target='msg' @(263,96)->(263,99))","class BotHandler(): + if self.log_to_ctrlchan: + # somewhat hacky fix + if target != CTRLCHAN: + self.connection.send_raw((""PRIVMSG %s :(%s) <%s> %s"" % (CTRLCHAN, target, nick, log))\ + .replace(""\n"", """").replace(""\r"", """")) + self.logs[target].append([day, log]) + self.logfiles[target].write(log)","class BotHandler(): + if self.log_to_ctrlchan: + # somewhat hacky fix + if target != CTRLCHAN: + self.connection.send_raw((""PRIVMSG %s :(%s) <%s> %s"" % (CTRLCHAN, target, nick, msg))\ + .replace(""\n"", """").replace(""\r"", """")) + self.logs[target].append([day, log]) + self.logfiles[target].write(log)" +348,https://:@github.com/tjcsl/cslbot.git,b5c181736ff1adc6b665d2d4a80bd6141aaa549e,"@@ -331,7 +331,7 @@ class BotHandler(): + return + if cmdargs[0] != '#': + cmdargs = '#' + cmdargs +- if cmdargs in self.channels and len(cmd) > 0 and cmd[1] != ""force"": ++ if cmdargs in self.channels or len(cmd) > 0 and cmd[1] != ""force"": + send(""%s is already a member of %s"" % (NICK, cmdargs)) + return + c.join(cmd[0]) +",handler.py,"ReplaceText(target='or' @(334,36)->(334,39))","class BotHandler(): + return + if cmdargs[0] != '#': + cmdargs = '#' + cmdargs + if cmdargs in self.channels and len(cmd) > 0 and cmd[1] != ""force"": + send(""%s is already a member of %s"" % (NICK, cmdargs)) + return + c.join(cmd[0])","class BotHandler(): + return + if cmdargs[0] != '#': + cmdargs = '#' + cmdargs + if cmdargs in self.channels or len(cmd) > 0 and cmd[1] != ""force"": + send(""%s is already a member of %s"" % (NICK, cmdargs)) + return + c.join(cmd[0])" +349,https://:@github.com/tjcsl/cslbot.git,20dab902837bb40599cb34afe152dfc780f2854e,"@@ -315,7 +315,7 @@ class BotHandler(): + # -pub + # -private + #log to sqlite logger +- self.logger.log(target, nick, isop, msg, msgtype) ++ self.logger.log(nick, target, isop, msg, msgtype) + + if self.log_to_ctrlchan: + ctrlchan = self.config['core']['ctrlchan'] +",handler.py,"ArgSwap(idxs=0<->1 @(318,8)->(318,23))","class BotHandler(): + # -pub + # -private + #log to sqlite logger + self.logger.log(target, nick, isop, msg, msgtype) + + if self.log_to_ctrlchan: + ctrlchan = self.config['core']['ctrlchan']","class BotHandler(): + # -pub + # -private + #log to sqlite logger + self.logger.log(nick, target, isop, msg, msgtype) + + if self.log_to_ctrlchan: + ctrlchan = self.config['core']['ctrlchan']" +350,https://:@github.com/tjcsl/cslbot.git,7b544654a37dd0ca467157c76aaa51bb6e9a73e8,"@@ -442,7 +442,7 @@ class BotHandler(): + if cmd_obj.is_limited() and self.abusecheck(send, nick, cmd_obj.limit, msgtype, cmd[len(cmdchar):]): + return + args = self.do_args(cmd_obj.args, send, nick, target, e.source, c, cmd_name, msgtype) +- cmd_obj.run(send, cmdargs, args, cmd_name, target, nick, self.db.get()) ++ cmd_obj.run(send, cmdargs, args, cmd_name, nick, target, self.db.get()) + # special commands + if cmd.startswith(cmdchar): + if cmd[len(cmdchar):] == 'reload': +",handler.py,"ArgSwap(idxs=4<->5 @(445,16)->(445,27))","class BotHandler(): + if cmd_obj.is_limited() and self.abusecheck(send, nick, cmd_obj.limit, msgtype, cmd[len(cmdchar):]): + return + args = self.do_args(cmd_obj.args, send, nick, target, e.source, c, cmd_name, msgtype) + cmd_obj.run(send, cmdargs, args, cmd_name, target, nick, self.db.get()) + # special commands + if cmd.startswith(cmdchar): + if cmd[len(cmdchar):] == 'reload':","class BotHandler(): + if cmd_obj.is_limited() and self.abusecheck(send, nick, cmd_obj.limit, msgtype, cmd[len(cmdchar):]): + return + args = self.do_args(cmd_obj.args, send, nick, target, e.source, c, cmd_name, msgtype) + cmd_obj.run(send, cmdargs, args, cmd_name, nick, target, self.db.get()) + # special commands + if cmd.startswith(cmdchar): + if cmd[len(cmdchar):] == 'reload':" +351,https://:@github.com/tjcsl/cslbot.git,8d5e5ff45a32d6849e0daf38414e818b4d8e4a96,"@@ -38,7 +38,7 @@ def cmd(send, msg, args): + name = 'passthrough' + else: + name = name[4:] +- names.append(i) ++ names.append(name) + send(""Current filter(s): %s"" % "", "".join(names)) + elif msg == 'list': + send(""Available filters are %s"" % "", "".join(output_filters.keys())) +",commands/filter.py,"ReplaceText(target='name' @(41,25)->(41,26))","def cmd(send, msg, args): + name = 'passthrough' + else: + name = name[4:] + names.append(i) + send(""Current filter(s): %s"" % "", "".join(names)) + elif msg == 'list': + send(""Available filters are %s"" % "", "".join(output_filters.keys()))","def cmd(send, msg, args): + name = 'passthrough' + else: + name = name[4:] + names.append(name) + send(""Current filter(s): %s"" % "", "".join(names)) + elif msg == 'list': + send(""Available filters are %s"" % "", "".join(output_filters.keys()))" +352,https://:@github.com/tjcsl/cslbot.git,0e38c8226ab070d321cbed3ade449c2833d0f36e,"@@ -154,7 +154,7 @@ def handle_accept(handler, cmd): + return ""Missing argument."" + if not cmd[1].isdigit(): + return ""Not A Valid Positive Integer"" +- elif not handler.issues or len(handler.issues) < int(cmd[1]): ++ elif not handler.issues or len(handler.issues) <= int(cmd[1]): + return ""Not a valid issue"" + else: + num = int(cmd[1]) +",helpers/control.py,"ReplaceText(target='<=' @(157,51)->(157,52))","def handle_accept(handler, cmd): + return ""Missing argument."" + if not cmd[1].isdigit(): + return ""Not A Valid Positive Integer"" + elif not handler.issues or len(handler.issues) < int(cmd[1]): + return ""Not a valid issue"" + else: + num = int(cmd[1])","def handle_accept(handler, cmd): + return ""Missing argument."" + if not cmd[1].isdigit(): + return ""Not A Valid Positive Integer"" + elif not handler.issues or len(handler.issues) <= int(cmd[1]): + return ""Not a valid issue"" + else: + num = int(cmd[1])" +353,https://:@github.com/tjcsl/cslbot.git,1694edfac9e6ee93ce648c78be52d19360b7e364,"@@ -54,7 +54,7 @@ def do_add_quote(cmd, conn, isadmin, send, args): + cursor = conn.execute('INSERT INTO quotes(quote, nick, submitter) VALUES(?,?,?)', (quote[0], quote[1], args['nick'])) + qid = cursor.lastrowid + if isadmin: +- cursor.execute('UPDATE quotes SET approved=1 WHERE id=?', (qid,)) ++ conn.execute('UPDATE quotes SET approved=1 WHERE id=?', (qid,)) + send(""Added quote %d!"" % qid) + else: + send(""Quote submitted for approval."", target=args['nick']) +",commands/quote.py,"ReplaceText(target='conn' @(57,8)->(57,14))","def do_add_quote(cmd, conn, isadmin, send, args): + cursor = conn.execute('INSERT INTO quotes(quote, nick, submitter) VALUES(?,?,?)', (quote[0], quote[1], args['nick'])) + qid = cursor.lastrowid + if isadmin: + cursor.execute('UPDATE quotes SET approved=1 WHERE id=?', (qid,)) + send(""Added quote %d!"" % qid) + else: + send(""Quote submitted for approval."", target=args['nick'])","def do_add_quote(cmd, conn, isadmin, send, args): + cursor = conn.execute('INSERT INTO quotes(quote, nick, submitter) VALUES(?,?,?)', (quote[0], quote[1], args['nick'])) + qid = cursor.lastrowid + if isadmin: + conn.execute('UPDATE quotes SET approved=1 WHERE id=?', (qid,)) + send(""Added quote %d!"" % qid) + else: + send(""Quote submitted for approval."", target=args['nick'])" +354,https://:@github.com/tjcsl/cslbot.git,aa3079c68c6bfed92fe95cf92dbed87d1f3c91d2,"@@ -33,7 +33,7 @@ def handle_traceback(ex, c, target, config, source=""the bot""): + errtarget = ctrlchan if prettyerrors else target + if prettyerrors: + if name == 'CSLException': +- c.privmsg(target, ""%s -- %s"" % (name, output)) ++ c.privmsg(target, ""%s -- %s"" % (source, output)) + else: + c.privmsg(target, ""An %s has occured in %s. See the control channel for details."" % (name, source)) + c.privmsg(errtarget, '%s -- %s in %s on line %s: %s' % (source, name, trace[0], trace[1], output)) +",helpers/traceback.py,"ReplaceText(target='source' @(36,44)->(36,48))","def handle_traceback(ex, c, target, config, source=""the bot""): + errtarget = ctrlchan if prettyerrors else target + if prettyerrors: + if name == 'CSLException': + c.privmsg(target, ""%s -- %s"" % (name, output)) + else: + c.privmsg(target, ""An %s has occured in %s. See the control channel for details."" % (name, source)) + c.privmsg(errtarget, '%s -- %s in %s on line %s: %s' % (source, name, trace[0], trace[1], output))","def handle_traceback(ex, c, target, config, source=""the bot""): + errtarget = ctrlchan if prettyerrors else target + if prettyerrors: + if name == 'CSLException': + c.privmsg(target, ""%s -- %s"" % (source, output)) + else: + c.privmsg(target, ""An %s has occured in %s. See the control channel for details."" % (name, source)) + c.privmsg(errtarget, '%s -- %s in %s on line %s: %s' % (source, name, trace[0], trace[1], output))" +355,https://:@github.com/tjcsl/cslbot.git,8bd3d1038ba16c4c097b51c1bdce1a54a5fb43af,"@@ -38,7 +38,7 @@ def get_definition(msg): + elif not index.isdigit() or int(index) >= len(data) or int(index) == 0: + output = ""Invalid Index"" + else: +- output = data[int(index)+1]['definition'] ++ output = data[int(index)-1]['definition'] + output = output.splitlines() + return ' '.join(output) + +",commands/urban.py,"ReplaceText(target='-' @(41,32)->(41,33))","def get_definition(msg): + elif not index.isdigit() or int(index) >= len(data) or int(index) == 0: + output = ""Invalid Index"" + else: + output = data[int(index)+1]['definition'] + output = output.splitlines() + return ' '.join(output) + ","def get_definition(msg): + elif not index.isdigit() or int(index) >= len(data) or int(index) == 0: + output = ""Invalid Index"" + else: + output = data[int(index)-1]['definition'] + output = output.splitlines() + return ' '.join(output) + " +356,https://:@github.com/tjcsl/cslbot.git,a72f1944cc07392f2f1c023448bfc0eceb6cd8cd,"@@ -40,7 +40,7 @@ def get_definition(msg): + output = ""UrbanDictionary doesn't have an answer for you."" + elif index is None: + output = data[0]['definition'] +- elif not index.isdigit() or int(index) >= len(data) or int(index) == 0: ++ elif not index.isdigit() or int(index) > len(data) or int(index) == 0: + output = ""Invalid Index"" + else: + output = data[int(index)-1]['definition'] +",commands/urban.py,"ReplaceText(target='>' @(43,43)->(43,45))","def get_definition(msg): + output = ""UrbanDictionary doesn't have an answer for you."" + elif index is None: + output = data[0]['definition'] + elif not index.isdigit() or int(index) >= len(data) or int(index) == 0: + output = ""Invalid Index"" + else: + output = data[int(index)-1]['definition']","def get_definition(msg): + output = ""UrbanDictionary doesn't have an answer for you."" + elif index is None: + output = data[0]['definition'] + elif not index.isdigit() or int(index) > len(data) or int(index) == 0: + output = ""Invalid Index"" + else: + output = data[int(index)-1]['definition']" +357,https://:@github.com/tjcsl/cslbot.git,ffc2cedcd394bf7076f4e8882d7f8773fc2a529b,"@@ -24,7 +24,7 @@ from helpers.command import Command + def cmd(send, msg, args): + """"""Finds a random quote from tjbash.org given search criteria + """""" +- if len(msg) < 0: ++ if len(msg) == 0: + url = 'http://tjbash.org/random1' + else: + url = 'http://tjbash.org/search?query=' +",commands/tjbash.py,"ReplaceText(target='==' @(27,16)->(27,17))","from helpers.command import Command + def cmd(send, msg, args): + """"""Finds a random quote from tjbash.org given search criteria + """""" + if len(msg) < 0: + url = 'http://tjbash.org/random1' + else: + url = 'http://tjbash.org/search?query='","from helpers.command import Command + def cmd(send, msg, args): + """"""Finds a random quote from tjbash.org given search criteria + """""" + if len(msg) == 0: + url = 'http://tjbash.org/random1' + else: + url = 'http://tjbash.org/search?query='" +358,https://:@github.com/tjcsl/cslbot.git,0a9fcb6ce10d7d7dca87496e3abb02faa1c35794,"@@ -87,7 +87,7 @@ def build_markov(cursor, speaker, cmdchar, ctrlchan): + def get_markov(cursor, speaker, handler, cmdchar, ctrlchan): + markov = cursor.query(Babble).filter(Babble.nick == speaker).first() + if not markov: +- update_markov(cursor, speaker, cmdchar, ctrlchan) ++ update_markov(handler, speaker, cmdchar, ctrlchan) + markov = cursor.query(Babble).filter(Babble.nick == speaker).first() + elif time.time() - markov.time > CACHE_LIFE: + handler.workers.defer(0, False, update_markov, handler, speaker, cmdchar, ctrlchan) +",commands/babble.py,"ReplaceText(target='handler' @(90,22)->(90,28))","def build_markov(cursor, speaker, cmdchar, ctrlchan): + def get_markov(cursor, speaker, handler, cmdchar, ctrlchan): + markov = cursor.query(Babble).filter(Babble.nick == speaker).first() + if not markov: + update_markov(cursor, speaker, cmdchar, ctrlchan) + markov = cursor.query(Babble).filter(Babble.nick == speaker).first() + elif time.time() - markov.time > CACHE_LIFE: + handler.workers.defer(0, False, update_markov, handler, speaker, cmdchar, ctrlchan)","def build_markov(cursor, speaker, cmdchar, ctrlchan): + def get_markov(cursor, speaker, handler, cmdchar, ctrlchan): + markov = cursor.query(Babble).filter(Babble.nick == speaker).first() + if not markov: + update_markov(handler, speaker, cmdchar, ctrlchan) + markov = cursor.query(Babble).filter(Babble.nick == speaker).first() + elif time.time() - markov.time > CACHE_LIFE: + handler.workers.defer(0, False, update_markov, handler, speaker, cmdchar, ctrlchan)" +359,https://:@github.com/ThibHlln/smartpy.git,6e02ac69689bff3802de8dcc5b15237996379aae,"@@ -26,7 +26,7 @@ def nash_sutcliffe(evaluation, simulation): + + + def groundwater_constraint(evaluation, simulation): +- if (evaluation[0] - 0.1 <= simulation[0]) or (simulation[0] <= evaluation[0] + 0.1): ++ if (evaluation[0] - 0.1 <= simulation[0]) and (simulation[0] <= evaluation[0] + 0.1): + return 1.0 + else: + return 0.0 +",SMARTobjective.py,"ReplaceText(target='and' @(29,46)->(29,48))","def nash_sutcliffe(evaluation, simulation): + + + def groundwater_constraint(evaluation, simulation): + if (evaluation[0] - 0.1 <= simulation[0]) or (simulation[0] <= evaluation[0] + 0.1): + return 1.0 + else: + return 0.0","def nash_sutcliffe(evaluation, simulation): + + + def groundwater_constraint(evaluation, simulation): + if (evaluation[0] - 0.1 <= simulation[0]) and (simulation[0] <= evaluation[0] + 0.1): + return 1.0 + else: + return 0.0" +360,https://:@github.com/satellogic/orbit-predictor.git,672c75a9b64b6735c08bd5270855588e3d514065,"@@ -30,7 +30,7 @@ from orbit_predictor.predictors.base import CartesianPredictor, logger + class TLEPredictor(CartesianPredictor): + + def __init__(self, sate_id, source): +- super(TLEPredictor, self).__init__(source, sate_id) ++ super(TLEPredictor, self).__init__(sate_id, source) + self._iterations = 0 + + def _propagate_eci(self, when_utc=None): +",orbit_predictor/predictors/tle.py,"ArgSwap(idxs=0<->1 @(33,8)->(33,42))","from orbit_predictor.predictors.base import CartesianPredictor, logger + class TLEPredictor(CartesianPredictor): + + def __init__(self, sate_id, source): + super(TLEPredictor, self).__init__(source, sate_id) + self._iterations = 0 + + def _propagate_eci(self, when_utc=None):","from orbit_predictor.predictors.base import CartesianPredictor, logger + class TLEPredictor(CartesianPredictor): + + def __init__(self, sate_id, source): + super(TLEPredictor, self).__init__(sate_id, source) + self._iterations = 0 + + def _propagate_eci(self, when_utc=None):" +361,https://:@github.com/dipu-bd/lightnovel-crawler.git,773695654f273c9f7191817c4dd64e8322325809,"@@ -39,7 +39,7 @@ class LightNovelOnline(Crawler): + logger.debug('Visiting %s', self.novel_url) + soup = self.get_soup(self.novel_url) + +- self.novel_id = urlparse(self.novel_url).path.split('/')[1] ++ self.novel_id = urlparse(self.novel_url).path.split('/')[-1] + logger.info(""Novel Id: %s"", self.novel_id) + + self.novel_title = soup.select_one( +",lncrawl/sources/lightnovelonline.py,"ReplaceText(target='-1' @(42,65)->(42,66))","class LightNovelOnline(Crawler): + logger.debug('Visiting %s', self.novel_url) + soup = self.get_soup(self.novel_url) + + self.novel_id = urlparse(self.novel_url).path.split('/')[1] + logger.info(""Novel Id: %s"", self.novel_id) + + self.novel_title = soup.select_one(","class LightNovelOnline(Crawler): + logger.debug('Visiting %s', self.novel_url) + soup = self.get_soup(self.novel_url) + + self.novel_id = urlparse(self.novel_url).path.split('/')[-1] + logger.info(""Novel Id: %s"", self.novel_id) + + self.novel_title = soup.select_one(" +362,https://:@github.com/raphaelm/python-sepaxml.git,024a11dd1e26d08bbeb028a2a13dabcb509011ec,"@@ -54,7 +54,7 @@ def make_id(name): + 12 char rand hex string. + """""" + r = get_rand_string(12) +- if len(name) <= 22: ++ if len(name) > 22: + name = name[:22] + return name + ""-"" + r + +",sepadd/utils.py,"ReplaceText(target='>' @(57,17)->(57,19))","def make_id(name): + 12 char rand hex string. + """""" + r = get_rand_string(12) + if len(name) <= 22: + name = name[:22] + return name + ""-"" + r + ","def make_id(name): + 12 char rand hex string. + """""" + r = get_rand_string(12) + if len(name) > 22: + name = name[:22] + return name + ""-"" + r + " +363,https://:@github.com/raphaelm/python-sepaxml.git,98934ba5c863ffbc2bc770a34dd9ddea8edf2577,"@@ -70,7 +70,7 @@ def int_to_decimal_str(integer): + @return string The amount in currency with full stop decimal separator + """""" + int_string = str(integer) +- if len(int_string) < 2: ++ if len(int_string) <= 2: + return ""0."" + int_string.zfill(2) + else: + return int_string[:-2] + ""."" + int_string[-2:] +",sepaxml/utils.py,"ReplaceText(target='<=' @(73,23)->(73,24))","def int_to_decimal_str(integer): + @return string The amount in currency with full stop decimal separator + """""" + int_string = str(integer) + if len(int_string) < 2: + return ""0."" + int_string.zfill(2) + else: + return int_string[:-2] + ""."" + int_string[-2:]","def int_to_decimal_str(integer): + @return string The amount in currency with full stop decimal separator + """""" + int_string = str(integer) + if len(int_string) <= 2: + return ""0."" + int_string.zfill(2) + else: + return int_string[:-2] + ""."" + int_string[-2:]" +364,https://:@github.com/scikit-image/scikit-image.git,2585a323ac57004179b0ba643f953162650f39ee,"@@ -51,7 +51,7 @@ def peak_local_max(image, min_distance=10, threshold='deprecated', + threshold_rel = threshold + # find top corner candidates above a threshold + corner_threshold = max(np.max(image.ravel()) * threshold_rel, threshold_abs) +- image_t = (image >= corner_threshold) * 1 ++ image_t = (image > corner_threshold) * 1 + + # get coordinates of peaks + coordinates = np.transpose(image_t.nonzero()) +",skimage/feature/peak.py,"ReplaceText(target='>' @(54,21)->(54,23))","def peak_local_max(image, min_distance=10, threshold='deprecated', + threshold_rel = threshold + # find top corner candidates above a threshold + corner_threshold = max(np.max(image.ravel()) * threshold_rel, threshold_abs) + image_t = (image >= corner_threshold) * 1 + + # get coordinates of peaks + coordinates = np.transpose(image_t.nonzero())","def peak_local_max(image, min_distance=10, threshold='deprecated', + threshold_rel = threshold + # find top corner candidates above a threshold + corner_threshold = max(np.max(image.ravel()) * threshold_rel, threshold_abs) + image_t = (image > corner_threshold) * 1 + + # get coordinates of peaks + coordinates = np.transpose(image_t.nonzero())" +365,https://:@github.com/scikit-image/scikit-image.git,8084faf1f69c2c4ba79b6e85c7a2a06e1e7c77b8,"@@ -133,7 +133,7 @@ def reconstruction(seed, mask, method='dilation', selem=None, offset=None): + if offset == None: + if not all([d % 2 == 1 for d in selem.shape]): + ValueError(""Footprint dimensions must all be odd"") +- offset = np.array([d / 2 for d in selem.shape]) ++ offset = np.array([d // 2 for d in selem.shape]) + # Cross out the center of the selem + selem[[slice(d, d + 1) for d in offset]] = False + +",skimage/morphology/greyreconstruct.py,"ReplaceText(target='//' @(136,29)->(136,30))","def reconstruction(seed, mask, method='dilation', selem=None, offset=None): + if offset == None: + if not all([d % 2 == 1 for d in selem.shape]): + ValueError(""Footprint dimensions must all be odd"") + offset = np.array([d / 2 for d in selem.shape]) + # Cross out the center of the selem + selem[[slice(d, d + 1) for d in offset]] = False + ","def reconstruction(seed, mask, method='dilation', selem=None, offset=None): + if offset == None: + if not all([d % 2 == 1 for d in selem.shape]): + ValueError(""Footprint dimensions must all be odd"") + offset = np.array([d // 2 for d in selem.shape]) + # Cross out the center of the selem + selem[[slice(d, d + 1) for d in offset]] = False + " +366,https://:@github.com/scikit-image/scikit-image.git,d1629aec0f1a861106d54cb015b238e7fe542936,"@@ -28,7 +28,7 @@ def approximate_polygon(coords, tolerance): + ---------- + .. [1] http://en.wikipedia.org/wiki/Ramer-Douglas-Peucker_algorithm + """""" +- if tolerance == 0: ++ if tolerance <= 0: + return coords + + chain = np.zeros(coords.shape[0], 'bool') +",skimage/measure/_polygon.py,"ReplaceText(target='<=' @(31,17)->(31,19))","def approximate_polygon(coords, tolerance): + ---------- + .. [1] http://en.wikipedia.org/wiki/Ramer-Douglas-Peucker_algorithm + """""" + if tolerance == 0: + return coords + + chain = np.zeros(coords.shape[0], 'bool')","def approximate_polygon(coords, tolerance): + ---------- + .. [1] http://en.wikipedia.org/wiki/Ramer-Douglas-Peucker_algorithm + """""" + if tolerance <= 0: + return coords + + chain = np.zeros(coords.shape[0], 'bool')" +367,https://:@github.com/scikit-image/scikit-image.git,22f94d8707d3d9d2a36493403cbaeb61213dd68b,"@@ -163,7 +163,7 @@ def rotate(image, angle, resize=False, order=1, mode='constant', cval=0.): + tform = tform1 + tform2 + tform3 + + output_shape = None +- if not resize: ++ if resize: + # determine shape of output image + corners = np.array([[1, 1], [1, rows], [cols, rows], [cols, 1]]) + corners = tform(corners - 1) +",skimage/transform/_warps.py,"ReplaceText(target='' @(166,7)->(166,11))","def rotate(image, angle, resize=False, order=1, mode='constant', cval=0.): + tform = tform1 + tform2 + tform3 + + output_shape = None + if not resize: + # determine shape of output image + corners = np.array([[1, 1], [1, rows], [cols, rows], [cols, 1]]) + corners = tform(corners - 1)","def rotate(image, angle, resize=False, order=1, mode='constant', cval=0.): + tform = tform1 + tform2 + tform3 + + output_shape = None + if resize: + # determine shape of output image + corners = np.array([[1, 1], [1, rows], [cols, rows], [cols, 1]]) + corners = tform(corners - 1)" +368,https://:@github.com/scikit-image/scikit-image.git,794a4d7daebfdcb217fbf0a73b9d42e256ce45cd,"@@ -1085,7 +1085,7 @@ def _validate_lengths(narray, number_elements): + normshp = _normalize_shape(narray, number_elements) + for i in normshp: + chk = [1 if x is None else x for x in i] +- chk = [1 if x > 0 else -1 for x in chk] ++ chk = [1 if x >= 0 else -1 for x in chk] + if (chk[0] < 0) or (chk[1] < 0): + fmt = ""%s cannot contain negative values."" + raise ValueError(fmt % (number_elements,)) +",skimage/util/arraypad.py,"ReplaceText(target='>=' @(1088,22)->(1088,23))","def _validate_lengths(narray, number_elements): + normshp = _normalize_shape(narray, number_elements) + for i in normshp: + chk = [1 if x is None else x for x in i] + chk = [1 if x > 0 else -1 for x in chk] + if (chk[0] < 0) or (chk[1] < 0): + fmt = ""%s cannot contain negative values."" + raise ValueError(fmt % (number_elements,))","def _validate_lengths(narray, number_elements): + normshp = _normalize_shape(narray, number_elements) + for i in normshp: + chk = [1 if x is None else x for x in i] + chk = [1 if x >= 0 else -1 for x in chk] + if (chk[0] < 0) or (chk[1] < 0): + fmt = ""%s cannot contain negative values."" + raise ValueError(fmt % (number_elements,))" +369,https://:@github.com/scikit-image/scikit-image.git,5f46fd01be76ac8c7252ab35ba58609e81ad0ca0,"@@ -124,7 +124,7 @@ def _star_filter_kernel(m, n): + def _suppress_lines(feature_mask, image, sigma, line_threshold): + Axx, Axy, Ayy = _compute_auto_correlation(image, sigma) + feature_mask[(Axx + Ayy) * (Axx + Ayy) +- < line_threshold * (Axx * Ayy - Axy * Axy)] = 0 ++ > line_threshold * (Axx * Ayy - Axy * Axy)] = 0 + return feature_mask + + +",skimage/feature/censure.py,"ReplaceText(target='>' @(127,17)->(127,18))","def _star_filter_kernel(m, n): + def _suppress_lines(feature_mask, image, sigma, line_threshold): + Axx, Axy, Ayy = _compute_auto_correlation(image, sigma) + feature_mask[(Axx + Ayy) * (Axx + Ayy) + < line_threshold * (Axx * Ayy - Axy * Axy)] = 0 + return feature_mask + + ","def _star_filter_kernel(m, n): + def _suppress_lines(feature_mask, image, sigma, line_threshold): + Axx, Axy, Ayy = _compute_auto_correlation(image, sigma) + feature_mask[(Axx + Ayy) * (Axx + Ayy) + > line_threshold * (Axx * Ayy - Axy * Axy)] = 0 + return feature_mask + + " +370,https://:@github.com/scikit-image/scikit-image.git,05aeb7c7fe89a70fa18294d69c9e12dd58fa5c08,"@@ -159,7 +159,7 @@ def reconstruction(seed, mask, method='dilation', selem=None, offset=None): + # Create a list of strides across the array to get the neighbors within + # a flattened array + value_stride = np.array(images.strides[1:]) / images.dtype.itemsize +- image_stride = images.strides[0] / images.dtype.itemsize ++ image_stride = images.strides[0] // images.dtype.itemsize + selem_mgrid = np.mgrid[[slice(-o, d - o) + for d, o in zip(selem.shape, offset)]] + selem_offsets = selem_mgrid[:, selem].transpose() +",skimage/morphology/greyreconstruct.py,"ReplaceText(target='//' @(162,37)->(162,38))","def reconstruction(seed, mask, method='dilation', selem=None, offset=None): + # Create a list of strides across the array to get the neighbors within + # a flattened array + value_stride = np.array(images.strides[1:]) / images.dtype.itemsize + image_stride = images.strides[0] / images.dtype.itemsize + selem_mgrid = np.mgrid[[slice(-o, d - o) + for d, o in zip(selem.shape, offset)]] + selem_offsets = selem_mgrid[:, selem].transpose()","def reconstruction(seed, mask, method='dilation', selem=None, offset=None): + # Create a list of strides across the array to get the neighbors within + # a flattened array + value_stride = np.array(images.strides[1:]) / images.dtype.itemsize + image_stride = images.strides[0] // images.dtype.itemsize + selem_mgrid = np.mgrid[[slice(-o, d - o) + for d, o in zip(selem.shape, offset)]] + selem_offsets = selem_mgrid[:, selem].transpose()" +371,https://:@github.com/scikit-image/scikit-image.git,05fbc3fbfcc00157841c18b15b171d6477bfb5da,"@@ -119,7 +119,7 @@ def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=None, + spacing = np.array(spacing, np.double) + if not isinstance(sigma, coll.Iterable): + sigma = np.array([sigma, sigma, sigma], np.double) +- elif isinstance(spacing, (list, tuple)): ++ elif isinstance(sigma, (list, tuple)): + sigma = np.array(sigma, np.double) + if (sigma > 0).any(): + sigma /= spacing.astype(np.double) +",skimage/segmentation/slic_superpixels.py,"ReplaceText(target='sigma' @(122,20)->(122,27))","def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=None, + spacing = np.array(spacing, np.double) + if not isinstance(sigma, coll.Iterable): + sigma = np.array([sigma, sigma, sigma], np.double) + elif isinstance(spacing, (list, tuple)): + sigma = np.array(sigma, np.double) + if (sigma > 0).any(): + sigma /= spacing.astype(np.double)","def slic(image, n_segments=100, compactness=10., max_iter=10, sigma=None, + spacing = np.array(spacing, np.double) + if not isinstance(sigma, coll.Iterable): + sigma = np.array([sigma, sigma, sigma], np.double) + elif isinstance(sigma, (list, tuple)): + sigma = np.array(sigma, np.double) + if (sigma > 0).any(): + sigma /= spacing.astype(np.double)" +372,https://:@github.com/scikit-image/scikit-image.git,1ca0eef825188ac5e9fc84b232b4783c166933ac,"@@ -94,7 +94,7 @@ def view_as_blocks(arr_in, block_shape): + + arr_in = np.ascontiguousarray(arr_in) + +- new_shape = tuple(arr_shape / block_shape) + tuple(block_shape) ++ new_shape = tuple(arr_shape // block_shape) + tuple(block_shape) + new_strides = tuple(arr_in.strides * block_shape) + arr_in.strides + + arr_out = as_strided(arr_in, shape=new_shape, strides=new_strides) +",skimage/util/shape.py,"ReplaceText(target='//' @(97,32)->(97,33))","def view_as_blocks(arr_in, block_shape): + + arr_in = np.ascontiguousarray(arr_in) + + new_shape = tuple(arr_shape / block_shape) + tuple(block_shape) + new_strides = tuple(arr_in.strides * block_shape) + arr_in.strides + + arr_out = as_strided(arr_in, shape=new_shape, strides=new_strides)","def view_as_blocks(arr_in, block_shape): + + arr_in = np.ascontiguousarray(arr_in) + + new_shape = tuple(arr_shape // block_shape) + tuple(block_shape) + new_strides = tuple(arr_in.strides * block_shape) + arr_in.strides + + arr_out = as_strided(arr_in, shape=new_shape, strides=new_strides)" +373,https://:@github.com/scikit-image/scikit-image.git,a38b1c12579214cf77785e9c85f30202b2048c4f,"@@ -136,7 +136,7 @@ def _clahe(image, ntiles_x, ntiles_y, clip_limit, nbins=128): + image = pad(image, ((0, h_pad), (0, w_pad)), mode='reflect') + h_inner, w_inner = image.shape + +- bin_size = 1 + NR_OF_GREY / nbins ++ bin_size = 1 + NR_OF_GREY // nbins + lut = np.arange(NR_OF_GREY) + lut //= bin_size + img_blocks = view_as_blocks(image, (height, width)) +",skimage/exposure/_adapthist.py,"ReplaceText(target='//' @(139,30)->(139,31))","def _clahe(image, ntiles_x, ntiles_y, clip_limit, nbins=128): + image = pad(image, ((0, h_pad), (0, w_pad)), mode='reflect') + h_inner, w_inner = image.shape + + bin_size = 1 + NR_OF_GREY / nbins + lut = np.arange(NR_OF_GREY) + lut //= bin_size + img_blocks = view_as_blocks(image, (height, width))","def _clahe(image, ntiles_x, ntiles_y, clip_limit, nbins=128): + image = pad(image, ((0, h_pad), (0, w_pad)), mode='reflect') + h_inner, w_inner = image.shape + + bin_size = 1 + NR_OF_GREY // nbins + lut = np.arange(NR_OF_GREY) + lut //= bin_size + img_blocks = view_as_blocks(image, (height, width))" +374,https://:@github.com/scikit-image/scikit-image.git,9a192bf1cb899632253619385ad9814dbd61f63a,"@@ -16,7 +16,7 @@ from skimage import graph, data, io, segmentation, color + img = data.coffee() + labels = segmentation.slic(img, compactness=30, n_segments=400) + g = graph.rag_mean_color(img, labels) +-labels2 = graph.merge_hierarchical(g, labels, 40) ++labels2 = graph.merge_hierarchical(labels, g, 40) + g2 = graph.rag_mean_color(img, labels2) + + out = color.label2rgb(labels2, img, kind='avg') +",doc/examples/plot_rag_merge.py,"ArgSwap(idxs=0<->1 @(19,10)->(19,34))","from skimage import graph, data, io, segmentation, color + img = data.coffee() + labels = segmentation.slic(img, compactness=30, n_segments=400) + g = graph.rag_mean_color(img, labels) + labels2 = graph.merge_hierarchical(g, labels, 40) + g2 = graph.rag_mean_color(img, labels2) + + out = color.label2rgb(labels2, img, kind='avg')","from skimage import graph, data, io, segmentation, color + img = data.coffee() + labels = segmentation.slic(img, compactness=30, n_segments=400) + g = graph.rag_mean_color(img, labels) + labels2 = graph.merge_hierarchical(labels, g, 40) + g2 = graph.rag_mean_color(img, labels2) + + out = color.label2rgb(labels2, img, kind='avg')" +375,https://:@github.com/scikit-image/scikit-image.git,4bdde3d2aef2dd184e0b907983a15167326aec55,"@@ -254,7 +254,7 @@ class ImageCollection(object): + if ((self.conserve_memory and n != self._cached) or + (self.data[idx] is None)): + if self._frame_index: +- fname, img_num = self._frame_index[idx] ++ fname, img_num = self._frame_index[n] + self.data[idx] = self.load_func(fname, img_num=img_num, + **self.load_func_kwargs) + else: +",skimage/io/collection.py,"ReplaceText(target='n' @(257,55)->(257,58))","class ImageCollection(object): + if ((self.conserve_memory and n != self._cached) or + (self.data[idx] is None)): + if self._frame_index: + fname, img_num = self._frame_index[idx] + self.data[idx] = self.load_func(fname, img_num=img_num, + **self.load_func_kwargs) + else:","class ImageCollection(object): + if ((self.conserve_memory and n != self._cached) or + (self.data[idx] is None)): + if self._frame_index: + fname, img_num = self._frame_index[n] + self.data[idx] = self.load_func(fname, img_num=img_num, + **self.load_func_kwargs) + else:" +376,https://:@github.com/scikit-image/scikit-image.git,84bcb583d76c1ec507b3d5794b6705d06383ced8,"@@ -288,7 +288,7 @@ def hessian_matrix_eigvals(Hxx, Hxy, Hyy): + + """""" + +- return _image_orthogonal_matrix22_eigvals(Hyy, Hxy, Hyy) ++ return _image_orthogonal_matrix22_eigvals(Hxx, Hxy, Hyy) + + + def corner_kitchen_rosenfeld(image, mode='constant', cval=0): +",skimage/feature/corner.py,"ReplaceText(target='Hxx' @(291,46)->(291,49))","def hessian_matrix_eigvals(Hxx, Hxy, Hyy): + + """""" + + return _image_orthogonal_matrix22_eigvals(Hyy, Hxy, Hyy) + + + def corner_kitchen_rosenfeld(image, mode='constant', cval=0):","def hessian_matrix_eigvals(Hxx, Hxy, Hyy): + + """""" + + return _image_orthogonal_matrix22_eigvals(Hxx, Hxy, Hyy) + + + def corner_kitchen_rosenfeld(image, mode='constant', cval=0):" +377,https://:@github.com/scikit-image/scikit-image.git,33e36542d5f457a50c5fa00371fb9fe18a620f15,"@@ -84,7 +84,7 @@ def hough_line_peaks(hspace, angles, dists, min_distance=9, min_angle=10, + -min_angle:min_angle + 1] + + for dist_idx, angle_idx in coords: +- accum = hspace[dist_idx, angle_idx] ++ accum = hspace_max[dist_idx, angle_idx] + if accum > threshold: + # absolute coordinate grid for local neighbourhood suppression + dist_nh = dist_idx + dist_ext +",skimage/transform/hough_transform.py,"ReplaceText(target='hspace_max' @(87,16)->(87,22))","def hough_line_peaks(hspace, angles, dists, min_distance=9, min_angle=10, + -min_angle:min_angle + 1] + + for dist_idx, angle_idx in coords: + accum = hspace[dist_idx, angle_idx] + if accum > threshold: + # absolute coordinate grid for local neighbourhood suppression + dist_nh = dist_idx + dist_ext","def hough_line_peaks(hspace, angles, dists, min_distance=9, min_angle=10, + -min_angle:min_angle + 1] + + for dist_idx, angle_idx in coords: + accum = hspace_max[dist_idx, angle_idx] + if accum > threshold: + # absolute coordinate grid for local neighbourhood suppression + dist_nh = dist_idx + dist_ext" +378,https://:@github.com/scikit-image/scikit-image.git,bc52e4a411ab6d4aa10d38281e979158e6f21f19,"@@ -105,7 +105,7 @@ def hough_line_peaks(hspace, angles, dists, min_distance=9, min_angle=10, + angle_nh[angle_high] -= cols + + # suppress neighbourhood +- hspace[dist_nh, angle_nh] = 0 ++ hspace_max[dist_nh, angle_nh] = 0 + + # add current line to peaks + hspace_peaks.append(accum) +",skimage/transform/hough_transform.py,"ReplaceText(target='hspace_max' @(108,12)->(108,18))","def hough_line_peaks(hspace, angles, dists, min_distance=9, min_angle=10, + angle_nh[angle_high] -= cols + + # suppress neighbourhood + hspace[dist_nh, angle_nh] = 0 + + # add current line to peaks + hspace_peaks.append(accum)","def hough_line_peaks(hspace, angles, dists, min_distance=9, min_angle=10, + angle_nh[angle_high] -= cols + + # suppress neighbourhood + hspace_max[dist_nh, angle_nh] = 0 + + # add current line to peaks + hspace_peaks.append(accum)" +379,https://:@github.com/scikit-image/scikit-image.git,2fb59b92435b9f67c091871cba701323b784ade7,"@@ -48,7 +48,7 @@ def imread(fname, dtype=None, img_num=None, **kwargs): + im = Image.open(f) + return pil_to_ndarray(im, dtype=dtype, img_num=img_num) + else: +- im = Image.open(f) ++ im = Image.open(fname) + return pil_to_ndarray(im, dtype=dtype, img_num=img_num) + + +",skimage/io/_plugins/pil_plugin.py,"ReplaceText(target='fname' @(51,24)->(51,25))","def imread(fname, dtype=None, img_num=None, **kwargs): + im = Image.open(f) + return pil_to_ndarray(im, dtype=dtype, img_num=img_num) + else: + im = Image.open(f) + return pil_to_ndarray(im, dtype=dtype, img_num=img_num) + + ","def imread(fname, dtype=None, img_num=None, **kwargs): + im = Image.open(f) + return pil_to_ndarray(im, dtype=dtype, img_num=img_num) + else: + im = Image.open(fname) + return pil_to_ndarray(im, dtype=dtype, img_num=img_num) + + " +380,https://:@github.com/scikit-image/scikit-image.git,4ee3b2c5ac89f946a9b4bbf26665411bb7241ff4,"@@ -20,7 +20,7 @@ image = data.astronaut() + rows, cols, dim = image.shape + pyramid = tuple(pyramid_gaussian(image, downscale=2)) + +-composite_image = np.zeros((rows, cols + cols / 2, 3), dtype=np.double) ++composite_image = np.zeros((rows, cols + cols // 2, 3), dtype=np.double) + + composite_image[:rows, :cols, :] = pyramid[0] + +",doc/examples/transform/plot_pyramid.py,"ReplaceText(target='//' @(23,46)->(23,47))","image = data.astronaut() + rows, cols, dim = image.shape + pyramid = tuple(pyramid_gaussian(image, downscale=2)) + + composite_image = np.zeros((rows, cols + cols / 2, 3), dtype=np.double) + + composite_image[:rows, :cols, :] = pyramid[0] + ","image = data.astronaut() + rows, cols, dim = image.shape + pyramid = tuple(pyramid_gaussian(image, downscale=2)) + + composite_image = np.zeros((rows, cols + cols // 2, 3), dtype=np.double) + + composite_image[:rows, :cols, :] = pyramid[0] + " +381,https://:@github.com/scikit-image/scikit-image.git,472a420d86ff363cbb11df4e4b76ec090e0d015c,"@@ -634,7 +634,7 @@ def skeletonize_3d(image, *, img=None): + raise ValueError(""skeletonize_3d can only handle 2D or 3D images; "" + ""got image.ndim = %s instead."" % image.ndim) + image = np.ascontiguousarray(image) +- image = img_as_ubyte(img, force_copy=False) ++ image = img_as_ubyte(image, force_copy=False) + + # make an in image 3D and pad it w/ zeros to simplify dealing w/ boundaries + # NB: careful here to not clobber the original *and* minimize copying +",skimage/morphology/_skeletonize.py,"ReplaceText(target='image' @(637,25)->(637,28))","def skeletonize_3d(image, *, img=None): + raise ValueError(""skeletonize_3d can only handle 2D or 3D images; "" + ""got image.ndim = %s instead."" % image.ndim) + image = np.ascontiguousarray(image) + image = img_as_ubyte(img, force_copy=False) + + # make an in image 3D and pad it w/ zeros to simplify dealing w/ boundaries + # NB: careful here to not clobber the original *and* minimize copying","def skeletonize_3d(image, *, img=None): + raise ValueError(""skeletonize_3d can only handle 2D or 3D images; "" + ""got image.ndim = %s instead."" % image.ndim) + image = np.ascontiguousarray(image) + image = img_as_ubyte(image, force_copy=False) + + # make an in image 3D and pad it w/ zeros to simplify dealing w/ boundaries + # NB: careful here to not clobber the original *and* minimize copying" +382,https://:@github.com/scikit-image/scikit-image.git,1539f238e52610f5e7607d5b447b5c491e3455eb,"@@ -242,7 +242,7 @@ def test_arraymap_update(): + in_values = np.unique(np.random.randint(0, 200, size=5)) + out_values = np.random.random(len(in_values)) + m = ArrayMap(in_values, out_values) +- image = np.random.randint(1, len(in_values), size=(512, 512)) ++ image = np.random.randint(1, len(m), size=(512, 512)) + assert np.all(m[image] < 1) # missing values map to 0. + m[1:] += 1 + assert np.all(m[image] >= 1) +",skimage/segmentation/tests/test_join.py,"ReplaceText(target='m' @(245,37)->(245,46))","def test_arraymap_update(): + in_values = np.unique(np.random.randint(0, 200, size=5)) + out_values = np.random.random(len(in_values)) + m = ArrayMap(in_values, out_values) + image = np.random.randint(1, len(in_values), size=(512, 512)) + assert np.all(m[image] < 1) # missing values map to 0. + m[1:] += 1 + assert np.all(m[image] >= 1)","def test_arraymap_update(): + in_values = np.unique(np.random.randint(0, 200, size=5)) + out_values = np.random.random(len(in_values)) + m = ArrayMap(in_values, out_values) + image = np.random.randint(1, len(m), size=(512, 512)) + assert np.all(m[image] < 1) # missing values map to 0. + m[1:] += 1 + assert np.all(m[image] >= 1)" +383,https://:@github.com/globusonline/agamemnon.git,6460e336b2a3fd359364f85e39d6e3222077621e,"@@ -233,7 +233,7 @@ class DataStore(object): + source_node_key = value + elif column.startswith('source__'): + source_attributes[column[8:]] = value +- source = prim.Node(self, source_node_type, source_node_key, values) ++ source = prim.Node(self, source_node_type, source_node_key, source_attributes) + rel_key = RELATIONSHIP_KEY_PATTERN % (rel_type, rel_key) + return self.get_outgoing_relationship(rel_type, source, (rel_key, values)) + +",agamemnon/factory.py,"ReplaceText(target='source_attributes' @(236,68)->(236,74))","class DataStore(object): + source_node_key = value + elif column.startswith('source__'): + source_attributes[column[8:]] = value + source = prim.Node(self, source_node_type, source_node_key, values) + rel_key = RELATIONSHIP_KEY_PATTERN % (rel_type, rel_key) + return self.get_outgoing_relationship(rel_type, source, (rel_key, values)) + ","class DataStore(object): + source_node_key = value + elif column.startswith('source__'): + source_attributes[column[8:]] = value + source = prim.Node(self, source_node_type, source_node_key, source_attributes) + rel_key = RELATIONSHIP_KEY_PATTERN % (rel_type, rel_key) + return self.get_outgoing_relationship(rel_type, source, (rel_key, values)) + " +384,https://:@github.com/chiptopher/guet.git,f95c54917b51e65f47789534ab88ecbede1838eb,"@@ -11,6 +11,6 @@ def _recursive_directory_find(path: Path, directory_name: str) -> str: + raise FileNotFoundError() + joined_with_driectory = path.joinpath(directory_name) + if joined_with_driectory.is_dir(): +- return str(joined_with_driectory) ++ return str(path) + else: + return _recursive_directory_find(path.parent, directory_name) +",guet/util/_recursive_directory_find.py,"ReplaceText(target='path' @(14,19)->(14,40))","def _recursive_directory_find(path: Path, directory_name: str) -> str: + raise FileNotFoundError() + joined_with_driectory = path.joinpath(directory_name) + if joined_with_driectory.is_dir(): + return str(joined_with_driectory) + else: + return _recursive_directory_find(path.parent, directory_name)","def _recursive_directory_find(path: Path, directory_name: str) -> str: + raise FileNotFoundError() + joined_with_driectory = path.joinpath(directory_name) + if joined_with_driectory.is_dir(): + return str(path) + else: + return _recursive_directory_find(path.parent, directory_name)" +385,https://:@github.com/justinsalamon/scaper.git,520ae608ebcbcc5e5438ca5c7967dc2479454038,"@@ -193,7 +193,7 @@ def generate_from_jams(jams_infile, audio_outfile, fg_path=None, bg_path=None, + tfm.trim(sliceop['slice_start'], sliceop['slice_end']) + tfm.build(audio_file, tmpfiles[-1].name) + # Copy result back to original file +- shutil.copyfile(tmpfiles[-1].name, audio_outfile) ++ shutil.copyfile(tmpfiles[-1].name, audio_file) + + # Optionally save new jams file + if jams_outfile is not None: +",scaper/core.py,"ReplaceText(target='audio_file' @(196,55)->(196,68))","def generate_from_jams(jams_infile, audio_outfile, fg_path=None, bg_path=None, + tfm.trim(sliceop['slice_start'], sliceop['slice_end']) + tfm.build(audio_file, tmpfiles[-1].name) + # Copy result back to original file + shutil.copyfile(tmpfiles[-1].name, audio_outfile) + + # Optionally save new jams file + if jams_outfile is not None:","def generate_from_jams(jams_infile, audio_outfile, fg_path=None, bg_path=None, + tfm.trim(sliceop['slice_start'], sliceop['slice_end']) + tfm.build(audio_file, tmpfiles[-1].name) + # Copy result back to original file + shutil.copyfile(tmpfiles[-1].name, audio_file) + + # Optionally save new jams file + if jams_outfile is not None:" +386,https://:@github.com/markokr/rarfile.git,7fd6b2ca3efb81f7c4dffa6b6cef347b7d6ba043,"@@ -833,7 +833,7 @@ class RarFile: + if dirs: + dirs.sort(reverse=True) + for dst, inf in dirs: +- self._set_attrs(dst, inf) ++ self._set_attrs(inf, dst) + + def testrar(self, pwd=None): + """"""Read all files and test CRC. +",rarfile.py,"ArgSwap(idxs=0<->1 @(836,16)->(836,31))","class RarFile: + if dirs: + dirs.sort(reverse=True) + for dst, inf in dirs: + self._set_attrs(dst, inf) + + def testrar(self, pwd=None): + """"""Read all files and test CRC.","class RarFile: + if dirs: + dirs.sort(reverse=True) + for dst, inf in dirs: + self._set_attrs(inf, dst) + + def testrar(self, pwd=None): + """"""Read all files and test CRC." +387,https://:@github.com/rougier/freetype-py.git,b21f15fb02eb44a656c250357665d1d7dc50bef6,"@@ -44,7 +44,7 @@ if __name__ == '__main__': + y = height-baseline-top + kerning = face.get_kerning(previous, c) + x += (kerning.x >> 6) +- Z[y:y+h,x:x+w] |= numpy.array(bitmap.buffer).reshape(h,w) ++ Z[y:y+h,x:x+w] += numpy.array(bitmap.buffer).reshape(h,w) + x += (slot.advance.x >> 6) + previous = c + +",examples/hello-world.py,"ReplaceText(target='+=' @(47,23)->(47,25))","if __name__ == '__main__': + y = height-baseline-top + kerning = face.get_kerning(previous, c) + x += (kerning.x >> 6) + Z[y:y+h,x:x+w] |= numpy.array(bitmap.buffer).reshape(h,w) + x += (slot.advance.x >> 6) + previous = c + ","if __name__ == '__main__': + y = height-baseline-top + kerning = face.get_kerning(previous, c) + x += (kerning.x >> 6) + Z[y:y+h,x:x+w] += numpy.array(bitmap.buffer).reshape(h,w) + x += (slot.advance.x >> 6) + previous = c + " +388,https://:@github.com/piotrmaslanka/satella.git,24018c366401278a79da72097f1c594c188f5220,"@@ -15,7 +15,7 @@ def _merge(v1, v2): + + if isinstance(v1, list) and isinstance(v2, list): + v1.extend(v2) +- return v2 ++ return v1 + + raise TypeError + +",satella/coding/algos.py,"ReplaceText(target='v1' @(18,15)->(18,17))","def _merge(v1, v2): + + if isinstance(v1, list) and isinstance(v2, list): + v1.extend(v2) + return v2 + + raise TypeError + ","def _merge(v1, v2): + + if isinstance(v1, list) and isinstance(v2, list): + v1.extend(v2) + return v1 + + raise TypeError + " +389,https://:@github.com/piotrmaslanka/satella.git,4828537442e39bd6592413a5b4a2421a079edc91,"@@ -194,7 +194,7 @@ class Heap(object): + :return: Iterator + """""" + while self: +- if self.heap[0] >= less: ++ if self.heap[0] < less: + return + yield self.pop() + +",satella/coding/structures.py,"ReplaceText(target='<' @(197,28)->(197,30))","class Heap(object): + :return: Iterator + """""" + while self: + if self.heap[0] >= less: + return + yield self.pop() + ","class Heap(object): + :return: Iterator + """""" + while self: + if self.heap[0] < less: + return + yield self.pop() + " +390,https://:@github.com/piotrmaslanka/satella.git,fab19fa60841455e2ec0ec4493c618b7f5225f7d,"@@ -35,7 +35,7 @@ class MeasurableMixin: + elapsed = value_getter() - future.old_value + self.handle(logging_level, elapsed, **labels) + +- future.add_done_callback(future) ++ future.add_done_callback(on_future_done) + + def measure(self, include_exceptions: bool = True, + logging_level: MetricLevel = MetricLevel.RUNTIME, +",satella/instrumentation/metrics/metric_types/measurable_mixin.py,"ReplaceText(target='on_future_done' @(38,33)->(38,39))","class MeasurableMixin: + elapsed = value_getter() - future.old_value + self.handle(logging_level, elapsed, **labels) + + future.add_done_callback(future) + + def measure(self, include_exceptions: bool = True, + logging_level: MetricLevel = MetricLevel.RUNTIME,","class MeasurableMixin: + elapsed = value_getter() - future.old_value + self.handle(logging_level, elapsed, **labels) + + future.add_done_callback(on_future_done) + + def measure(self, include_exceptions: bool = True, + logging_level: MetricLevel = MetricLevel.RUNTIME," +391,https://:@github.com/piotrmaslanka/satella.git,a9b866bd76586a440918130d52ca933529ac521a,"@@ -117,7 +117,7 @@ class Proxy(tp.Generic[T]): + return self.__obj or other + + def __and__(self, other): +- return self.__obj or other ++ return self.__obj and other + + def __le__(self, other): + return self.__obj <= other +",satella/coding/structures/proxy.py,"ReplaceText(target='and' @(120,26)->(120,28))","class Proxy(tp.Generic[T]): + return self.__obj or other + + def __and__(self, other): + return self.__obj or other + + def __le__(self, other): + return self.__obj <= other","class Proxy(tp.Generic[T]): + return self.__obj or other + + def __and__(self, other): + return self.__obj and other + + def __le__(self, other): + return self.__obj <= other" +392,https://:@github.com/dmlc/keras.git,2662d81a9c925501831f0acb805c9e8adcde0a32,"@@ -160,7 +160,7 @@ class Adam(Optimizer): + m_b_t = m_t / (1 - beta_1_t) + v_b_t = v_t / (1 - beta_2_t) + +- p_t = p - self.lr * m_b_t / (T.sqrt(v_t) + self.epsilon) ++ p_t = p - self.lr * m_b_t / (T.sqrt(v_b_t) + self.epsilon) + + updates.append((m, m_t)) + updates.append((v, v_t)) +",keras/optimizers.py,"ReplaceText(target='v_b_t' @(163,48)->(163,51))","class Adam(Optimizer): + m_b_t = m_t / (1 - beta_1_t) + v_b_t = v_t / (1 - beta_2_t) + + p_t = p - self.lr * m_b_t / (T.sqrt(v_t) + self.epsilon) + + updates.append((m, m_t)) + updates.append((v, v_t))","class Adam(Optimizer): + m_b_t = m_t / (1 - beta_1_t) + v_b_t = v_t / (1 - beta_2_t) + + p_t = p - self.lr * m_b_t / (T.sqrt(v_b_t) + self.epsilon) + + updates.append((m, m_t)) + updates.append((v, v_t))" +393,https://:@github.com/dmlc/keras.git,cc10c4d907d959eb9009ad502c727542a5259613,"@@ -69,7 +69,7 @@ def skipgrams(sequence, vocabulary_size, + if not wi: + continue + if sampling_table is not None: +- if sampling_table[i] < random.random(): ++ if sampling_table[wi] < random.random(): + continue + + window_start = max(0, i-window_size) +",keras/preprocessing/sequence.py,"ReplaceText(target='wi' @(72,30)->(72,31))","def skipgrams(sequence, vocabulary_size, + if not wi: + continue + if sampling_table is not None: + if sampling_table[i] < random.random(): + continue + + window_start = max(0, i-window_size)","def skipgrams(sequence, vocabulary_size, + if not wi: + continue + if sampling_table is not None: + if sampling_table[wi] < random.random(): + continue + + window_start = max(0, i-window_size)" +394,https://:@github.com/dmlc/keras.git,e3695591704a21c6d0d6236c11c1bad7de4e314c,"@@ -58,7 +58,7 @@ class SimpleRNN(Layer): + mask = T.addbroadcast(mask[:, :, np.newaxis], 2) + + mask_tm1 = alloc_zeros_matrix(*mask.shape) +- mask_tm1 = T.addbroadcast(T.set_subtensor(mask[1:, :, :], mask[:-1, :, :]), 2) ++ mask_tm1 = T.addbroadcast(T.set_subtensor(mask_tm1[1:, :, :], mask[:-1, :, :]), 2) + + # scan = theano symbolic loop. + # See: http://deeplearning.net/software/theano/library/scan.html +",keras/layers/recurrent.py,"ReplaceText(target='mask_tm1' @(61,50)->(61,54))","class SimpleRNN(Layer): + mask = T.addbroadcast(mask[:, :, np.newaxis], 2) + + mask_tm1 = alloc_zeros_matrix(*mask.shape) + mask_tm1 = T.addbroadcast(T.set_subtensor(mask[1:, :, :], mask[:-1, :, :]), 2) + + # scan = theano symbolic loop. + # See: http://deeplearning.net/software/theano/library/scan.html","class SimpleRNN(Layer): + mask = T.addbroadcast(mask[:, :, np.newaxis], 2) + + mask_tm1 = alloc_zeros_matrix(*mask.shape) + mask_tm1 = T.addbroadcast(T.set_subtensor(mask_tm1[1:, :, :], mask[:-1, :, :]), 2) + + # scan = theano symbolic loop. + # See: http://deeplearning.net/software/theano/library/scan.html" +395,https://:@github.com/dmlc/keras.git,c315b0d7a95b6677452300bdefd526b444951819,"@@ -218,7 +218,7 @@ class GaussianNoise(MaskedLayer): + + def get_output(self, train=False): + X = self.get_input(train) +- if train or self.sigma == 0: ++ if not train or self.sigma == 0: + return X + else: + return X + srng.normal(size=X.shape, avg=0.0, std=self.sigma, +",keras/layers/core.py,"ReplaceText(target='not ' @(221,11)->(221,11))","class GaussianNoise(MaskedLayer): + + def get_output(self, train=False): + X = self.get_input(train) + if train or self.sigma == 0: + return X + else: + return X + srng.normal(size=X.shape, avg=0.0, std=self.sigma,","class GaussianNoise(MaskedLayer): + + def get_output(self, train=False): + X = self.get_input(train) + if not train or self.sigma == 0: + return X + else: + return X + srng.normal(size=X.shape, avg=0.0, std=self.sigma," +396,https://:@github.com/dmlc/keras.git,46a2fb6fd8e52b02df78f1416cc9fbd4b3156604,"@@ -42,7 +42,7 @@ class Optimizer(object): + grads = [clip_norm(g, self.clipnorm, norm) for g in grads] + + if hasattr(self, 'clipvalue') and self.clipvalue > 0: +- grads = [T.clip(g, self.clipvalue, -self.clipvalue) for g in grads] ++ grads = [T.clip(g, -self.clipvalue, self.clipvalue) for g in grads] + + return grads + +",keras/optimizers.py,"ArgSwap(idxs=1<->2 @(45,21)->(45,27))","class Optimizer(object): + grads = [clip_norm(g, self.clipnorm, norm) for g in grads] + + if hasattr(self, 'clipvalue') and self.clipvalue > 0: + grads = [T.clip(g, self.clipvalue, -self.clipvalue) for g in grads] + + return grads + ","class Optimizer(object): + grads = [clip_norm(g, self.clipnorm, norm) for g in grads] + + if hasattr(self, 'clipvalue') and self.clipvalue > 0: + grads = [T.clip(g, -self.clipvalue, self.clipvalue) for g in grads] + + return grads + " +397,https://:@github.com/dmlc/keras.git,c2534964b76015eb3d76261b025c7556b354764c,"@@ -158,7 +158,7 @@ class SimpleRNN(Recurrent): + assert len(states) == 1 + prev_output = states[0] + h = K.dot(x, self.W) + self.b +- output = self.activation(h * K.dot(prev_output, self.U)) ++ output = self.activation(h + K.dot(prev_output, self.U)) + return output, [output] + + def get_config(self): +",keras/layers/recurrent.py,"ReplaceText(target='+' @(161,35)->(161,36))","class SimpleRNN(Recurrent): + assert len(states) == 1 + prev_output = states[0] + h = K.dot(x, self.W) + self.b + output = self.activation(h * K.dot(prev_output, self.U)) + return output, [output] + + def get_config(self):","class SimpleRNN(Recurrent): + assert len(states) == 1 + prev_output = states[0] + h = K.dot(x, self.W) + self.b + output = self.activation(h + K.dot(prev_output, self.U)) + return output, [output] + + def get_config(self):" +398,https://:@github.com/dmlc/keras.git,3d51a26749937cb1a1aec40c20bc505e82809dce,"@@ -449,7 +449,7 @@ class Graph(Layer): + self.namespace.add(sh_name) + self.nodes[sh_name] = sh + self.node_config.append({'name': sh_name, +- 'inputs': [s], ++ 'inputs': [name], + 'create_output': create_output}) + if create_output: + self.add_output(sh_name, input=sh_name) +",keras/layers/containers.py,"ReplaceText(target='name' @(452,52)->(452,53))","class Graph(Layer): + self.namespace.add(sh_name) + self.nodes[sh_name] = sh + self.node_config.append({'name': sh_name, + 'inputs': [s], + 'create_output': create_output}) + if create_output: + self.add_output(sh_name, input=sh_name)","class Graph(Layer): + self.namespace.add(sh_name) + self.nodes[sh_name] = sh + self.node_config.append({'name': sh_name, + 'inputs': [name], + 'create_output': create_output}) + if create_output: + self.add_output(sh_name, input=sh_name)" +399,https://:@github.com/dmlc/keras.git,42b3d37a54545882699283b5764cf3c997f8d9cd,"@@ -43,7 +43,7 @@ def test_skipgrams(): + couples, labels = skipgrams(np.arange(5), vocabulary_size=5, window_size=1, + categorical=True) + for couple in couples: +- assert couple[0] - couple[1] < 3 ++ assert couple[0] - couple[1] <= 3 + for l in labels: + assert len(l) == 2 + +",tests/keras/preprocessing/test_sequence.py,"ReplaceText(target='<=' @(46,37)->(46,38))","def test_skipgrams(): + couples, labels = skipgrams(np.arange(5), vocabulary_size=5, window_size=1, + categorical=True) + for couple in couples: + assert couple[0] - couple[1] < 3 + for l in labels: + assert len(l) == 2 + ","def test_skipgrams(): + couples, labels = skipgrams(np.arange(5), vocabulary_size=5, window_size=1, + categorical=True) + for couple in couples: + assert couple[0] - couple[1] <= 3 + for l in labels: + assert len(l) == 2 + " +400,https://:@github.com/dmlc/keras.git,e2e281e14f619d9ade61c46567e2c599db070f16,"@@ -23,7 +23,7 @@ def test_unitnorm_constraint(): + lookup.compile(loss='binary_crossentropy', optimizer='sgd', + class_mode='binary') + lookup.train_on_batch(X1, np.array([[1], [0]], dtype='int32')) +- norm = np.linalg.norm(K.get_value(lookup.params[0]), axis=1) ++ norm = np.linalg.norm(K.get_value(lookup.params[0]), axis=0) + assert_allclose(norm, np.ones_like(norm).astype('float32'), rtol=1e-05) + + +",tests/keras/layers/test_embeddings.py,"ReplaceText(target='0' @(26,62)->(26,63))","def test_unitnorm_constraint(): + lookup.compile(loss='binary_crossentropy', optimizer='sgd', + class_mode='binary') + lookup.train_on_batch(X1, np.array([[1], [0]], dtype='int32')) + norm = np.linalg.norm(K.get_value(lookup.params[0]), axis=1) + assert_allclose(norm, np.ones_like(norm).astype('float32'), rtol=1e-05) + + ","def test_unitnorm_constraint(): + lookup.compile(loss='binary_crossentropy', optimizer='sgd', + class_mode='binary') + lookup.train_on_batch(X1, np.array([[1], [0]], dtype='int32')) + norm = np.linalg.norm(K.get_value(lookup.params[0]), axis=0) + assert_allclose(norm, np.ones_like(norm).astype('float32'), rtol=1e-05) + + " +401,https://:@github.com/dmlc/keras.git,e2e281e14f619d9ade61c46567e2c599db070f16,"@@ -54,7 +54,7 @@ def test_identity_oddballs(): + def test_unitnorm(): + unitnorm_instance = constraints.unitnorm() + normalized = unitnorm_instance(K.variable(example_array)) +- norm_of_normalized = np.sqrt(np.sum(K.eval(normalized)**2, axis=1)) ++ norm_of_normalized = np.sqrt(np.sum(K.eval(normalized)**2, axis=0)) + # in the unit norm constraint, it should be equal to 1. + difference = norm_of_normalized - 1. + largest_difference = np.max(np.abs(difference)) +",tests/keras/test_constraints.py,"ReplaceText(target='0' @(57,68)->(57,69))","def test_identity_oddballs(): + def test_unitnorm(): + unitnorm_instance = constraints.unitnorm() + normalized = unitnorm_instance(K.variable(example_array)) + norm_of_normalized = np.sqrt(np.sum(K.eval(normalized)**2, axis=1)) + # in the unit norm constraint, it should be equal to 1. + difference = norm_of_normalized - 1. + largest_difference = np.max(np.abs(difference))","def test_identity_oddballs(): + def test_unitnorm(): + unitnorm_instance = constraints.unitnorm() + normalized = unitnorm_instance(K.variable(example_array)) + norm_of_normalized = np.sqrt(np.sum(K.eval(normalized)**2, axis=0)) + # in the unit norm constraint, it should be equal to 1. + difference = norm_of_normalized - 1. + largest_difference = np.max(np.abs(difference))" +402,https://:@github.com/dmlc/keras.git,f4af11c7300816ca28b6b707fdf7d64b00430074,"@@ -52,7 +52,7 @@ def pad_sequences(sequences, maxlen=None, dtype='int32', padding='pre', truncati + elif truncating == 'post': + trunc = s[:maxlen] + else: +- raise ValueError(""Truncating type '%s' not understood"" % padding) ++ raise ValueError(""Truncating type '%s' not understood"" % truncating) + + # check `trunc` has expected shape + trunc = np.asarray(trunc, dtype=dtype) +",keras/preprocessing/sequence.py,"ReplaceText(target='truncating' @(55,69)->(55,76))","def pad_sequences(sequences, maxlen=None, dtype='int32', padding='pre', truncati + elif truncating == 'post': + trunc = s[:maxlen] + else: + raise ValueError(""Truncating type '%s' not understood"" % padding) + + # check `trunc` has expected shape + trunc = np.asarray(trunc, dtype=dtype)","def pad_sequences(sequences, maxlen=None, dtype='int32', padding='pre', truncati + elif truncating == 'post': + trunc = s[:maxlen] + else: + raise ValueError(""Truncating type '%s' not understood"" % truncating) + + # check `trunc` has expected shape + trunc = np.asarray(trunc, dtype=dtype)" +403,https://:@github.com/dmlc/keras.git,b61235b77f87288d62ddd8ce4aae88b76babf887,"@@ -153,7 +153,7 @@ def check_array_lengths(X, Y, W): + raise Exception('All input arrays (x) should have ' + 'the same number of samples.') + set_y = set(y_lengths) +- if len(set_x) != 1: ++ if len(set_y) != 1: + raise Exception('All target arrays (y) should have ' + 'the same number of samples.') + set_w = set(w_lengths) +",keras/engine/training.py,"ReplaceText(target='set_y' @(156,11)->(156,16))","def check_array_lengths(X, Y, W): + raise Exception('All input arrays (x) should have ' + 'the same number of samples.') + set_y = set(y_lengths) + if len(set_x) != 1: + raise Exception('All target arrays (y) should have ' + 'the same number of samples.') + set_w = set(w_lengths)","def check_array_lengths(X, Y, W): + raise Exception('All input arrays (x) should have ' + 'the same number of samples.') + set_y = set(y_lengths) + if len(set_y) != 1: + raise Exception('All target arrays (y) should have ' + 'the same number of samples.') + set_w = set(w_lengths)" +404,https://:@github.com/dmlc/keras.git,98974efa5f51d6f55afbf2bc125d6fd090bcf782,"@@ -510,7 +510,7 @@ class Model(Container): + 'it should have one entry per model outputs. ' + 'The model has ' + str(len(self.outputs)) + + ' outputs, but you passed loss_weights=' + +- str(loss)) ++ str(loss_weights)) + loss_weights_list = loss_weights + else: + raise Exception('Could not interpret loss_weights argument: ' + +",keras/engine/training.py,"ReplaceText(target='loss_weights' @(513,36)->(513,40))","class Model(Container): + 'it should have one entry per model outputs. ' + 'The model has ' + str(len(self.outputs)) + + ' outputs, but you passed loss_weights=' + + str(loss)) + loss_weights_list = loss_weights + else: + raise Exception('Could not interpret loss_weights argument: ' +","class Model(Container): + 'it should have one entry per model outputs. ' + 'The model has ' + str(len(self.outputs)) + + ' outputs, but you passed loss_weights=' + + str(loss_weights)) + loss_weights_list = loss_weights + else: + raise Exception('Could not interpret loss_weights argument: ' +" +405,https://:@github.com/dmlc/keras.git,48ae7217e482a1a3624d6e5380c972a653cacfaf,"@@ -1136,7 +1136,7 @@ def rnn(step_function, inputs, initial_states, + + if mask is not None: + if go_backwards: +- mask = tf.reverse(mask, [True] + [False] * (ndim - 1)) ++ mask = tf.reverse(mask, [True] + [False] * (ndim - 2)) + + # Transpose not supported by bool tensor types, hence round-trip to uint8. + mask = tf.cast(mask, tf.uint8) +",keras/backend/tensorflow_backend.py,"ReplaceText(target='2' @(1139,67)->(1139,68))","def rnn(step_function, inputs, initial_states, + + if mask is not None: + if go_backwards: + mask = tf.reverse(mask, [True] + [False] * (ndim - 1)) + + # Transpose not supported by bool tensor types, hence round-trip to uint8. + mask = tf.cast(mask, tf.uint8)","def rnn(step_function, inputs, initial_states, + + if mask is not None: + if go_backwards: + mask = tf.reverse(mask, [True] + [False] * (ndim - 2)) + + # Transpose not supported by bool tensor types, hence round-trip to uint8. + mask = tf.cast(mask, tf.uint8)" +406,https://:@github.com/dmlc/keras.git,41741c38e5f29ebf69fe9bd82a604eba3c0b97e5,"@@ -1261,7 +1261,7 @@ def rnn(step_function, inputs, initial_states, + new_state = new_states[0] + else: + # return dummy state, otherwise _dynamic_rnn_loop breaks +- new_state = output ++ new_state = state + return output, new_state + + _step.state_size = state_size * nb_states +",keras/backend/tensorflow_backend.py,"ReplaceText(target='state' @(1264,32)->(1264,38))","def rnn(step_function, inputs, initial_states, + new_state = new_states[0] + else: + # return dummy state, otherwise _dynamic_rnn_loop breaks + new_state = output + return output, new_state + + _step.state_size = state_size * nb_states","def rnn(step_function, inputs, initial_states, + new_state = new_states[0] + else: + # return dummy state, otherwise _dynamic_rnn_loop breaks + new_state = state + return output, new_state + + _step.state_size = state_size * nb_states" +407,https://:@github.com/dmlc/keras.git,80fbbc3a6a2a30f391bad2aa85e7558c50ca0709,"@@ -411,7 +411,7 @@ class ImageDataGenerator(object): + + if self.zca_whitening: + flatX = np.reshape(X, (X.shape[0], X.shape[1] * X.shape[2] * X.shape[3])) +- sigma = np.dot(flatX.T, flatX) / flatX.shape[1] ++ sigma = np.dot(flatX.T, flatX) / flatX.shape[0] + U, S, V = linalg.svd(sigma) + self.principal_components = np.dot(np.dot(U, np.diag(1. / np.sqrt(S + 10e-7))), U.T) + +",keras/preprocessing/image.py,"ReplaceText(target='0' @(414,57)->(414,58))","class ImageDataGenerator(object): + + if self.zca_whitening: + flatX = np.reshape(X, (X.shape[0], X.shape[1] * X.shape[2] * X.shape[3])) + sigma = np.dot(flatX.T, flatX) / flatX.shape[1] + U, S, V = linalg.svd(sigma) + self.principal_components = np.dot(np.dot(U, np.diag(1. / np.sqrt(S + 10e-7))), U.T) + ","class ImageDataGenerator(object): + + if self.zca_whitening: + flatX = np.reshape(X, (X.shape[0], X.shape[1] * X.shape[2] * X.shape[3])) + sigma = np.dot(flatX.T, flatX) / flatX.shape[0] + U, S, V = linalg.svd(sigma) + self.principal_components = np.dot(np.dot(U, np.diag(1. / np.sqrt(S + 10e-7))), U.T) + " +408,https://:@github.com/dmlc/keras.git,7bd5c862a271f125a76fa1ada7f0d9ae27159549,"@@ -209,7 +209,7 @@ def check_loss_and_target_compatibility(targets, losses, output_shapes): + 'which does expect integer targets.') + if loss.__name__ in key_losses: + for target_dim, out_dim in zip(y.shape[1:], shape[1:]): +- if target_dim is not None and target_dim != out_dim: ++ if out_dim is not None and target_dim != out_dim: + raise Exception('A target array with shape ' + str(y.shape) + + ' was passed for an output of shape ' + str(shape) + + ' while using as loss `' + loss.__name__ + '`. ' +",keras/engine/training.py,"ReplaceText(target='out_dim' @(212,19)->(212,29))","def check_loss_and_target_compatibility(targets, losses, output_shapes): + 'which does expect integer targets.') + if loss.__name__ in key_losses: + for target_dim, out_dim in zip(y.shape[1:], shape[1:]): + if target_dim is not None and target_dim != out_dim: + raise Exception('A target array with shape ' + str(y.shape) + + ' was passed for an output of shape ' + str(shape) + + ' while using as loss `' + loss.__name__ + '`. '","def check_loss_and_target_compatibility(targets, losses, output_shapes): + 'which does expect integer targets.') + if loss.__name__ in key_losses: + for target_dim, out_dim in zip(y.shape[1:], shape[1:]): + if out_dim is not None and target_dim != out_dim: + raise Exception('A target array with shape ' + str(y.shape) + + ' was passed for an output of shape ' + str(shape) + + ' while using as loss `' + loss.__name__ + '`. '" +409,https://:@github.com/dmlc/keras.git,cb4f93913eb871a5e234db0c31f885daff87ecdf,"@@ -67,7 +67,7 @@ def _obtain_input_shape(input_shape, default_size, min_size, dim_ordering, inclu + if input_shape is not None: + if len(input_shape) != 3: + raise ValueError('`input_shape` must be a tuple of three integers.') +- if input_shape[1] != 3: ++ if input_shape[0] != 3: + raise ValueError('The input must have 3 channels; got ' + '`input_shape=' + str(input_shape) + '`') + if ((input_shape[1] is not None and input_shape[1] < min_size) or +",keras/applications/imagenet_utils.py,"ReplaceText(target='0' @(70,31)->(70,32))","def _obtain_input_shape(input_shape, default_size, min_size, dim_ordering, inclu + if input_shape is not None: + if len(input_shape) != 3: + raise ValueError('`input_shape` must be a tuple of three integers.') + if input_shape[1] != 3: + raise ValueError('The input must have 3 channels; got ' + '`input_shape=' + str(input_shape) + '`') + if ((input_shape[1] is not None and input_shape[1] < min_size) or","def _obtain_input_shape(input_shape, default_size, min_size, dim_ordering, inclu + if input_shape is not None: + if len(input_shape) != 3: + raise ValueError('`input_shape` must be a tuple of three integers.') + if input_shape[0] != 3: + raise ValueError('The input must have 3 channels; got ' + '`input_shape=' + str(input_shape) + '`') + if ((input_shape[1] is not None and input_shape[1] < min_size) or" +410,https://:@github.com/dmlc/keras.git,82ca6d418588ccd61d663ec8029937290b62d583,"@@ -120,7 +120,7 @@ X = X[indices] + y = y[indices] + + # Explicitly set apart 10% for validation data that we never train over +-split_at = len(X) - len(X) / 10 ++split_at = len(X) - len(X) // 10 + (X_train, X_val) = (slice_X(X, 0, split_at), slice_X(X, split_at)) + (y_train, y_val) = (y[:split_at], y[split_at:]) + +",examples/addition_rnn.py,"ReplaceText(target='//' @(123,27)->(123,28))","X = X[indices] + y = y[indices] + + # Explicitly set apart 10% for validation data that we never train over + split_at = len(X) - len(X) / 10 + (X_train, X_val) = (slice_X(X, 0, split_at), slice_X(X, split_at)) + (y_train, y_val) = (y[:split_at], y[split_at:]) + ","X = X[indices] + y = y[indices] + + # Explicitly set apart 10% for validation data that we never train over + split_at = len(X) - len(X) // 10 + (X_train, X_val) = (slice_X(X, 0, split_at), slice_X(X, split_at)) + (y_train, y_val) = (y[:split_at], y[split_at:]) + " +411,https://:@github.com/dmlc/keras.git,7c34add25d0f6a773f1c74d1d8bb50f4482afc76,"@@ -1875,7 +1875,7 @@ def set_value(x, value): + """"""Sets the value of a variable, + from a Numpy array. It returns `None`. + """""" +- if isinstance(x, Number): ++ if isinstance(value, Number): + value = [value] + x.bind(mx.nd.array(value)) + +",keras/backend/mxnet_backend.py,"ReplaceText(target='value' @(1878,18)->(1878,19))","def set_value(x, value): + """"""Sets the value of a variable, + from a Numpy array. It returns `None`. + """""" + if isinstance(x, Number): + value = [value] + x.bind(mx.nd.array(value)) + ","def set_value(x, value): + """"""Sets the value of a variable, + from a Numpy array. It returns `None`. + """""" + if isinstance(value, Number): + value = [value] + x.bind(mx.nd.array(value)) + " +412,https://:@github.com/incountry/sdk-python.git,e98e4243dae300a5ae9cab87347fa61bb87b51a9,"@@ -28,6 +28,6 @@ storage = Storage( + + while not migration_complete: + migration_res = storage.migrate(country=COUNTRY, limit=50) +- if migration_res[""total_left""] <= 0: ++ if migration_res[""total_left""] == 0: + migration_complete = True + time.sleep(1) +",examples/full_migration.py,"ReplaceText(target='==' @(31,35)->(31,37))","storage = Storage( + + while not migration_complete: + migration_res = storage.migrate(country=COUNTRY, limit=50) + if migration_res[""total_left""] <= 0: + migration_complete = True + time.sleep(1)","storage = Storage( + + while not migration_complete: + migration_res = storage.migrate(country=COUNTRY, limit=50) + if migration_res[""total_left""] == 0: + migration_complete = True + time.sleep(1)" +413,https://:@github.com/knockrentals/scrapy-elasticsearch.git,1c5c20459e68544eeb8a0490b9f7b14895861b24,"@@ -96,7 +96,7 @@ class ElasticSearchPipeline(object): + + self.items_buffer.append(index_action) + +- if len(self.items_buffer) == self.settings.get('ELASTICSEARCH_BUFFER_LENGTH', 500): ++ if len(self.items_buffer) >= self.settings.get('ELASTICSEARCH_BUFFER_LENGTH', 500): + self.send_items() + self.items_buffer = [] + +",scrapyelasticsearch/scrapyelasticsearch.py,"ReplaceText(target='>=' @(99,34)->(99,36))","class ElasticSearchPipeline(object): + + self.items_buffer.append(index_action) + + if len(self.items_buffer) == self.settings.get('ELASTICSEARCH_BUFFER_LENGTH', 500): + self.send_items() + self.items_buffer = [] + ","class ElasticSearchPipeline(object): + + self.items_buffer.append(index_action) + + if len(self.items_buffer) >= self.settings.get('ELASTICSEARCH_BUFFER_LENGTH', 500): + self.send_items() + self.items_buffer = [] + " +414,https://:@github.com/smithlabcode/ribotricer.git,805255ef81f4c94dcaf9f0c63ba39f0de7f14eea,"@@ -149,7 +149,7 @@ def detect_orfs_cmd(bam, ribocop_index, prefix, stranded, read_lengths, + sys.exit('Error: cannot convert psite_offsets into integers') + if len(read_lengths) != len(psite_offsets): + sys.exit('Error: psite_offsets must match read_lengths') +- if not all(x > 0 for x in psite_offsets): ++ if not all(x >= 0 for x in psite_offsets): + sys.exit('Error: P-site offset must be >= 0') + if not all(x > y for (x, y) in zip(read_lengths, psite_offsets)): + sys.exit('Error: P-site offset must be smaller than read length') +",RiboCop/cli.py,"ReplaceText(target='>=' @(152,21)->(152,22))","def detect_orfs_cmd(bam, ribocop_index, prefix, stranded, read_lengths, + sys.exit('Error: cannot convert psite_offsets into integers') + if len(read_lengths) != len(psite_offsets): + sys.exit('Error: psite_offsets must match read_lengths') + if not all(x > 0 for x in psite_offsets): + sys.exit('Error: P-site offset must be >= 0') + if not all(x > y for (x, y) in zip(read_lengths, psite_offsets)): + sys.exit('Error: P-site offset must be smaller than read length')","def detect_orfs_cmd(bam, ribocop_index, prefix, stranded, read_lengths, + sys.exit('Error: cannot convert psite_offsets into integers') + if len(read_lengths) != len(psite_offsets): + sys.exit('Error: psite_offsets must match read_lengths') + if not all(x >= 0 for x in psite_offsets): + sys.exit('Error: P-site offset must be >= 0') + if not all(x > y for (x, y) in zip(read_lengths, psite_offsets)): + sys.exit('Error: P-site offset must be smaller than read length')" +415,https://:@github.com/smithlabcode/ribotricer.git,9e9c9497eb5c2669bd272729e19f47e2cbf2b3db,"@@ -321,7 +321,7 @@ def prepare_orfs(gtf, fasta, prefix, min_orf_length, start_codons, + for orf in tqdm(candidate_orfs): + coordinate = ','.join( + ['{}-{}'.format(iv.start, iv.end) for iv in orf.intervals]) +- to_write = formatter.format(orf.oid, orf.category, orf.tid, orf.ttype, ++ to_write += formatter.format(orf.oid, orf.category, orf.tid, orf.ttype, + orf.gid, orf.gname, orf.gtype, orf.chrom, + orf.strand, coordinate) + +",RiboCop/prepare_orfs.py,"ReplaceText(target='+=' @(324,17)->(324,18))","def prepare_orfs(gtf, fasta, prefix, min_orf_length, start_codons, + for orf in tqdm(candidate_orfs): + coordinate = ','.join( + ['{}-{}'.format(iv.start, iv.end) for iv in orf.intervals]) + to_write = formatter.format(orf.oid, orf.category, orf.tid, orf.ttype, + orf.gid, orf.gname, orf.gtype, orf.chrom, + orf.strand, coordinate) + ","def prepare_orfs(gtf, fasta, prefix, min_orf_length, start_codons, + for orf in tqdm(candidate_orfs): + coordinate = ','.join( + ['{}-{}'.format(iv.start, iv.end) for iv in orf.intervals]) + to_write += formatter.format(orf.oid, orf.category, orf.tid, orf.ttype, + orf.gid, orf.gname, orf.gtype, orf.chrom, + orf.strand, coordinate) + " +416,https://:@github.com/pughlab/ConsensusCruncher.git,3622410b893b07afb4e423a4537eab33da26a55d,"@@ -147,7 +147,7 @@ def main(): + sscs_bam = pysam.AlignmentFile(args.infile, ""rb"") + dcs_bam = pysam.AlignmentFile(args.outfile, ""wb"", template=sscs_bam) + +- if re.search('dcs.sc', args.outfile) is None: ++ if re.search('dcs.sc', args.outfile) is not None: + sscs_singleton_bam = pysam.AlignmentFile('{}.sscs.sc.singleton.bam'.format(args.outfile.split('.dcs.sc')[0]), + ""wb"", template=sscs_bam) + dcs_header = ""DCS - Singleton Correction"" +",ConsensusCruncher/DCS_maker.py,"ReplaceText(target=' is not ' @(150,40)->(150,44))","def main(): + sscs_bam = pysam.AlignmentFile(args.infile, ""rb"") + dcs_bam = pysam.AlignmentFile(args.outfile, ""wb"", template=sscs_bam) + + if re.search('dcs.sc', args.outfile) is None: + sscs_singleton_bam = pysam.AlignmentFile('{}.sscs.sc.singleton.bam'.format(args.outfile.split('.dcs.sc')[0]), + ""wb"", template=sscs_bam) + dcs_header = ""DCS - Singleton Correction""","def main(): + sscs_bam = pysam.AlignmentFile(args.infile, ""rb"") + dcs_bam = pysam.AlignmentFile(args.outfile, ""wb"", template=sscs_bam) + + if re.search('dcs.sc', args.outfile) is not None: + sscs_singleton_bam = pysam.AlignmentFile('{}.sscs.sc.singleton.bam'.format(args.outfile.split('.dcs.sc')[0]), + ""wb"", template=sscs_bam) + dcs_header = ""DCS - Singleton Correction""" +417,https://:@github.com/django-guardian/django-guardian.git,f60306eb93fd276879806d6e78557bdb5d1ce34f,"@@ -172,7 +172,7 @@ def get_obj_perms_model(obj, base_cls, generic_cls): + for attr in fields: + model = getattr(attr, 'related_model', None) + if (model and issubclass(model, base_cls) and +- model is not generic_cls and getattr(attr, 'enabled', True)): ++ model is not generic_cls and getattr(model, 'enabled', True)): + # if model is generic one it would be returned anyway + if not model.objects.is_generic(): + # make sure that content_object's content_type is same as +",guardian/utils.py,"ReplaceText(target='model' @(175,53)->(175,57))","def get_obj_perms_model(obj, base_cls, generic_cls): + for attr in fields: + model = getattr(attr, 'related_model', None) + if (model and issubclass(model, base_cls) and + model is not generic_cls and getattr(attr, 'enabled', True)): + # if model is generic one it would be returned anyway + if not model.objects.is_generic(): + # make sure that content_object's content_type is same as","def get_obj_perms_model(obj, base_cls, generic_cls): + for attr in fields: + model = getattr(attr, 'related_model', None) + if (model and issubclass(model, base_cls) and + model is not generic_cls and getattr(model, 'enabled', True)): + # if model is generic one it would be returned anyway + if not model.objects.is_generic(): + # make sure that content_object's content_type is same as" +418,https://:@github.com/podhmo/magicalimport.git,293f619fee3f401ebe0daf55f001354ecf2a2124,"@@ -69,7 +69,7 @@ def import_symbol(sym, here=None, sep="":"", ns=None): + sym = ""{}:{}"".format(ns, sym) + module_path, fn_name = sym.rsplit(sep, 2) + try: +- module = import_module(sym, here=here, sep=sep) ++ module = import_module(module_path, here=here, sep=sep) + return getattr(module, fn_name) + except (ImportError, AttributeError) as e: + sys.stderr.write(""could not import {!r}\n{}\n"".format(sym, e)) +",magicalimport/__init__.py,"ReplaceText(target='module_path' @(72,31)->(72,34))","def import_symbol(sym, here=None, sep="":"", ns=None): + sym = ""{}:{}"".format(ns, sym) + module_path, fn_name = sym.rsplit(sep, 2) + try: + module = import_module(sym, here=here, sep=sep) + return getattr(module, fn_name) + except (ImportError, AttributeError) as e: + sys.stderr.write(""could not import {!r}\n{}\n"".format(sym, e))","def import_symbol(sym, here=None, sep="":"", ns=None): + sym = ""{}:{}"".format(ns, sym) + module_path, fn_name = sym.rsplit(sep, 2) + try: + module = import_module(module_path, here=here, sep=sep) + return getattr(module, fn_name) + except (ImportError, AttributeError) as e: + sys.stderr.write(""could not import {!r}\n{}\n"".format(sym, e))" +419,https://:@github.com/sigmavirus24/betamax.git,9d84fcffbdf41133dbdd686490c993d63e0243fc,"@@ -112,7 +112,7 @@ def deserialize_response(serialized): + for header_name, header_list in serialized['headers'].items(): + if isinstance(header_list, list): + for header_value in header_list: +- header_dict.add(header_name, header_list) ++ header_dict.add(header_name, header_value) + else: + header_dict.add(header_name, header_list) + r.headers = CaseInsensitiveDict(header_dict) +",betamax/cassette/util.py,"ReplaceText(target='header_value' @(115,45)->(115,56))","def deserialize_response(serialized): + for header_name, header_list in serialized['headers'].items(): + if isinstance(header_list, list): + for header_value in header_list: + header_dict.add(header_name, header_list) + else: + header_dict.add(header_name, header_list) + r.headers = CaseInsensitiveDict(header_dict)","def deserialize_response(serialized): + for header_name, header_list in serialized['headers'].items(): + if isinstance(header_list, list): + for header_value in header_list: + header_dict.add(header_name, header_value) + else: + header_dict.add(header_name, header_list) + r.headers = CaseInsensitiveDict(header_dict)" +420,https://:@github.com/CodyKochmann/generators.git,0c99248a9a96a675d6995855c4a9ae0efebef329,"@@ -17,7 +17,7 @@ def itemgetter(iterable, indexes): + for i,x in enumerate(iterable): + if i in positive_indexes: + out[i]=x +- negative_index_buffer.append(i) ++ negative_index_buffer.append(x) + out.update({ni:negative_index_buffer[ni] for ni in negative_indexes}) + else: + # if just positive results +",generators/itemgetter.py,"ReplaceText(target='x' @(20,41)->(20,42))","def itemgetter(iterable, indexes): + for i,x in enumerate(iterable): + if i in positive_indexes: + out[i]=x + negative_index_buffer.append(i) + out.update({ni:negative_index_buffer[ni] for ni in negative_indexes}) + else: + # if just positive results","def itemgetter(iterable, indexes): + for i,x in enumerate(iterable): + if i in positive_indexes: + out[i]=x + negative_index_buffer.append(x) + out.update({ni:negative_index_buffer[ni] for ni in negative_indexes}) + else: + # if just positive results" +421,https://:@github.com/reiinakano/xcessiv.git,b197e370a6f8a46f6ba3e9b77fb76f150f28edd5,"@@ -146,7 +146,7 @@ def evaluate_stacked_ensemble(path, ensemble_id): + ) + preds = [] + trues_list = [] +- for train_index, test_index in cv.split(X, y): ++ for train_index, test_index in cv.split(secondary_features, y): + X_train, X_test = secondary_features[train_index], secondary_features[test_index] + y_train, y_test = y[train_index], y[test_index] + est = est.fit(X_train, y_train) +",xcessiv/rqtasks.py,"ReplaceText(target='secondary_features' @(149,52)->(149,53))","def evaluate_stacked_ensemble(path, ensemble_id): + ) + preds = [] + trues_list = [] + for train_index, test_index in cv.split(X, y): + X_train, X_test = secondary_features[train_index], secondary_features[test_index] + y_train, y_test = y[train_index], y[test_index] + est = est.fit(X_train, y_train)","def evaluate_stacked_ensemble(path, ensemble_id): + ) + preds = [] + trues_list = [] + for train_index, test_index in cv.split(secondary_features, y): + X_train, X_test = secondary_features[train_index], secondary_features[test_index] + y_train, y_test = y[train_index], y[test_index] + est = est.fit(X_train, y_train)" +422,https://:@github.com/MosesofEgypt/mozzarilla.git,5c0f1e29111be71edbb67ef13094a0cdc83d760c,"@@ -684,7 +684,7 @@ def _compile_model_animations(self): + print(error) + + self.update() +- if messagebox.askyesno( ++ if not messagebox.askyesno( + ""Model_animations compilation failed"", + ""Errors occurred while compiling animations(check console). "" + ""Do you want to save the model_animations tag anyway?"", +",mozzarilla/tools/animations_compiler_window.py,"ReplaceText(target='not ' @(687,15)->(687,15))","def _compile_model_animations(self): + print(error) + + self.update() + if messagebox.askyesno( + ""Model_animations compilation failed"", + ""Errors occurred while compiling animations(check console). "" + ""Do you want to save the model_animations tag anyway?"",","def _compile_model_animations(self): + print(error) + + self.update() + if not messagebox.askyesno( + ""Model_animations compilation failed"", + ""Errors occurred while compiling animations(check console). "" + ""Do you want to save the model_animations tag anyway?""," +423,https://:@github.com/HeeroYui/lutin.git,9fc593fb59a192ddf5f50a96e2a6cba76dab73b6,"@@ -23,7 +23,7 @@ class System(system.System): + # no check needed ==> just add this: + self.add_module_depend(['c']) + self.add_export_flag('link-lib', 'X11') +- if env.get_isolate_system() == False: ++ if env.get_isolate_system() == True: + self.add_header_file([ + ""/usr/include/X11/*"" + ], +",lutin/z_system/lutinSystem_Linux_X11.py,"ReplaceText(target='True' @(26,33)->(26,38))","class System(system.System): + # no check needed ==> just add this: + self.add_module_depend(['c']) + self.add_export_flag('link-lib', 'X11') + if env.get_isolate_system() == False: + self.add_header_file([ + ""/usr/include/X11/*"" + ],","class System(system.System): + # no check needed ==> just add this: + self.add_module_depend(['c']) + self.add_export_flag('link-lib', 'X11') + if env.get_isolate_system() == True: + self.add_header_file([ + ""/usr/include/X11/*"" + ]," +424,https://:@github.com/sanger-pathogens/ariba.git,8625628cf307e533bb6e778d9b8e936e48cef727,"@@ -294,7 +294,7 @@ class ReferenceData: + def sanity_check(self, outprefix): + variants_only_removed = self._remove_bad_genes(self.seq_dicts['variants_only'], outprefix + '.00.check_fasta_variants_only.log') + presence_absence_removed = self._remove_bad_genes(self.seq_dicts['presence_absence'], outprefix + '.00.check_fasta_presence_absence.log') +- self._filter_bad_variant_data(outprefix + '.01.check_variants', variants_only_removed, presence_absence_removed) ++ self._filter_bad_variant_data(outprefix + '.01.check_variants', presence_absence_removed, variants_only_removed) + + + @classmethod +",ariba/reference_data.py,"ArgSwap(idxs=1<->2 @(297,8)->(297,37))","class ReferenceData: + def sanity_check(self, outprefix): + variants_only_removed = self._remove_bad_genes(self.seq_dicts['variants_only'], outprefix + '.00.check_fasta_variants_only.log') + presence_absence_removed = self._remove_bad_genes(self.seq_dicts['presence_absence'], outprefix + '.00.check_fasta_presence_absence.log') + self._filter_bad_variant_data(outprefix + '.01.check_variants', variants_only_removed, presence_absence_removed) + + + @classmethod","class ReferenceData: + def sanity_check(self, outprefix): + variants_only_removed = self._remove_bad_genes(self.seq_dicts['variants_only'], outprefix + '.00.check_fasta_variants_only.log') + presence_absence_removed = self._remove_bad_genes(self.seq_dicts['presence_absence'], outprefix + '.00.check_fasta_presence_absence.log') + self._filter_bad_variant_data(outprefix + '.01.check_variants', presence_absence_removed, variants_only_removed) + + + @classmethod" +425,https://:@github.com/sanger-pathogens/ariba.git,c70bc90299a1c5a85f20127ac8c750925219316b,"@@ -192,7 +192,7 @@ class Summary: + if self.show_known_het and (cluster, variant) in all_het_snps: + rows[filename][cluster][key + '.%'] = 'NA' + +- if self.show_known_het and (ref_name, variant) in all_het_snps and key + '.%' not in rows[filename][cluster]: ++ if self.show_known_het and (cluster, variant) in all_het_snps and key + '.%' not in rows[filename][cluster]: + rows[filename][cluster][key + '.%'] = 'NA' + + for key, wanted in self.cluster_columns.items(): +",ariba/summary.py,"ReplaceText(target='cluster' @(195,52)->(195,60))","class Summary: + if self.show_known_het and (cluster, variant) in all_het_snps: + rows[filename][cluster][key + '.%'] = 'NA' + + if self.show_known_het and (ref_name, variant) in all_het_snps and key + '.%' not in rows[filename][cluster]: + rows[filename][cluster][key + '.%'] = 'NA' + + for key, wanted in self.cluster_columns.items():","class Summary: + if self.show_known_het and (cluster, variant) in all_het_snps: + rows[filename][cluster][key + '.%'] = 'NA' + + if self.show_known_het and (cluster, variant) in all_het_snps and key + '.%' not in rows[filename][cluster]: + rows[filename][cluster][key + '.%'] = 'NA' + + for key, wanted in self.cluster_columns.items():" +426,https://:@github.com/sanger-pathogens/ariba.git,1fd2c639e7b24a69252390744ae4e1a9e49db5dd,"@@ -47,7 +47,7 @@ class MlstReporter: + depths = [int(x) for x in d['smtls_nts_depth'].split(',')] + depths.sort() + het_pc = round(100.0 * depths[-1] / sum(depths), 2) +- if results['hetmin'] == '.' or results['hetmin'] < het_pc: ++ if results['hetmin'] == '.' or results['hetmin'] > het_pc: + results['hetmin'] = het_pc + if len(het_data): + results['hets'] = '.'.join(het_data) +",ariba/mlst_reporter.py,"ReplaceText(target='>' @(50,69)->(50,70))","class MlstReporter: + depths = [int(x) for x in d['smtls_nts_depth'].split(',')] + depths.sort() + het_pc = round(100.0 * depths[-1] / sum(depths), 2) + if results['hetmin'] == '.' or results['hetmin'] < het_pc: + results['hetmin'] = het_pc + if len(het_data): + results['hets'] = '.'.join(het_data)","class MlstReporter: + depths = [int(x) for x in d['smtls_nts_depth'].split(',')] + depths.sort() + het_pc = round(100.0 * depths[-1] / sum(depths), 2) + if results['hetmin'] == '.' or results['hetmin'] > het_pc: + results['hetmin'] = het_pc + if len(het_data): + results['hets'] = '.'.join(het_data)" +427,https://:@github.com/urschrei/pyzotero.git,cdfd191116363c947fc0a0d0b4f37849d709f9f2,"@@ -40,7 +40,7 @@ def check(): + return library_version == git_version + + if __name__ == '__main__': +- if check(): ++ if not check(): + sys.exit(1) + else: + sys.exit(0) +",pre-deploy.py,"ReplaceText(target='not ' @(43,7)->(43,7))","def check(): + return library_version == git_version + + if __name__ == '__main__': + if check(): + sys.exit(1) + else: + sys.exit(0)","def check(): + return library_version == git_version + + if __name__ == '__main__': + if not check(): + sys.exit(1) + else: + sys.exit(0)" +428,https://:@github.com/lyft/confidant.git,5de06bb144ad392dba5ef9c75603eb9587dfcfe3,"@@ -410,7 +410,7 @@ def update_credential(id): + include_credential_pairs=True, + ) + credential_response.permissions = permissions +- return credential_response_schema.dumps(permissions) ++ return credential_response_schema.dumps(credential_response) + + + @blueprint.route('/v1/credentials//', methods=['PUT']) +",confidant/routes/credentials.py,"ReplaceText(target='credential_response' @(413,44)->(413,55))","def update_credential(id): + include_credential_pairs=True, + ) + credential_response.permissions = permissions + return credential_response_schema.dumps(permissions) + + + @blueprint.route('/v1/credentials//', methods=['PUT'])","def update_credential(id): + include_credential_pairs=True, + ) + credential_response.permissions = permissions + return credential_response_schema.dumps(credential_response) + + + @blueprint.route('/v1/credentials//', methods=['PUT'])" +429,https://:@github.com/cloudenvy/cloudenvy.git,a19f6f84832b1dfddbf5ad7b1e84790842b22712,"@@ -35,7 +35,7 @@ class Files(cloudenvy.envy.Command): + logging.info(""Copying file from '%s' to '%s'"", + local_path, remote_path) + +- if os.path.exists(local_path): ++ if not os.path.exists(local_path): + logging.error(""Local file '%s' not found."", local_path) + + dest_dir = _parse_directory(remote_path) +",cloudenvy/commands/files.py,"ReplaceText(target='not ' @(38,23)->(38,23))","class Files(cloudenvy.envy.Command): + logging.info(""Copying file from '%s' to '%s'"", + local_path, remote_path) + + if os.path.exists(local_path): + logging.error(""Local file '%s' not found."", local_path) + + dest_dir = _parse_directory(remote_path)","class Files(cloudenvy.envy.Command): + logging.info(""Copying file from '%s' to '%s'"", + local_path, remote_path) + + if not os.path.exists(local_path): + logging.error(""Local file '%s' not found."", local_path) + + dest_dir = _parse_directory(remote_path)" +430,https://:@github.com/WeiXuanChan/autoD.git,e163474f70ed6a02f39cd6edaa298271e5f23327,"@@ -520,7 +520,7 @@ class Imaginary(AD): + class Absolute(AD): + def __init__(self,func): + self.func=func +- self.abs=(Real(func)**2.-Imaginary(func)**2.)**0.5 ++ self.abs=(Real(func)**2.+Imaginary(func)**2.)**0.5 + try: + self.dependent=func.dependent[:] + except AttributeError: +",autoD.py,"ReplaceText(target='+' @(523,32)->(523,33))","class Imaginary(AD): + class Absolute(AD): + def __init__(self,func): + self.func=func + self.abs=(Real(func)**2.-Imaginary(func)**2.)**0.5 + try: + self.dependent=func.dependent[:] + except AttributeError:","class Imaginary(AD): + class Absolute(AD): + def __init__(self,func): + self.func=func + self.abs=(Real(func)**2.+Imaginary(func)**2.)**0.5 + try: + self.dependent=func.dependent[:] + except AttributeError:" +431,https://:@github.com/dwavesystems/dimod.git,79979454139757bd49c1e31c67d890c1d5efeee2,"@@ -279,7 +279,7 @@ class PolyScaleComposite(ComposedPolySampler): + # we need to know how much we scaled by, which we can do by looking + # at the biases + try: +- v = next((v for v, bias in poly.items() if bias)) ++ v = next((v for v, bias in original.items() if bias)) + except StopIteration: + # nothing to scale + scalar = 1 +",dimod/reference/composites/higherordercomposites.py,"ReplaceText(target='original' @(282,43)->(282,47))","class PolyScaleComposite(ComposedPolySampler): + # we need to know how much we scaled by, which we can do by looking + # at the biases + try: + v = next((v for v, bias in poly.items() if bias)) + except StopIteration: + # nothing to scale + scalar = 1","class PolyScaleComposite(ComposedPolySampler): + # we need to know how much we scaled by, which we can do by looking + # at the biases + try: + v = next((v for v, bias in original.items() if bias)) + except StopIteration: + # nothing to scale + scalar = 1" +432,https://:@github.com/dwavesystems/dimod.git,c21ee99ab65a519b822689361fcfcc66ffb890f2,"@@ -2146,7 +2146,7 @@ class TestSerialization(unittest.TestCase): + new = dimod.BinaryQuadraticModel.from_serializable(bqm.to_serializable(use_bytes=True)) + + self.assertEqual(bqm, new) +- self.assertEqual(bqm.info, {""tag"": 5}) ++ self.assertEqual(new.info, {""tag"": 5}) + + + class TestZeroField(unittest.TestCase): +",tests/test_binary_quadratic_model.py,"ReplaceText(target='new' @(2149,25)->(2149,28))","class TestSerialization(unittest.TestCase): + new = dimod.BinaryQuadraticModel.from_serializable(bqm.to_serializable(use_bytes=True)) + + self.assertEqual(bqm, new) + self.assertEqual(bqm.info, {""tag"": 5}) + + + class TestZeroField(unittest.TestCase):","class TestSerialization(unittest.TestCase): + new = dimod.BinaryQuadraticModel.from_serializable(bqm.to_serializable(use_bytes=True)) + + self.assertEqual(bqm, new) + self.assertEqual(new.info, {""tag"": 5}) + + + class TestZeroField(unittest.TestCase):" +433,https://:@github.com/dwavesystems/dimod.git,ceee47e049c2c3305d459c6ae865a430dbd113e9,"@@ -197,7 +197,7 @@ def ran_r(r, graph, cls=BinaryQuadraticModel, seed=None): + rvals = np.empty(2*r) + rvals[0:r] = range(-r, 0) + rvals[r:] = range(1, r+1) +- qdata = rnd.choice(rvals, size=len(variables)) ++ qdata = rnd.choice(rvals, size=len(irow)) + + offset = 0 + +",dimod/generators/random.py,"ReplaceText(target='irow' @(200,39)->(200,48))","def ran_r(r, graph, cls=BinaryQuadraticModel, seed=None): + rvals = np.empty(2*r) + rvals[0:r] = range(-r, 0) + rvals[r:] = range(1, r+1) + qdata = rnd.choice(rvals, size=len(variables)) + + offset = 0 + ","def ran_r(r, graph, cls=BinaryQuadraticModel, seed=None): + rvals = np.empty(2*r) + rvals[0:r] = range(-r, 0) + rvals[r:] = range(1, r+1) + qdata = rnd.choice(rvals, size=len(irow)) + + offset = 0 + " +434,https://:@github.com/dvdotsenko/jsonrpc.py.git,92ad90db194c878cb2023e97758671d72c976797,"@@ -75,7 +75,7 @@ class JSONPRCWSGIApplicationTestSuite(TestCase): + + response_json = responses_data[0] + assert 'error' not in response_json +- assert response_json['id'] == request2['id'] ++ assert response_json['id'] == request1['id'] + assert response_json['result'] == 5 + + response_json = responses_data[1] +",tests/test_wsgi_application.py,"ReplaceText(target='request1' @(78,38)->(78,46))","class JSONPRCWSGIApplicationTestSuite(TestCase): + + response_json = responses_data[0] + assert 'error' not in response_json + assert response_json['id'] == request2['id'] + assert response_json['result'] == 5 + + response_json = responses_data[1]","class JSONPRCWSGIApplicationTestSuite(TestCase): + + response_json = responses_data[0] + assert 'error' not in response_json + assert response_json['id'] == request1['id'] + assert response_json['result'] == 5 + + response_json = responses_data[1]" +435,https://:@github.com/MarSoft/ses-mailer-2.git,8c1b6aafc09412a6b6b2b1a69337ccbd99fc43f2,"@@ -264,7 +264,7 @@ class Mail(object): + for ob in optional_blocks: + if ob in blocks: + if ob == ""format"" and \ +- mail_params[ob].lower() not in [""html"", ""text""]: ++ blocks[ob].lower() not in [""html"", ""text""]: + continue + mail_params[ob] = blocks[ob] + return mail_params +",ses_mailer.py,"ReplaceText(target='blocks' @(267,24)->(267,35))","class Mail(object): + for ob in optional_blocks: + if ob in blocks: + if ob == ""format"" and \ + mail_params[ob].lower() not in [""html"", ""text""]: + continue + mail_params[ob] = blocks[ob] + return mail_params","class Mail(object): + for ob in optional_blocks: + if ob in blocks: + if ob == ""format"" and \ + blocks[ob].lower() not in [""html"", ""text""]: + continue + mail_params[ob] = blocks[ob] + return mail_params" +436,https://:@github.com/interpretml/interpret.git,dfae1d47394d50472e25717c53c245cbe9f8a5ad,"@@ -1067,7 +1067,7 @@ class BaseEBM(BaseEstimator): + ""scores_range"": bounds, + } + feature_list.append(feature_dict) +- density_dict.append({}) ++ density_list.append({}) + + data_dict = { + ""type"": ""pairwise"", +",python/interpret/glassbox/ebm/ebm.py,"ReplaceText(target='density_list' @(1070,16)->(1070,28))","class BaseEBM(BaseEstimator): + ""scores_range"": bounds, + } + feature_list.append(feature_dict) + density_dict.append({}) + + data_dict = { + ""type"": ""pairwise"",","class BaseEBM(BaseEstimator): + ""scores_range"": bounds, + } + feature_list.append(feature_dict) + density_list.append({}) + + data_dict = { + ""type"": ""pairwise""," +437,https://:@gitlab.com/serial-lab/random-flavorpack.git,e69ba47e04a84e1746363a93d33bfe2ca9581cd5,"@@ -76,7 +76,7 @@ class RandomGenerator(Generator): + if maximum <= minimum: + raise ValueError( + _(""The maximum can not be less than the minimum."")) +- if start < minimum or start >= maximum: ++ if start < minimum or start > maximum: + raise ValueError( + _(""The start must be between the minimum and maximum!"")) + rnrange = maximum - minimum +",random_flavorpack/generators/random.py,"ReplaceText(target='>' @(79,36)->(79,38))","class RandomGenerator(Generator): + if maximum <= minimum: + raise ValueError( + _(""The maximum can not be less than the minimum."")) + if start < minimum or start >= maximum: + raise ValueError( + _(""The start must be between the minimum and maximum!"")) + rnrange = maximum - minimum","class RandomGenerator(Generator): + if maximum <= minimum: + raise ValueError( + _(""The maximum can not be less than the minimum."")) + if start < minimum or start > maximum: + raise ValueError( + _(""The start must be between the minimum and maximum!"")) + rnrange = maximum - minimum" +438,https://:@github.com/Ezibenroc/PyRoaringBitMap.git,7081ceba18ccaf2ee80d3c142e6e612cf77d17d2,"@@ -779,7 +779,7 @@ class OptimizationTest(unittest.TestCase): + self.assertGreater(bm2.shrink_to_fit(), 0) + self.assertEqual(bm2.shrink_to_fit(), 0) + bm3 = cls(bm1, optimize=True) +- self.assertEqual(bm2.shrink_to_fit(), 0) ++ self.assertEqual(bm3.shrink_to_fit(), 0) + + + class VersionTest(unittest.TestCase): +",test.py,"ReplaceText(target='bm3' @(782,25)->(782,28))","class OptimizationTest(unittest.TestCase): + self.assertGreater(bm2.shrink_to_fit(), 0) + self.assertEqual(bm2.shrink_to_fit(), 0) + bm3 = cls(bm1, optimize=True) + self.assertEqual(bm2.shrink_to_fit(), 0) + + + class VersionTest(unittest.TestCase):","class OptimizationTest(unittest.TestCase): + self.assertGreater(bm2.shrink_to_fit(), 0) + self.assertEqual(bm2.shrink_to_fit(), 0) + bm3 = cls(bm1, optimize=True) + self.assertEqual(bm3.shrink_to_fit(), 0) + + + class VersionTest(unittest.TestCase):" +439,https://:@github.com/Cavenfish/autogamess.git,09def521ebf6c9686479439d71aee114d554a5de,"@@ -136,8 +136,8 @@ def new_project(maindir, csvfile, ebasis_dir, initial_coords_dict=None, + + #Run Input Builder function + save_dir = maindir + 'inputs/' +- input_builder(csvfile, initial_coords_dict, ebasis_dir, +- save_dir, title.replace('/', '\n')) ++ input_builder(csvfile, save_dir, ebasis_dir, ++ initial_coords_dict, title.replace('/', '\n')) + + + return +",autogamess/new_project.py,"ArgSwap(idxs=1<->3 @(139,4)->(139,17))","def new_project(maindir, csvfile, ebasis_dir, initial_coords_dict=None, + + #Run Input Builder function + save_dir = maindir + 'inputs/' + input_builder(csvfile, initial_coords_dict, ebasis_dir, + save_dir, title.replace('/', '\n')) + + + return","def new_project(maindir, csvfile, ebasis_dir, initial_coords_dict=None, + + #Run Input Builder function + save_dir = maindir + 'inputs/' + input_builder(csvfile, save_dir, ebasis_dir, + initial_coords_dict, title.replace('/', '\n')) + + + return" +440,https://:@github.com/Cavenfish/autogamess.git,4dcbf5d1a0f9059f8bdbc1a346c8f9cced70f62d,"@@ -136,7 +136,7 @@ def new_project(maindir, csvfile, ebasis_dir, initial_coords_dict=None, + + #Run Input Builder function + save_dir = maindir + 'inputs/' +- input_builder(csvfile, save_dir, ebasis_dir, ++ input_builder(csvfile, ebasis_dir, save_dir, + initial_coords_dict, title.replace('/', '\n')) + + +",autogamess/new_project.py,"ArgSwap(idxs=1<->2 @(139,4)->(139,17))","def new_project(maindir, csvfile, ebasis_dir, initial_coords_dict=None, + + #Run Input Builder function + save_dir = maindir + 'inputs/' + input_builder(csvfile, save_dir, ebasis_dir, + initial_coords_dict, title.replace('/', '\n')) + + ","def new_project(maindir, csvfile, ebasis_dir, initial_coords_dict=None, + + #Run Input Builder function + save_dir = maindir + 'inputs/' + input_builder(csvfile, ebasis_dir, save_dir, + initial_coords_dict, title.replace('/', '\n')) + + " +441,https://:@github.com/Cavenfish/autogamess.git,3890ccfd3dc7e723a37b8b5308d59a8de0b6f807,"@@ -306,6 +306,6 @@ def fill_spreadsheets(projdir=False, sorteddir=False, sheetsdir=False): + if vsc in df: + df[vsc].to_excel(writer, sheet_name=vsc, startrow=6) + if cmp in df: +- df[cmp].to_excel(writer, sheet_name=vsc, startrow=6) ++ df[cmp].to_excel(writer, sheet_name=cmp, startrow=6) + + return +",autogamess/fill_spreadsheets.py,"ReplaceText(target='cmp' @(309,52)->(309,55))","def fill_spreadsheets(projdir=False, sorteddir=False, sheetsdir=False): + if vsc in df: + df[vsc].to_excel(writer, sheet_name=vsc, startrow=6) + if cmp in df: + df[cmp].to_excel(writer, sheet_name=vsc, startrow=6) + + return","def fill_spreadsheets(projdir=False, sorteddir=False, sheetsdir=False): + if vsc in df: + df[vsc].to_excel(writer, sheet_name=vsc, startrow=6) + if cmp in df: + df[cmp].to_excel(writer, sheet_name=cmp, startrow=6) + + return" +442,https://:@github.com/EntilZha/ScalaFunctional.git,8426ff978b84cb4125052ad842ae5db64eaf42f3,"@@ -185,6 +185,6 @@ class TestStreams(unittest.TestCase): + + # test insert into a connection + with sqlite3.connect(tmp_path) as conn: +- seq(elements).to_sqlite3(tmp_path, insert_sql) ++ seq(elements).to_sqlite3(conn, insert_sql) + result = seq.sqlite3(conn, ""SELECT id, name FROM user;"").to_list() + self.assertListEqual(elements, result) +",functional/test/test_streams.py,"ReplaceText(target='conn' @(188,37)->(188,45))","class TestStreams(unittest.TestCase): + + # test insert into a connection + with sqlite3.connect(tmp_path) as conn: + seq(elements).to_sqlite3(tmp_path, insert_sql) + result = seq.sqlite3(conn, ""SELECT id, name FROM user;"").to_list() + self.assertListEqual(elements, result)","class TestStreams(unittest.TestCase): + + # test insert into a connection + with sqlite3.connect(tmp_path) as conn: + seq(elements).to_sqlite3(conn, insert_sql) + result = seq.sqlite3(conn, ""SELECT id, name FROM user;"").to_list() + self.assertListEqual(elements, result)" +443,https://:@github.com/wesselb/stheno.git,32d55bf855f88067e689684eaa5d6f9e8c7604d6,"@@ -80,7 +80,7 @@ class Kernel(Referentiable): + def feat_map(x): + scale = 2 * B.pi / B.cast(period, x.dtype) + return B.concatenate((B.sin(x * scale), +- B.cos(x * scale)), axis=0) ++ B.cos(x * scale)), axis=1) + + return Kernel(lambda x, y: self.f(feat_map(x), feat_map(y))) + +",stheno/kernel.py,"ReplaceText(target='1' @(83,59)->(83,60))","class Kernel(Referentiable): + def feat_map(x): + scale = 2 * B.pi / B.cast(period, x.dtype) + return B.concatenate((B.sin(x * scale), + B.cos(x * scale)), axis=0) + + return Kernel(lambda x, y: self.f(feat_map(x), feat_map(y))) + ","class Kernel(Referentiable): + def feat_map(x): + scale = 2 * B.pi / B.cast(period, x.dtype) + return B.concatenate((B.sin(x * scale), + B.cos(x * scale)), axis=1) + + return Kernel(lambda x, y: self.f(feat_map(x), feat_map(y))) + " +444,https://:@github.com/djgagne/hagelslag.git,7ef4f68645a7b7146f21813f2b39a0a7208b0fdb,"@@ -19,7 +19,7 @@ class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): +- core_labels, n_labels = label(data <= self.max_intensity) ++ core_labels, n_labels = label(data >= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + +",hagelslag/processing/Watershed.py,"ReplaceText(target='>=' @(22,43)->(22,45))","class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): + core_labels, n_labels = label(data <= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + ","class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): + core_labels, n_labels = label(data >= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + " +445,https://:@github.com/djgagne/hagelslag.git,28dbda86b4244802a1651a808dfcfe0dbdeb62e3,"@@ -19,7 +19,7 @@ class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): +- core_labels, n_labels = label(data >= self.max_intensity) ++ core_labels, n_labels = label(data <= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + +",hagelslag/processing/Watershed.py,"ReplaceText(target='<=' @(22,43)->(22,45))","class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): + core_labels, n_labels = label(data >= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + ","class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): + core_labels, n_labels = label(data <= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + " +446,https://:@github.com/djgagne/hagelslag.git,be189c11c1135f782bb30529f58dff78e99f4c8e,"@@ -19,7 +19,7 @@ class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): +- core_labels, n_labels = label(data <= self.max_intensity) ++ core_labels, n_labels = label(data >= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + +",hagelslag/processing/Watershed.py,"ReplaceText(target='>=' @(22,43)->(22,45))","class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): + core_labels, n_labels = label(data <= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + ","class Watershed(object): + self.max_intensity = max_intensity + + def label(self, data): + core_labels, n_labels = label(data >= self.max_intensity) + ws_labels = watershed(data.max() - data, markers=core_labels, mask=data >= self.min_intensity) + return ws_labels + " +447,https://:@github.com/ICRAR/daliuge.git,72b08c308f61bc4e9006976fc9e63f3638fad9e8,"@@ -604,7 +604,7 @@ def chiles_pg(): + total_bandwidth = 480 + num_obs = 8 # the same as num of data island + subband_width = 60 # MHz +- num_subb = total_bandwidth / subband_width ++ num_subb = total_bandwidth // subband_width + subband_dict = collections.defaultdict(list) # for corner turning + img_list = [] + start_freq = 940 +",test/graphsRepository.py,"ReplaceText(target='//' @(607,31)->(607,32))","def chiles_pg(): + total_bandwidth = 480 + num_obs = 8 # the same as num of data island + subband_width = 60 # MHz + num_subb = total_bandwidth / subband_width + subband_dict = collections.defaultdict(list) # for corner turning + img_list = [] + start_freq = 940","def chiles_pg(): + total_bandwidth = 480 + num_obs = 8 # the same as num of data island + subband_width = 60 # MHz + num_subb = total_bandwidth // subband_width + subband_dict = collections.defaultdict(list) # for corner turning + img_list = [] + start_freq = 940" +448,https://:@github.com/ICRAR/daliuge.git,00eb7a92f6679df09650e2e8054e9163f0089785,"@@ -115,7 +115,7 @@ class TestDM(unittest.TestCase): + a.setCompleted() + + for dm, drop in (dm1,a), (dm2,b), (dm2,c): +- self.assertEqual(DROPStates.COMPLETED, dm.get_drop_property(sessionId, 'status', drop.uid)) ++ self.assertEqual(DROPStates.COMPLETED, dm.get_drop_property(sessionId, drop.uid, 'status')) + self.assertEqual(a.checksum, int(droputils.allDropContents(c))) + + for dropProxy in a,b,c: +",test/manager/test_dm.py,"ArgSwap(idxs=1<->2 @(118,51)->(118,71))","class TestDM(unittest.TestCase): + a.setCompleted() + + for dm, drop in (dm1,a), (dm2,b), (dm2,c): + self.assertEqual(DROPStates.COMPLETED, dm.get_drop_property(sessionId, 'status', drop.uid)) + self.assertEqual(a.checksum, int(droputils.allDropContents(c))) + + for dropProxy in a,b,c:","class TestDM(unittest.TestCase): + a.setCompleted() + + for dm, drop in (dm1,a), (dm2,b), (dm2,c): + self.assertEqual(DROPStates.COMPLETED, dm.get_drop_property(sessionId, drop.uid, 'status')) + self.assertEqual(a.checksum, int(droputils.allDropContents(c))) + + for dropProxy in a,b,c:" +449,https://:@github.com/ICRAR/daliuge.git,a45bf6f0b7e2fa2627b7e4faa18324aa1087d8f5,"@@ -167,7 +167,7 @@ class DockerTests(unittest.TestCase): + c = FileDROP('c', 'c') + b.addInput(a) + b.addOutput(c) +- with DROPWaiterCtx(self, b, 100): ++ with DROPWaiterCtx(self, c, 100): + a.setCompleted() + self.assertEqual(six.b(a.dataURL), droputils.allDropContents(c)) + +",test/apps/test_docker.py,"ReplaceText(target='c' @(170,33)->(170,34))","class DockerTests(unittest.TestCase): + c = FileDROP('c', 'c') + b.addInput(a) + b.addOutput(c) + with DROPWaiterCtx(self, b, 100): + a.setCompleted() + self.assertEqual(six.b(a.dataURL), droputils.allDropContents(c)) + ","class DockerTests(unittest.TestCase): + c = FileDROP('c', 'c') + b.addInput(a) + b.addOutput(c) + with DROPWaiterCtx(self, c, 100): + a.setCompleted() + self.assertEqual(six.b(a.dataURL), droputils.allDropContents(c)) + " +450,https://:@github.com/ICRAR/daliuge.git,882b2feb9672662c5347bf0b11ce06b0e7529be8,"@@ -512,7 +512,7 @@ class LogParser(object): + for dim_log_f in possible_logs: + if (os.path.exists(dim_log_f)): + self._dim_log_f = [dim_log_f] +- if (dim_log_f == possible_logs[1]): ++ if (dim_log_f == possible_logs[0]): + cluster_log = os.path.join(log_dir, '0', 'start_dlg_cluster.log') + if (os.path.exists(cluster_log)): + self._dim_log_f.append(cluster_log) +",dlg/deploy/pawsey/scale_test.py,"ReplaceText(target='0' @(515,47)->(515,48))","class LogParser(object): + for dim_log_f in possible_logs: + if (os.path.exists(dim_log_f)): + self._dim_log_f = [dim_log_f] + if (dim_log_f == possible_logs[1]): + cluster_log = os.path.join(log_dir, '0', 'start_dlg_cluster.log') + if (os.path.exists(cluster_log)): + self._dim_log_f.append(cluster_log)","class LogParser(object): + for dim_log_f in possible_logs: + if (os.path.exists(dim_log_f)): + self._dim_log_f = [dim_log_f] + if (dim_log_f == possible_logs[0]): + cluster_log = os.path.join(log_dir, '0', 'start_dlg_cluster.log') + if (os.path.exists(cluster_log)): + self._dim_log_f.append(cluster_log)" +451,https://:@github.com/ICRAR/daliuge.git,f1204971537d6fa5e972cd96c963f907166dd291,"@@ -952,7 +952,7 @@ class KFamilyPartition(Partition): + kwargs['weight'] = self_global_dag.node[u].get('weight', 5) + self._dag.add_node(u, **kwargs) + for k in self._w_attr: +- self._tmp_max_dop[_w_attr] = get_max_weighted_antichain(self._dag, w_attr=k)[0] ++ self._tmp_max_dop[k] = get_max_weighted_antichain(self._dag, w_attr=k)[0] + self._max_dop = self._tmp_max_dop + + def can_merge(self, that, u, v): +",dlg/dropmake/scheduler.py,"ReplaceText(target='k' @(955,30)->(955,37))","class KFamilyPartition(Partition): + kwargs['weight'] = self_global_dag.node[u].get('weight', 5) + self._dag.add_node(u, **kwargs) + for k in self._w_attr: + self._tmp_max_dop[_w_attr] = get_max_weighted_antichain(self._dag, w_attr=k)[0] + self._max_dop = self._tmp_max_dop + + def can_merge(self, that, u, v):","class KFamilyPartition(Partition): + kwargs['weight'] = self_global_dag.node[u].get('weight', 5) + self._dag.add_node(u, **kwargs) + for k in self._w_attr: + self._tmp_max_dop[k] = get_max_weighted_antichain(self._dag, w_attr=k)[0] + self._max_dop = self._tmp_max_dop + + def can_merge(self, that, u, v):" +452,https://:@github.com/ICRAR/daliuge.git,6a91d4338a9a90bc2413e4e78c9ed8ca02264ae4,"@@ -2225,7 +2225,7 @@ def partition(pgt, algo, num_partitions=1, num_islands=1, + + elif algo == ALGO_MIN_NUM_PARTS: + time_greedy = 1 - time_greedy / 100.0 # assuming between 1 to 100 +- pgt = MinNumPartsPGTP(pgt, deadline, num_partitions, partition_label, max_dop, merge_parts=could_merge, optimistic_factor=time_greedy) ++ pgt = MinNumPartsPGTP(pgt, deadline, num_partitions, partition_label, max_cpu, merge_parts=could_merge, optimistic_factor=time_greedy) + + elif algo == ALGO_PSO: + pgt = PSOPGTP(pgt, partition_label, max_dop, deadline=deadline, topk=topk, swarm_size=swarm_size, merge_parts=could_merge) +",dlg/dropmake/pg_generator.py,"ReplaceText(target='max_cpu' @(2228,79)->(2228,86))","def partition(pgt, algo, num_partitions=1, num_islands=1, + + elif algo == ALGO_MIN_NUM_PARTS: + time_greedy = 1 - time_greedy / 100.0 # assuming between 1 to 100 + pgt = MinNumPartsPGTP(pgt, deadline, num_partitions, partition_label, max_dop, merge_parts=could_merge, optimistic_factor=time_greedy) + + elif algo == ALGO_PSO: + pgt = PSOPGTP(pgt, partition_label, max_dop, deadline=deadline, topk=topk, swarm_size=swarm_size, merge_parts=could_merge)","def partition(pgt, algo, num_partitions=1, num_islands=1, + + elif algo == ALGO_MIN_NUM_PARTS: + time_greedy = 1 - time_greedy / 100.0 # assuming between 1 to 100 + pgt = MinNumPartsPGTP(pgt, deadline, num_partitions, partition_label, max_cpu, merge_parts=could_merge, optimistic_factor=time_greedy) + + elif algo == ALGO_PSO: + pgt = PSOPGTP(pgt, partition_label, max_dop, deadline=deadline, topk=topk, swarm_size=swarm_size, merge_parts=could_merge)" +453,https://:@github.com/ICRAR/daliuge.git,885ea31e59129d694329161da7acf7e8f2654348,"@@ -96,7 +96,7 @@ def check_hosts(ips, port, timeout=None, check_with_session=False, retry=1): + logger.info(""Host %s:%d is running"", ip, port) + return ip + logger.warning(""Failed to contact host %s:%d"", ip, port) +- ntries -= 0 ++ ntries -= 1 + return None + + # Don't return None values +",dlg/deploy/pawsey/start_dfms_cluster.py,"ReplaceText(target='1' @(99,22)->(99,23))","def check_hosts(ips, port, timeout=None, check_with_session=False, retry=1): + logger.info(""Host %s:%d is running"", ip, port) + return ip + logger.warning(""Failed to contact host %s:%d"", ip, port) + ntries -= 0 + return None + + # Don't return None values","def check_hosts(ips, port, timeout=None, check_with_session=False, retry=1): + logger.info(""Host %s:%d is running"", ip, port) + return ip + logger.warning(""Failed to contact host %s:%d"", ip, port) + ntries -= 1 + return None + + # Don't return None values" +454,https://:@github.com/ICRAR/daliuge.git,ca615527deef8c147aaad3c64755b5f3d89b65b8,"@@ -56,7 +56,7 @@ def timed_import(module_name): + """"""Imports `module_name` and log how long it took to import it"""""" + start = time.time() + module = importlib.import_module(module_name) +- logger.info('Imported %s in %.3f seconds', module, time.time() - start) ++ logger.info('Imported %s in %.3f seconds', module_name, time.time() - start) + return module + + +",dlg/utils.py,"ReplaceText(target='module_name' @(59,47)->(59,53))","def timed_import(module_name): + """"""Imports `module_name` and log how long it took to import it"""""" + start = time.time() + module = importlib.import_module(module_name) + logger.info('Imported %s in %.3f seconds', module, time.time() - start) + return module + + ","def timed_import(module_name): + """"""Imports `module_name` and log how long it took to import it"""""" + start = time.time() + module = importlib.import_module(module_name) + logger.info('Imported %s in %.3f seconds', module_name, time.time() - start) + return module + + " +455,https://:@github.com/JRCSTU/co2mpas-ta.git,8e8557c3590acc6942bcabc7167de3767681e48b,"@@ -419,7 +419,7 @@ def define_alternator_status_model( + if soc < dn_soc or (prev_status == 1 and soc < up_soc): + status = 1 + +- elif has_energy_recuperation and gear_box_power_in >= 0: ++ elif has_energy_recuperation and gear_box_power_in < 0: + status = 2 + + return status +",co2mpas/functions/physical/electrics/__init__.py,"ReplaceText(target='<' @(422,63)->(422,65))","def define_alternator_status_model( + if soc < dn_soc or (prev_status == 1 and soc < up_soc): + status = 1 + + elif has_energy_recuperation and gear_box_power_in >= 0: + status = 2 + + return status","def define_alternator_status_model( + if soc < dn_soc or (prev_status == 1 and soc < up_soc): + status = 1 + + elif has_energy_recuperation and gear_box_power_in < 0: + status = 2 + + return status" +456,https://:@github.com/JRCSTU/co2mpas-ta.git,b155780da4cd2489da6c06da12e0c4df41534ab5,"@@ -2766,8 +2766,8 @@ class Dispatcher(object): + + elif node_id in dists: # The node w already estimated. + if dist < dists[node_id]: # Error for negative paths. +- raise DispatcherError('Contradictory paths found: ' +- 'negative weights?', self) ++ raise DispatcherError(self, 'Contradictory paths found: ' ++ 'negative weights?') + elif node_id not in seen or dist < seen[node_id]: # Check min dist. + seen[node_id] = dist # Update dist. + +",co2mpas/dispatcher/__init__.py,"ArgSwap(idxs=0<->1 @(2769,22)->(2769,37))","class Dispatcher(object): + + elif node_id in dists: # The node w already estimated. + if dist < dists[node_id]: # Error for negative paths. + raise DispatcherError('Contradictory paths found: ' + 'negative weights?', self) + elif node_id not in seen or dist < seen[node_id]: # Check min dist. + seen[node_id] = dist # Update dist. + ","class Dispatcher(object): + + elif node_id in dists: # The node w already estimated. + if dist < dists[node_id]: # Error for negative paths. + raise DispatcherError(self, 'Contradictory paths found: ' + 'negative weights?') + elif node_id not in seen or dist < seen[node_id]: # Check min dist. + seen[node_id] = dist # Update dist. + " +457,https://:@github.com/JRCSTU/co2mpas-ta.git,46830a3edd1490d499b8f0e788ce87efe873d264,"@@ -225,7 +225,7 @@ def _predict_electrics( + alternator_current = calculate_alternator_current( + alternator_status, on_engine, gear_box_power_in, + alternator_current_model, engine_start_current, +- prev_battery_current, acceleration) ++ battery_state_of_charge, acceleration) + + battery_current = calculate_battery_current( + electric_load, alternator_current, alternator_nominal_voltage, +",co2mpas/functions/co2mpas_model/physical/electrics/electrics_prediction.py,"ReplaceText(target='battery_state_of_charge' @(228,8)->(228,28))","def _predict_electrics( + alternator_current = calculate_alternator_current( + alternator_status, on_engine, gear_box_power_in, + alternator_current_model, engine_start_current, + prev_battery_current, acceleration) + + battery_current = calculate_battery_current( + electric_load, alternator_current, alternator_nominal_voltage,","def _predict_electrics( + alternator_current = calculate_alternator_current( + alternator_status, on_engine, gear_box_power_in, + alternator_current_model, engine_start_current, + battery_state_of_charge, acceleration) + + battery_current = calculate_battery_current( + electric_load, alternator_current, alternator_nominal_voltage," +458,https://:@github.com/JRCSTU/co2mpas-ta.git,45e4f0782888c84b9c99842db88457353b45efb3,"@@ -240,7 +240,7 @@ def define_data_schema(read=True): + 'f0_uncorrected': positive, + 'f2': positive, + 'f0': positive, +- 'correct_f0': positive, ++ 'correct_f0': _bool, + + 'co2_emission_low': positive, + 'co2_emission_medium': positive, +",co2mpas/functions/io/schema.py,"ReplaceText(target='_bool' @(243,22)->(243,30))","def define_data_schema(read=True): + 'f0_uncorrected': positive, + 'f2': positive, + 'f0': positive, + 'correct_f0': positive, + + 'co2_emission_low': positive, + 'co2_emission_medium': positive,","def define_data_schema(read=True): + 'f0_uncorrected': positive, + 'f2': positive, + 'f0': positive, + 'correct_f0': _bool, + + 'co2_emission_low': positive, + 'co2_emission_medium': positive," +459,https://:@github.com/JRCSTU/co2mpas-ta.git,3fcd6ce4395980ea879bde8f1270e390e750a8ee,"@@ -3020,7 +3020,7 @@ class Dispatcher(object): + self._meet[dsp_id] = initial_dist # Set view distance. + + # Check if inputs are satisfied. +- if self.check_wait_in(node['wait_inputs'], node_id): ++ if self.check_wait_in(node['wait_inputs'], dsp_id): + return False # Pass the node + + if dsp_id not in distances: +",co2mpas/dispatcher/__init__.py,"ReplaceText(target='dsp_id' @(3023,51)->(3023,58))","class Dispatcher(object): + self._meet[dsp_id] = initial_dist # Set view distance. + + # Check if inputs are satisfied. + if self.check_wait_in(node['wait_inputs'], node_id): + return False # Pass the node + + if dsp_id not in distances:","class Dispatcher(object): + self._meet[dsp_id] = initial_dist # Set view distance. + + # Check if inputs are satisfied. + if self.check_wait_in(node['wait_inputs'], dsp_id): + return False # Pass the node + + if dsp_id not in distances:" +460,https://:@github.com/JRCSTU/co2mpas-ta.git,e3346285e51b0bba0d909746146e0be70c3090eb,"@@ -87,7 +87,7 @@ def calculate_full_load(full_load_speeds, full_load_powers, idle_engine_speed): + """""" + + pn = np.array((full_load_speeds, full_load_powers)) +- max_speed_at_max_power, max_power = pn[:, np.argmax(pn[0])] ++ max_speed_at_max_power, max_power = pn[:, np.argmax(pn[1])] + pn[1] /= max_power + idle = idle_engine_speed[0] + pn[0] = (pn[0] - idle) / (max_speed_at_max_power - idle) +",co2mpas/model/physical/engine/__init__.py,"ReplaceText(target='1' @(90,59)->(90,60))","def calculate_full_load(full_load_speeds, full_load_powers, idle_engine_speed): + """""" + + pn = np.array((full_load_speeds, full_load_powers)) + max_speed_at_max_power, max_power = pn[:, np.argmax(pn[0])] + pn[1] /= max_power + idle = idle_engine_speed[0] + pn[0] = (pn[0] - idle) / (max_speed_at_max_power - idle)","def calculate_full_load(full_load_speeds, full_load_powers, idle_engine_speed): + """""" + + pn = np.array((full_load_speeds, full_load_powers)) + max_speed_at_max_power, max_power = pn[:, np.argmax(pn[1])] + pn[1] /= max_power + idle = idle_engine_speed[0] + pn[0] = (pn[0] - idle) / (max_speed_at_max_power - idle)" +461,https://:@github.com/JRCSTU/co2mpas-ta.git,4154efcd8980a1790f2675afa14803991b4da76e,"@@ -1223,7 +1223,7 @@ def calibrate_co2_params( + + p = restrict_bounds(p) + +- p, s = calibrate_model_params(co2_error_function_on_phases, p) ++ p, s = calibrate_model_params(co2_error_function_on_emissions, p) + success.append((s, copy.deepcopy(p))) + _set_attr(p, vary) + +",co2mpas/model/physical/engine/co2_emission.py,"ReplaceText(target='co2_error_function_on_emissions' @(1226,34)->(1226,62))","def calibrate_co2_params( + + p = restrict_bounds(p) + + p, s = calibrate_model_params(co2_error_function_on_phases, p) + success.append((s, copy.deepcopy(p))) + _set_attr(p, vary) + ","def calibrate_co2_params( + + p = restrict_bounds(p) + + p, s = calibrate_model_params(co2_error_function_on_emissions, p) + success.append((s, copy.deepcopy(p))) + _set_attr(p, vary) + " +462,https://:@github.com/JRCSTU/co2mpas-ta.git,4c077512de9127f377b3802d2c82fe8ebd56f5c2,"@@ -703,7 +703,7 @@ def define_data_schema(read=True): + 'alternator_powers_demand': np_array, + 'alternator_statuses': np_array_int, + 'auxiliaries_power_losses': np_array, +- 'auxiliaries_torque_loss': positive, ++ 'auxiliaries_torque_loss': tuplefloat, + 'auxiliaries_torque_losses': np_array, + 'battery_currents': np_array, + 'clutch_tc_powers': np_array, +",co2mpas/io/schema.py,"ReplaceText(target='tuplefloat' @(706,35)->(706,43))","def define_data_schema(read=True): + 'alternator_powers_demand': np_array, + 'alternator_statuses': np_array_int, + 'auxiliaries_power_losses': np_array, + 'auxiliaries_torque_loss': positive, + 'auxiliaries_torque_losses': np_array, + 'battery_currents': np_array, + 'clutch_tc_powers': np_array,","def define_data_schema(read=True): + 'alternator_powers_demand': np_array, + 'alternator_statuses': np_array_int, + 'auxiliaries_power_losses': np_array, + 'auxiliaries_torque_loss': tuplefloat, + 'auxiliaries_torque_losses': np_array, + 'battery_currents': np_array, + 'clutch_tc_powers': np_array," +463,https://:@github.com/JRCSTU/co2mpas-ta.git,274f898a173aa42185fa5ef138035b4cb5994d28,"@@ -74,7 +74,7 @@ class TestGearBox(unittest.TestCase): + def test_calculate_torque_out(self): + wp, es, gbs = self.wp, self.es, self.ws + self.assertEquals( +- list(calculate_gear_box_torques(wp, es, gbs, 10)), list(self.tgb) ++ list(calculate_gear_box_torques(wp, gbs, es, 10)), list(self.tgb) + ) + + @unittest.skip(""to be reviewed"") +",tests/functions/test_gear_box.py,"ArgSwap(idxs=1<->2 @(77,17)->(77,43))","class TestGearBox(unittest.TestCase): + def test_calculate_torque_out(self): + wp, es, gbs = self.wp, self.es, self.ws + self.assertEquals( + list(calculate_gear_box_torques(wp, es, gbs, 10)), list(self.tgb) + ) + + @unittest.skip(""to be reviewed"")","class TestGearBox(unittest.TestCase): + def test_calculate_torque_out(self): + wp, es, gbs = self.wp, self.es, self.ws + self.assertEquals( + list(calculate_gear_box_torques(wp, gbs, es, 10)), list(self.tgb) + ) + + @unittest.skip(""to be reviewed"")" +464,https://:@github.com/JRCSTU/co2mpas-ta.git,739964622f68661a4dc35b8a60a30db5cb8475b2,"@@ -2608,7 +2608,7 @@ class Co2guiCmd(cmdlets.Cmd): + progr_bar.grid(column=1, row=1, sticky='nswe') + + if step is not None: +- if step < 0: ++ if step <= 0: + progr_var.set(-step) + else: + progr_var.set(progr_var.get() + step) +",co2mpas/co2gui/__init__.py,"ReplaceText(target='<=' @(2611,20)->(2611,21))","class Co2guiCmd(cmdlets.Cmd): + progr_bar.grid(column=1, row=1, sticky='nswe') + + if step is not None: + if step < 0: + progr_var.set(-step) + else: + progr_var.set(progr_var.get() + step)","class Co2guiCmd(cmdlets.Cmd): + progr_bar.grid(column=1, row=1, sticky='nswe') + + if step is not None: + if step <= 0: + progr_var.set(-step) + else: + progr_var.set(progr_var.get() + step)" +465,https://:@github.com/JRCSTU/co2mpas-ta.git,18af1fede3536121930c99ea0a2c94e8ffeb3bf7,"@@ -450,6 +450,6 @@ def calculate_drive_battery_currents_v2( + n_p, n_s = drive_battery_n_parallel_cells, drive_battery_n_series_cells + p = drive_battery_electric_powers + r0, ocv = drive_battery_r0, drive_battery_ocv +- x = ocv + np.nan_to_num(np.sqrt(ocv ** 2 - (4e3 * r0 / (n_s * n_p)) * p)) ++ x = ocv - np.nan_to_num(np.sqrt(ocv ** 2 - (4e3 * r0 / (n_s * n_p)) * p)) + x *= n_p / (2 * r0) + return x +",co2mpas/core/model/physical/electrics/batteries/drive.py,"ReplaceText(target='-' @(453,12)->(453,13))","def calculate_drive_battery_currents_v2( + n_p, n_s = drive_battery_n_parallel_cells, drive_battery_n_series_cells + p = drive_battery_electric_powers + r0, ocv = drive_battery_r0, drive_battery_ocv + x = ocv + np.nan_to_num(np.sqrt(ocv ** 2 - (4e3 * r0 / (n_s * n_p)) * p)) + x *= n_p / (2 * r0) + return x","def calculate_drive_battery_currents_v2( + n_p, n_s = drive_battery_n_parallel_cells, drive_battery_n_series_cells + p = drive_battery_electric_powers + r0, ocv = drive_battery_r0, drive_battery_ocv + x = ocv - np.nan_to_num(np.sqrt(ocv ** 2 - (4e3 * r0 / (n_s * n_p)) * p)) + x *= n_p / (2 * r0) + return x" +466,https://:@github.com/JRCSTU/co2mpas-ta.git,8f4cfb4afa97fc43a95b62b497f182fd72b0e379,"@@ -263,7 +263,7 @@ def calculate_service_battery_loads( + Service battery load vector [kW]. + :rtype: numpy.array + """""" +- p = service_battery_electric_powers - service_battery_electric_powers_supply ++ p = service_battery_electric_powers + service_battery_electric_powers_supply + return p + + +",co2mpas/core/model/physical/electrics/batteries/service/__init__.py,"ReplaceText(target='+' @(266,40)->(266,41))","def calculate_service_battery_loads( + Service battery load vector [kW]. + :rtype: numpy.array + """""" + p = service_battery_electric_powers - service_battery_electric_powers_supply + return p + + ","def calculate_service_battery_loads( + Service battery load vector [kW]. + :rtype: numpy.array + """""" + p = service_battery_electric_powers + service_battery_electric_powers_supply + return p + + " +467,https://:@github.com/JRCSTU/co2mpas-ta.git,52695d79acea053f5ff38a8a5d223f1907d33fb8,"@@ -46,7 +46,7 @@ def calculate_final_drive_ratios(final_drive_ratio, n_gears=1): + + # noinspection PyUnusedLocal,PyMissingOrEmptyDocstring + def is_not_manual_or_automatic(gear_box_type, *args): +- return gear_box_type in ('manual', 'automatic') ++ return gear_box_type not in ('manual', 'automatic') + + + dsp.add_function( +",co2mpas/core/model/physical/final_drive.py,"ReplaceText(target=' not in ' @(49,24)->(49,28))","def calculate_final_drive_ratios(final_drive_ratio, n_gears=1): + + # noinspection PyUnusedLocal,PyMissingOrEmptyDocstring + def is_not_manual_or_automatic(gear_box_type, *args): + return gear_box_type in ('manual', 'automatic') + + + dsp.add_function(","def calculate_final_drive_ratios(final_drive_ratio, n_gears=1): + + # noinspection PyUnusedLocal,PyMissingOrEmptyDocstring + def is_not_manual_or_automatic(gear_box_type, *args): + return gear_box_type not in ('manual', 'automatic') + + + dsp.add_function(" +468,https://:@github.com/JRCSTU/co2mpas-ta.git,401ec07523c5b34dacab9e73cf9a417dada880cb,"@@ -429,7 +429,7 @@ class CorrectGear: + + # 3.2 + j = i + np.searchsorted(times[i:], times[i] + 1) +- if not gear and up_clip(velocities, j + 1) >= up_clip(velocities, j): ++ if not gear and up_clip(velocities, j + 1) > up_clip(velocities, j): + gear = self.min_gear + + return gear +",co2mpas/core/model/physical/gear_box/at_gear/__init__.py,"ReplaceText(target='>' @(432,51)->(432,53))","class CorrectGear: + + # 3.2 + j = i + np.searchsorted(times[i:], times[i] + 1) + if not gear and up_clip(velocities, j + 1) >= up_clip(velocities, j): + gear = self.min_gear + + return gear","class CorrectGear: + + # 3.2 + j = i + np.searchsorted(times[i:], times[i] + 1) + if not gear and up_clip(velocities, j + 1) > up_clip(velocities, j): + gear = self.min_gear + + return gear" +469,https://:@github.com/JRCSTU/co2mpas-ta.git,745c3623fffca5cf7f84358f8fff87287a35525c,"@@ -125,7 +125,7 @@ def define_tau_function(after_treatment_temperature_threshold): + f = sci_sta.lognorm(max(s, dfl.EPS), 0, temp_mean).cdf + + def _tau_function(t0, t1, temp): +- return t0 - (t1 - t0) * f(temp + 273) ++ return t0 + (t1 - t0) * f(temp + 273) + + return _tau_function + +",co2mpas/core/model/physical/engine/fc.py,"ReplaceText(target='+' @(128,18)->(128,19))","def define_tau_function(after_treatment_temperature_threshold): + f = sci_sta.lognorm(max(s, dfl.EPS), 0, temp_mean).cdf + + def _tau_function(t0, t1, temp): + return t0 - (t1 - t0) * f(temp + 273) + + return _tau_function + ","def define_tau_function(after_treatment_temperature_threshold): + f = sci_sta.lognorm(max(s, dfl.EPS), 0, temp_mean).cdf + + def _tau_function(t0, t1, temp): + return t0 + (t1 - t0) * f(temp + 273) + + return _tau_function + " +470,https://:@github.com/RasaHQ/rasa.git,57d15923475ec8b5361cd6f84f327d864253746a,"@@ -33,7 +33,7 @@ def run_train(_config): + + def load_interpreter_for_model(nlp, config, persisted_path): + metadata = DataRouter.read_model_metadata(persisted_path, config) +- return DataRouter.create_interpreter(nlp, metadata) ++ return DataRouter.create_interpreter(metadata, nlp) + + + class ResponseTest(object): +",_pytest/utilities.py,"ArgSwap(idxs=0<->1 @(36,11)->(36,40))","def run_train(_config): + + def load_interpreter_for_model(nlp, config, persisted_path): + metadata = DataRouter.read_model_metadata(persisted_path, config) + return DataRouter.create_interpreter(nlp, metadata) + + + class ResponseTest(object):","def run_train(_config): + + def load_interpreter_for_model(nlp, config, persisted_path): + metadata = DataRouter.read_model_metadata(persisted_path, config) + return DataRouter.create_interpreter(metadata, nlp) + + + class ResponseTest(object):" +471,https://:@github.com/RasaHQ/rasa.git,bb0b24e56a97affbfa3db91be71782f293e9e5c2,"@@ -29,7 +29,7 @@ def test_luis_data_without_tokenizer(): + def test_wit_data(): + td = load_data('data/examples/wit/demo-flights.json', ""en"") + assert td.entity_examples != [] +- assert td.intent_examples != [] ++ assert td.intent_examples == [] + assert td.entity_synonyms == {} + + +",_pytest/test_training_data.py,"ReplaceText(target='==' @(32,30)->(32,32))","def test_luis_data_without_tokenizer(): + def test_wit_data(): + td = load_data('data/examples/wit/demo-flights.json', ""en"") + assert td.entity_examples != [] + assert td.intent_examples != [] + assert td.entity_synonyms == {} + + ","def test_luis_data_without_tokenizer(): + def test_wit_data(): + td = load_data('data/examples/wit/demo-flights.json', ""en"") + assert td.entity_examples != [] + assert td.intent_examples == [] + assert td.entity_synonyms == {} + + " +472,https://:@github.com/RasaHQ/rasa.git,12484270fb8c3c271d74c5b3269f287eaf2d7cfb,"@@ -84,7 +84,7 @@ class SklearnIntentClassifier(Component): + + # dirty str fix because sklearn is expecting str not instance of basestr... + tuned_parameters = [{'C': [1, 2, 5, 10, 20, 100], 'kernel': [str('linear')]}] +- cv_splits = max(2, min(MAX_CV_FOLDS, np.min(np.bincount(y)) / 5)) # aim for at least 5 examples in each fold ++ cv_splits = max(2, min(MAX_CV_FOLDS, np.min(np.bincount(y)) // 5)) # aim for at least 5 examples in each fold + + self.clf = GridSearchCV(SVC(C=1, probability=True), + param_grid=tuned_parameters, n_jobs=num_threads, +",rasa_nlu/classifiers/sklearn_intent_classifier.py,"ReplaceText(target='//' @(87,68)->(87,69))","class SklearnIntentClassifier(Component): + + # dirty str fix because sklearn is expecting str not instance of basestr... + tuned_parameters = [{'C': [1, 2, 5, 10, 20, 100], 'kernel': [str('linear')]}] + cv_splits = max(2, min(MAX_CV_FOLDS, np.min(np.bincount(y)) / 5)) # aim for at least 5 examples in each fold + + self.clf = GridSearchCV(SVC(C=1, probability=True), + param_grid=tuned_parameters, n_jobs=num_threads,","class SklearnIntentClassifier(Component): + + # dirty str fix because sklearn is expecting str not instance of basestr... + tuned_parameters = [{'C': [1, 2, 5, 10, 20, 100], 'kernel': [str('linear')]}] + cv_splits = max(2, min(MAX_CV_FOLDS, np.min(np.bincount(y)) // 5)) # aim for at least 5 examples in each fold + + self.clf = GridSearchCV(SVC(C=1, probability=True), + param_grid=tuned_parameters, n_jobs=num_threads," +473,https://:@github.com/RasaHQ/rasa.git,b5f9b6ad06ff52d75522b49c745f3e83c32ee7cd,"@@ -135,7 +135,7 @@ class TrainingData(object): + logger.info(""Training data stats: \n"" + + ""\t- intent examples: {} ({} distinct intents)\n"".format( + self.num_intent_examples, len(different_intents)) + +- ""\t- found intents: {}\n"".format(list_to_str(different_entities)) + ++ ""\t- found intents: {}\n"".format(list_to_str(different_intents)) + + ""\t- entity examples: {} ({} distinct entities)\n"".format( + self.num_entity_examples, len(different_entities)) + + ""\t- found entities: {}\n"".format(list_to_str(different_entities))) +",rasa_nlu/training_data.py,"ReplaceText(target='different_intents' @(138,65)->(138,83))","class TrainingData(object): + logger.info(""Training data stats: \n"" + + ""\t- intent examples: {} ({} distinct intents)\n"".format( + self.num_intent_examples, len(different_intents)) + + ""\t- found intents: {}\n"".format(list_to_str(different_entities)) + + ""\t- entity examples: {} ({} distinct entities)\n"".format( + self.num_entity_examples, len(different_entities)) + + ""\t- found entities: {}\n"".format(list_to_str(different_entities)))","class TrainingData(object): + logger.info(""Training data stats: \n"" + + ""\t- intent examples: {} ({} distinct intents)\n"".format( + self.num_intent_examples, len(different_intents)) + + ""\t- found intents: {}\n"".format(list_to_str(different_intents)) + + ""\t- entity examples: {} ({} distinct entities)\n"".format( + self.num_entity_examples, len(different_entities)) + + ""\t- found entities: {}\n"".format(list_to_str(different_entities)))" +474,https://:@github.com/RasaHQ/rasa.git,c5e10bd1c504146064183b6b87cfdf80d8617a4d,"@@ -28,7 +28,7 @@ class MarkdownToRasa: + entities = [] + utter = example_in_md + for regex in [ent_regex, ent_regex_with_value]: +- utter = re.sub(regex, r""\1"", example_in_md) # [text](entity) -> text ++ utter = re.sub(regex, r""\1"", utter) # [text](entity) -> text + ent_matches = re.finditer(regex, example_in_md) + for matchNum, match in enumerate(ent_matches): + if 'synonym' in match.groupdict(): +",rasa_nlu/utils/md_to_rasa.py,"ReplaceText(target='utter' @(31,41)->(31,54))","class MarkdownToRasa: + entities = [] + utter = example_in_md + for regex in [ent_regex, ent_regex_with_value]: + utter = re.sub(regex, r""\1"", example_in_md) # [text](entity) -> text + ent_matches = re.finditer(regex, example_in_md) + for matchNum, match in enumerate(ent_matches): + if 'synonym' in match.groupdict():","class MarkdownToRasa: + entities = [] + utter = example_in_md + for regex in [ent_regex, ent_regex_with_value]: + utter = re.sub(regex, r""\1"", utter) # [text](entity) -> text + ent_matches = re.finditer(regex, example_in_md) + for matchNum, match in enumerate(ent_matches): + if 'synonym' in match.groupdict():" +475,https://:@github.com/RasaHQ/rasa.git,571c59bc9fccca87aa1c29b56ddf874fce9b111a,"@@ -87,9 +87,9 @@ class Metadata(object): + return [] + + def for_component(self, name, defaults=None): +- return config.component_config_from_pipeline(self.get('pipeline', []), +- name, +- defaults) ++ return config.component_config_from_pipeline(name, ++ self.get('pipeline', []), ++ defaults) + + @property + def language(self): +",rasa_nlu/model.py,"ArgSwap(idxs=0<->1 @(90,15)->(90,52))","class Metadata(object): + return [] + + def for_component(self, name, defaults=None): + return config.component_config_from_pipeline(self.get('pipeline', []), + name, + defaults) + + @property + def language(self):","class Metadata(object): + return [] + + def for_component(self, name, defaults=None): + return config.component_config_from_pipeline(name, + self.get('pipeline', []), + defaults) + + @property + def language(self):" +476,https://:@github.com/RasaHQ/rasa.git,9a06d81201ca84812540bc4128111c55e22ffca7,"@@ -156,7 +156,7 @@ class RasaNLUModelConfig(object): + return json_to_string(self.__dict__, indent=4) + + def for_component(self, name, defaults=None): +- return component_config_from_pipeline(self.pipeline, name, defaults) ++ return component_config_from_pipeline(name, self.pipeline, defaults) + + @property + def component_names(self): +",rasa_nlu/config.py,"ArgSwap(idxs=0<->1 @(159,15)->(159,45))","class RasaNLUModelConfig(object): + return json_to_string(self.__dict__, indent=4) + + def for_component(self, name, defaults=None): + return component_config_from_pipeline(self.pipeline, name, defaults) + + @property + def component_names(self):","class RasaNLUModelConfig(object): + return json_to_string(self.__dict__, indent=4) + + def for_component(self, name, defaults=None): + return component_config_from_pipeline(name, self.pipeline, defaults) + + @property + def component_names(self):" +477,https://:@github.com/RasaHQ/rasa.git,2d92ef4002144ec4b3d66bd911c26642e5ab698f,"@@ -42,7 +42,7 @@ def create_argument_parser(): + description='evaluates a dialogue model') + parent_parser = argparse.ArgumentParser(add_help=False) + add_args_to_parser(parent_parser) +- cli.arguments.add_model_and_story_group(parser, ++ cli.arguments.add_model_and_story_group(parent_parser, + allow_pretrained_model=False) + utils.add_logging_option_arguments(parent_parser) + subparsers = parser.add_subparsers(help='mode', dest='mode') +",rasa_core/evaluate.py,"ReplaceText(target='parent_parser' @(45,44)->(45,50))","def create_argument_parser(): + description='evaluates a dialogue model') + parent_parser = argparse.ArgumentParser(add_help=False) + add_args_to_parser(parent_parser) + cli.arguments.add_model_and_story_group(parser, + allow_pretrained_model=False) + utils.add_logging_option_arguments(parent_parser) + subparsers = parser.add_subparsers(help='mode', dest='mode')","def create_argument_parser(): + description='evaluates a dialogue model') + parent_parser = argparse.ArgumentParser(add_help=False) + add_args_to_parser(parent_parser) + cli.arguments.add_model_and_story_group(parent_parser, + allow_pretrained_model=False) + utils.add_logging_option_arguments(parent_parser) + subparsers = parser.add_subparsers(help='mode', dest='mode')" +478,https://:@github.com/RasaHQ/rasa.git,665cf94ee30f44aac85e8ac3c5ed8b2b0694354a,"@@ -49,7 +49,7 @@ def create_argument_parser(): + description='evaluates a dialogue model') + parent_parser = argparse.ArgumentParser(add_help=False) + add_args_to_parser(parent_parser) +- cli.arguments.add_model_and_story_group(parser, ++ cli.arguments.add_model_and_story_group(parent_parser, + allow_pretrained_model=False) + utils.add_logging_option_arguments(parent_parser) + subparsers = parser.add_subparsers(help='mode', dest='mode') +",rasa_core/evaluate.py,"ReplaceText(target='parent_parser' @(52,44)->(52,50))","def create_argument_parser(): + description='evaluates a dialogue model') + parent_parser = argparse.ArgumentParser(add_help=False) + add_args_to_parser(parent_parser) + cli.arguments.add_model_and_story_group(parser, + allow_pretrained_model=False) + utils.add_logging_option_arguments(parent_parser) + subparsers = parser.add_subparsers(help='mode', dest='mode')","def create_argument_parser(): + description='evaluates a dialogue model') + parent_parser = argparse.ArgumentParser(add_help=False) + add_args_to_parser(parent_parser) + cli.arguments.add_model_and_story_group(parent_parser, + allow_pretrained_model=False) + utils.add_logging_option_arguments(parent_parser) + subparsers = parser.add_subparsers(help='mode', dest='mode')" +479,https://:@github.com/RasaHQ/rasa.git,37f446c8246c78339727f7b09bd2021906ec8d60,"@@ -174,7 +174,7 @@ def test_generate_training_data_original_and_augmented_trackers( + hasattr(t, 'is_augmented') or not t.is_augmented + ] + assert len(original_trackers) == 3 +- assert len(original_trackers) <= 33 ++ assert len(training_trackers) <= 33 + + + def test_visualize_training_data_graph(tmpdir, default_domain): +",tests/test_dsl.py,"ReplaceText(target='training_trackers' @(177,15)->(177,32))","def test_generate_training_data_original_and_augmented_trackers( + hasattr(t, 'is_augmented') or not t.is_augmented + ] + assert len(original_trackers) == 3 + assert len(original_trackers) <= 33 + + + def test_visualize_training_data_graph(tmpdir, default_domain):","def test_generate_training_data_original_and_augmented_trackers( + hasattr(t, 'is_augmented') or not t.is_augmented + ] + assert len(original_trackers) == 3 + assert len(training_trackers) <= 33 + + + def test_visualize_training_data_graph(tmpdir, default_domain):" +480,https://:@github.com/RasaHQ/rasa.git,31ab3bb5d10a09f8957455909311257b257f44dc,"@@ -218,7 +218,7 @@ class TestMemoizationPolicy(PolicyTestCollection): + assert recalled == default_domain.index_for_action(actions[0]) + + for tracker, states, actions \ +- in zip(trackers, all_states_augmented, all_actions_augmented): ++ in zip(augmented_trackers, all_states_augmented, all_actions_augmented): + recalled = trained_policy.recall(states, tracker, default_domain) + assert recalled == 0 + +",tests/test_policies.py,"ReplaceText(target='augmented_trackers' @(221,23)->(221,31))","class TestMemoizationPolicy(PolicyTestCollection): + assert recalled == default_domain.index_for_action(actions[0]) + + for tracker, states, actions \ + in zip(trackers, all_states_augmented, all_actions_augmented): + recalled = trained_policy.recall(states, tracker, default_domain) + assert recalled == 0 + ","class TestMemoizationPolicy(PolicyTestCollection): + assert recalled == default_domain.index_for_action(actions[0]) + + for tracker, states, actions \ + in zip(augmented_trackers, all_states_augmented, all_actions_augmented): + recalled = trained_policy.recall(states, tracker, default_domain) + assert recalled == 0 + " +481,https://:@github.com/RasaHQ/rasa.git,90a98e954b209a05a168e86e78d4ad90e12d8869,"@@ -31,7 +31,7 @@ def run(model: Text, endpoints: Text, connector: Text = None, + from rasa_core.utils import AvailableEndpoints + + model_path = get_model(model) +- core_path, nlu_path = get_model_subdirectories(model) ++ core_path, nlu_path = get_model_subdirectories(model_path) + _endpoints = AvailableEndpoints.read_endpoints(endpoints) + + if not connector and not credentials: +",rasa/run.py,"ReplaceText(target='model_path' @(34,51)->(34,56))","def run(model: Text, endpoints: Text, connector: Text = None, + from rasa_core.utils import AvailableEndpoints + + model_path = get_model(model) + core_path, nlu_path = get_model_subdirectories(model) + _endpoints = AvailableEndpoints.read_endpoints(endpoints) + + if not connector and not credentials:","def run(model: Text, endpoints: Text, connector: Text = None, + from rasa_core.utils import AvailableEndpoints + + model_path = get_model(model) + core_path, nlu_path = get_model_subdirectories(model_path) + _endpoints = AvailableEndpoints.read_endpoints(endpoints) + + if not connector and not credentials:" +482,https://:@github.com/RasaHQ/rasa.git,e43636652c80d0e9d81dc01f6a83ebfc5444ee12,"@@ -69,8 +69,8 @@ def test_core( + if os.path.exists(core_path) and os.path.exists(nlu_path): + _interpreter = NaturalLanguageInterpreter.create(nlu_path, _endpoints.nlu) + +- _agent = Agent.load(core_path, interpreter=_interpreter) +- ++ _agent = Agent.load(model_path, interpreter=_interpreter) ++ + kwargs = minimal_kwargs(kwargs, rasa.core.test, [""stories"", ""agent""]) + + loop.run_until_complete( +",rasa/test.py,"ReplaceText(target='model_path' @(72,28)->(72,37))","def test_core( + if os.path.exists(core_path) and os.path.exists(nlu_path): + _interpreter = NaturalLanguageInterpreter.create(nlu_path, _endpoints.nlu) + + _agent = Agent.load(core_path, interpreter=_interpreter) + + kwargs = minimal_kwargs(kwargs, rasa.core.test, [""stories"", ""agent""]) + + loop.run_until_complete(","def test_core( + if os.path.exists(core_path) and os.path.exists(nlu_path): + _interpreter = NaturalLanguageInterpreter.create(nlu_path, _endpoints.nlu) + + _agent = Agent.load(model_path, interpreter=_interpreter) + + kwargs = minimal_kwargs(kwargs, rasa.core.test, [""stories"", ""agent""]) + + loop.run_until_complete(" +483,https://:@github.com/RasaHQ/rasa.git,2d74a8355b63f587c6e1a7d69027a84982fe237d,"@@ -118,7 +118,7 @@ async def train_comparison_models( + file_importer, + train_path, + policy_config=policy_config, +- exclusion_percentage=current_run, ++ exclusion_percentage=percentage, + kwargs=kwargs, + dump_stories=dump_stories, + ) +",rasa/core/train.py,"ReplaceText(target='percentage' @(121,45)->(121,56))","async def train_comparison_models( + file_importer, + train_path, + policy_config=policy_config, + exclusion_percentage=current_run, + kwargs=kwargs, + dump_stories=dump_stories, + )","async def train_comparison_models( + file_importer, + train_path, + policy_config=policy_config, + exclusion_percentage=percentage, + kwargs=kwargs, + dump_stories=dump_stories, + )" +484,https://:@github.com/RasaHQ/rasa.git,3b51563dc49830f4e5f9a09ebd823c5f7eb563ef,"@@ -29,7 +29,7 @@ class Tokenizer(Component): + if ""use_cls_token"" in self.component_config: + self.use_cls_token = self.component_config[""use_cls_token""] + else: +- self.use_cls_token = False ++ self.use_cls_token = True + + def add_cls_token( + self, tokens: List[Token], attribute: Text = MESSAGE_TEXT_ATTRIBUTE +",rasa/nlu/tokenizers/tokenizer.py,"ReplaceText(target='True' @(32,33)->(32,38))","class Tokenizer(Component): + if ""use_cls_token"" in self.component_config: + self.use_cls_token = self.component_config[""use_cls_token""] + else: + self.use_cls_token = False + + def add_cls_token( + self, tokens: List[Token], attribute: Text = MESSAGE_TEXT_ATTRIBUTE","class Tokenizer(Component): + if ""use_cls_token"" in self.component_config: + self.use_cls_token = self.component_config[""use_cls_token""] + else: + self.use_cls_token = True + + def add_cls_token( + self, tokens: List[Token], attribute: Text = MESSAGE_TEXT_ATTRIBUTE" +485,https://:@github.com/RasaHQ/rasa.git,f96eb791fb2236695a98fd5a4f935c3c5d316fe3,"@@ -376,7 +376,7 @@ def test_intent_evaluation_report_large(tmpdir_factory): + + assert len(report.keys()) == 8 + assert report[""A""] == a_results +- assert result[""E""] == e_results ++ assert report[""E""] == e_results + + + def test_response_evaluation_report(tmpdir_factory): +",tests/nlu/base/test_evaluation.py,"ReplaceText(target='report' @(379,11)->(379,17))","def test_intent_evaluation_report_large(tmpdir_factory): + + assert len(report.keys()) == 8 + assert report[""A""] == a_results + assert result[""E""] == e_results + + + def test_response_evaluation_report(tmpdir_factory):","def test_intent_evaluation_report_large(tmpdir_factory): + + assert len(report.keys()) == 8 + assert report[""A""] == a_results + assert report[""E""] == e_results + + + def test_response_evaluation_report(tmpdir_factory):" +486,https://:@github.com/RasaHQ/rasa.git,ff9bb32d79e484cd2cfd7cde0acfa9d0006e14f8,"@@ -527,7 +527,7 @@ class DotProductLoss(tf.keras.layers.Layer): + + tiled = tf.tile(tf.expand_dims(x, 0), (batch_size, 1, 1)) + +- return tf.gather(tiled, idxs, batch_dims=-1) ++ return tf.gather(tiled, idxs, batch_dims=1) + + def _get_bad_mask( + self, labels: ""tf.Tensor"", target_labels: ""tf.Tensor"", idxs: ""tf.Tensor"" +",rasa/utils/tf_layers.py,"ReplaceText(target='1' @(530,49)->(530,51))","class DotProductLoss(tf.keras.layers.Layer): + + tiled = tf.tile(tf.expand_dims(x, 0), (batch_size, 1, 1)) + + return tf.gather(tiled, idxs, batch_dims=-1) + + def _get_bad_mask( + self, labels: ""tf.Tensor"", target_labels: ""tf.Tensor"", idxs: ""tf.Tensor""","class DotProductLoss(tf.keras.layers.Layer): + + tiled = tf.tile(tf.expand_dims(x, 0), (batch_size, 1, 1)) + + return tf.gather(tiled, idxs, batch_dims=1) + + def _get_bad_mask( + self, labels: ""tf.Tensor"", target_labels: ""tf.Tensor"", idxs: ""tf.Tensor""" +487,https://:@github.com/RasaHQ/rasa.git,75e04b5ec3cb1ac6925152f491db074a391a9378,"@@ -67,7 +67,7 @@ class SpacyFeaturizer(Featurizer): + non_zero_features = np.array([f for f in features if f.any()]) + + if self.pooling_operation == ""mean"": +- return np.mean(features, axis=0, keepdims=True) ++ return np.mean(non_zero_features, axis=0, keepdims=True) + elif self.pooling_operation == ""max"": + return np.max(features, axis=0, keepdims=True) + else: +",rasa/nlu/featurizers/dense_featurizer/spacy_featurizer.py,"ReplaceText(target='non_zero_features' @(70,27)->(70,35))","class SpacyFeaturizer(Featurizer): + non_zero_features = np.array([f for f in features if f.any()]) + + if self.pooling_operation == ""mean"": + return np.mean(features, axis=0, keepdims=True) + elif self.pooling_operation == ""max"": + return np.max(features, axis=0, keepdims=True) + else:","class SpacyFeaturizer(Featurizer): + non_zero_features = np.array([f for f in features if f.any()]) + + if self.pooling_operation == ""mean"": + return np.mean(non_zero_features, axis=0, keepdims=True) + elif self.pooling_operation == ""max"": + return np.max(features, axis=0, keepdims=True) + else:" +488,https://:@github.com/RasaHQ/rasa.git,ba4b8f70ffbb7bb4d3429c3b6aaa1f9fbcc3f632,"@@ -69,7 +69,7 @@ class SpacyFeaturizer(Featurizer): + if self.pooling_operation == ""mean"": + return np.mean(non_zero_features, axis=0, keepdims=True) + elif self.pooling_operation == ""max"": +- return np.max(features, axis=0, keepdims=True) ++ return np.max(non_zero_features, axis=0, keepdims=True) + else: + raise ValueError( + f""Invalid pooling operation specified. Available operations are "" +",rasa/nlu/featurizers/dense_featurizer/spacy_featurizer.py,"ReplaceText(target='non_zero_features' @(72,26)->(72,34))","class SpacyFeaturizer(Featurizer): + if self.pooling_operation == ""mean"": + return np.mean(non_zero_features, axis=0, keepdims=True) + elif self.pooling_operation == ""max"": + return np.max(features, axis=0, keepdims=True) + else: + raise ValueError( + f""Invalid pooling operation specified. Available operations are ""","class SpacyFeaturizer(Featurizer): + if self.pooling_operation == ""mean"": + return np.mean(non_zero_features, axis=0, keepdims=True) + elif self.pooling_operation == ""max"": + return np.max(non_zero_features, axis=0, keepdims=True) + else: + raise ValueError( + f""Invalid pooling operation specified. Available operations are """ +489,https://:@github.com/RasaHQ/rasa.git,a2552e73fc8e4a656f43796101121ff8963bc0da,"@@ -50,7 +50,7 @@ class EntityExtractor(Component): + # get indices of entity labels that belong to one word + for idx in range(1, len(entities)): + if entities[idx][""start""] == entities[idx - 1][""end""]: +- if entity_indices and entity_indices[-1][1] == idx - 1: ++ if entity_indices and entity_indices[-1][-1] == idx - 1: + entity_indices[-1].append(idx) + else: + entity_indices.append([idx - 1, idx]) +",rasa/nlu/extractors/extractor.py,"ReplaceText(target='-1' @(53,57)->(53,58))","class EntityExtractor(Component): + # get indices of entity labels that belong to one word + for idx in range(1, len(entities)): + if entities[idx][""start""] == entities[idx - 1][""end""]: + if entity_indices and entity_indices[-1][1] == idx - 1: + entity_indices[-1].append(idx) + else: + entity_indices.append([idx - 1, idx])","class EntityExtractor(Component): + # get indices of entity labels that belong to one word + for idx in range(1, len(entities)): + if entities[idx][""start""] == entities[idx - 1][""end""]: + if entity_indices and entity_indices[-1][-1] == idx - 1: + entity_indices[-1].append(idx) + else: + entity_indices.append([idx - 1, idx])" +490,https://:@github.com/RasaHQ/rasa.git,16ac7259b842e188c5c012bcaf6303e4bf4a4602,"@@ -223,7 +223,7 @@ class RasaModel(tf.keras.models.Model): + self.save(self.best_model_file, overwrite=True) + + if best_model_epoch >= 0: +- logger.info(f'The model of epoch {epoch} (out of {epochs} in total) will be stored!') ++ logger.info(f'The model of epoch {best_model_epoch} (out of {epochs} in total) will be stored!') + if self.model_summary_file is not None: + self._write_model_summary() + +",rasa/utils/tensorflow/models.py,"ReplaceText(target='best_model_epoch' @(226,46)->(226,51))","class RasaModel(tf.keras.models.Model): + self.save(self.best_model_file, overwrite=True) + + if best_model_epoch >= 0: + logger.info(f'The model of epoch {epoch} (out of {epochs} in total) will be stored!') + if self.model_summary_file is not None: + self._write_model_summary() + ","class RasaModel(tf.keras.models.Model): + self.save(self.best_model_file, overwrite=True) + + if best_model_epoch >= 0: + logger.info(f'The model of epoch {best_model_epoch} (out of {epochs} in total) will be stored!') + if self.model_summary_file is not None: + self._write_model_summary() + " +491,https://:@github.com/RasaHQ/rasa.git,194820a60d61607fc480a95d981cb570e9ec3d4f,"@@ -254,7 +254,7 @@ class RasaModel(tf.keras.models.Model): + val_results = self._get_metric_results(prefix=""val_"") + if self._does_model_improve(val_results): + logger.debug(f""Creating model checkpoint after training..."") +- best_model_epoch = epoch ++ best_model_epoch = epochs + self.save(self.best_model_file, overwrite=True) + + if best_model_epoch >= 0: +",rasa/utils/tensorflow/models.py,"ReplaceText(target='epochs' @(257,35)->(257,40))","class RasaModel(tf.keras.models.Model): + val_results = self._get_metric_results(prefix=""val_"") + if self._does_model_improve(val_results): + logger.debug(f""Creating model checkpoint after training..."") + best_model_epoch = epoch + self.save(self.best_model_file, overwrite=True) + + if best_model_epoch >= 0:","class RasaModel(tf.keras.models.Model): + val_results = self._get_metric_results(prefix=""val_"") + if self._does_model_improve(val_results): + logger.debug(f""Creating model checkpoint after training..."") + best_model_epoch = epochs + self.save(self.best_model_file, overwrite=True) + + if best_model_epoch >= 0:" +492,https://:@github.com/gbrammer/grizli.git,a14c6aef2fb7790a5418ac882e332cbddf3771d9,"@@ -87,7 +87,7 @@ def run_all(id, t0=None, t1=None, fwhm=1200, zr=[0.65, 1.6], dz=[0.004, 0.0002], + + if scale_photometry: + scl = mb.scale_to_photometry(z=fit.meta['z_map'][0], method='lm', templates=t0, order=scale_photometry*1) +- if scl.status == 0: ++ if scl.status > 0: + mb.pscale = scl.x + st.pscale = scl.x + +",grizli/fitting.py,"ReplaceText(target='>' @(90,22)->(90,24))","def run_all(id, t0=None, t1=None, fwhm=1200, zr=[0.65, 1.6], dz=[0.004, 0.0002], + + if scale_photometry: + scl = mb.scale_to_photometry(z=fit.meta['z_map'][0], method='lm', templates=t0, order=scale_photometry*1) + if scl.status == 0: + mb.pscale = scl.x + st.pscale = scl.x + ","def run_all(id, t0=None, t1=None, fwhm=1200, zr=[0.65, 1.6], dz=[0.004, 0.0002], + + if scale_photometry: + scl = mb.scale_to_photometry(z=fit.meta['z_map'][0], method='lm', templates=t0, order=scale_photometry*1) + if scl.status > 0: + mb.pscale = scl.x + st.pscale = scl.x + " +493,https://:@github.com/gbrammer/grizli.git,06b2bb1a51cc4090eb57f37798a4b6cb6b24b2c2,"@@ -2291,7 +2291,7 @@ For example, + # Pixel area map + pam = os.path.join(os.getenv('iref'), 'ir_wfc3_map.fits') + print('Pixel area map: {0}'.format(pam)) +- if not os.path.exists(badpix): ++ if not os.path.exists(pam): + os.system('curl -o {0} http://www.stsci.edu/hst/wfc3/pam/ir_wfc3_map.fits'.format(pam)) + + def fetch_config_files(ACS=False): +",grizli/utils.py,"ReplaceText(target='pam' @(2294,26)->(2294,32))","For example, + # Pixel area map + pam = os.path.join(os.getenv('iref'), 'ir_wfc3_map.fits') + print('Pixel area map: {0}'.format(pam)) + if not os.path.exists(badpix): + os.system('curl -o {0} http://www.stsci.edu/hst/wfc3/pam/ir_wfc3_map.fits'.format(pam)) + + def fetch_config_files(ACS=False):","For example, + # Pixel area map + pam = os.path.join(os.getenv('iref'), 'ir_wfc3_map.fits') + print('Pixel area map: {0}'.format(pam)) + if not os.path.exists(pam): + os.system('curl -o {0} http://www.stsci.edu/hst/wfc3/pam/ir_wfc3_map.fits'.format(pam)) + + def fetch_config_files(ACS=False):" +494,https://:@github.com/gbrammer/grizli.git,60c15addafcb4ac4a0e55bc697b4bb18d6463736,"@@ -229,7 +229,7 @@ def go(root='j010311+131615', maglim=[17,26], HOME_PATH='/Volumes/Pegasus/Grizli + ir_ref = None + + auto_script.drizzle_overlaps(root, filters=optical_filters, +- make_combined=(ir_ref is not None), ref_image=ir_ref) ++ make_combined=(ir_ref is None), ref_image=ir_ref) + + if ir_ref is None: + # Need +",grizli/pipeline/auto_script.py,"ReplaceText(target=' is ' @(232,33)->(232,41))","def go(root='j010311+131615', maglim=[17,26], HOME_PATH='/Volumes/Pegasus/Grizli + ir_ref = None + + auto_script.drizzle_overlaps(root, filters=optical_filters, + make_combined=(ir_ref is not None), ref_image=ir_ref) + + if ir_ref is None: + # Need ","def go(root='j010311+131615', maglim=[17,26], HOME_PATH='/Volumes/Pegasus/Grizli + ir_ref = None + + auto_script.drizzle_overlaps(root, filters=optical_filters, + make_combined=(ir_ref is None), ref_image=ir_ref) + + if ir_ref is None: + # Need " +495,https://:@github.com/gbrammer/grizli.git,e32899e470d02fa98365ca1ab1bfc70d6b64077b,"@@ -3420,7 +3420,7 @@ def field_rgb(root='j010514+021532', xsize=6, output_dpi=None, HOME_PATH='./', s + PATH_TO = '{0}/{1}/Prep'.format(HOME_PATH, root) + else: + PATH_TO = './' +- sci_files = glob.glob('./{1}-f*sci.fits'.format(HOME_PATH, root)) ++ sci_files = glob.glob('./{1}-f*sci.fits'.format(PATH_TO, root)) + + if filters is None: + filters = [file.split('_')[-3].split('-')[-1] for file in sci_files] +",grizli/pipeline/auto_script.py,"ReplaceText(target='PATH_TO' @(3423,56)->(3423,65))","def field_rgb(root='j010514+021532', xsize=6, output_dpi=None, HOME_PATH='./', s + PATH_TO = '{0}/{1}/Prep'.format(HOME_PATH, root) + else: + PATH_TO = './' + sci_files = glob.glob('./{1}-f*sci.fits'.format(HOME_PATH, root)) + + if filters is None: + filters = [file.split('_')[-3].split('-')[-1] for file in sci_files]","def field_rgb(root='j010514+021532', xsize=6, output_dpi=None, HOME_PATH='./', s + PATH_TO = '{0}/{1}/Prep'.format(HOME_PATH, root) + else: + PATH_TO = './' + sci_files = glob.glob('./{1}-f*sci.fits'.format(PATH_TO, root)) + + if filters is None: + filters = [file.split('_')[-3].split('-')[-1] for file in sci_files]" +496,https://:@github.com/gbrammer/grizli.git,27974fdbe2c948dee6777f6c6d333b46e1456a80,"@@ -575,7 +575,7 @@ class GroupFLT(): + is_cgs=False): + """"""TBD + """""" +- if cpu_count == 0: ++ if cpu_count <= 0: + cpu_count = mp.cpu_count() + + if fit_info is None: +",grizli/multifit.py,"ReplaceText(target='<=' @(578,21)->(578,23))","class GroupFLT(): + is_cgs=False): + """"""TBD + """""" + if cpu_count == 0: + cpu_count = mp.cpu_count() + + if fit_info is None:","class GroupFLT(): + is_cgs=False): + """"""TBD + """""" + if cpu_count <= 0: + cpu_count = mp.cpu_count() + + if fit_info is None:" +497,https://:@github.com/gbrammer/grizli.git,73b7211978b46ce1f7bcc1de111237c047fbe00e,"@@ -959,7 +959,7 @@ def parse_visits(field_root='', HOME_PATH='./', use_visit=True, combine_same_pa= + elif (combine_minexp > 0) & (not has_grism): + combined = [] + for visit in visits: +- if len(visit['files']) > combine_minexp*1: ++ if len(visit['files']) >= combine_minexp*1: + combined.append(copy.deepcopy(visit)) + else: + filter_pa = '-'.join(visit['product'].split('-')[-2:]) +",grizli/pipeline/auto_script.py,"ReplaceText(target='>=' @(962,35)->(962,36))","def parse_visits(field_root='', HOME_PATH='./', use_visit=True, combine_same_pa= + elif (combine_minexp > 0) & (not has_grism): + combined = [] + for visit in visits: + if len(visit['files']) > combine_minexp*1: + combined.append(copy.deepcopy(visit)) + else: + filter_pa = '-'.join(visit['product'].split('-')[-2:])","def parse_visits(field_root='', HOME_PATH='./', use_visit=True, combine_same_pa= + elif (combine_minexp > 0) & (not has_grism): + combined = [] + for visit in visits: + if len(visit['files']) >= combine_minexp*1: + combined.append(copy.deepcopy(visit)) + else: + filter_pa = '-'.join(visit['product'].split('-')[-2:])" +498,https://:@github.com/gbrammer/grizli.git,54178395a55d79f53bf11d651b53bb6bc3448eb6,"@@ -3386,7 +3386,7 @@ def make_filter_combinations(root, weight_fnu=True, filter_combinations=FILTER_C + + # UVIS + if filt_i.startswith('f') & filt_i.endswith('u'): +- filt_i = filt_i[:1] ++ filt_i = filt_i[:-1] + + band = None + for f in filter_combinations: +",grizli/pipeline/auto_script.py,"ReplaceText(target='-1' @(3389,29)->(3389,30))","def make_filter_combinations(root, weight_fnu=True, filter_combinations=FILTER_C + + # UVIS + if filt_i.startswith('f') & filt_i.endswith('u'): + filt_i = filt_i[:1] + + band = None + for f in filter_combinations:","def make_filter_combinations(root, weight_fnu=True, filter_combinations=FILTER_C + + # UVIS + if filt_i.startswith('f') & filt_i.endswith('u'): + filt_i = filt_i[:-1] + + band = None + for f in filter_combinations:" +499,https://:@github.com/PmagPy/PmagPy.git,153e127b39023f35ad6724b0e89609849ec48689,"@@ -33,7 +33,7 @@ def main(): + try: + fh_last = open(last_path, 'r+') + last_checked = pickle.load(fh_last) +- if last_checked > time.time() - 24*60*60: ++ if last_checked < time.time() - 24*60*60: + return # stop here because it's been less than 24 hours + else: + pickle.dump(time.time(), fh_last) +",check_updates.py,"ReplaceText(target='<' @(36,24)->(36,25))","def main(): + try: + fh_last = open(last_path, 'r+') + last_checked = pickle.load(fh_last) + if last_checked > time.time() - 24*60*60: + return # stop here because it's been less than 24 hours + else: + pickle.dump(time.time(), fh_last)","def main(): + try: + fh_last = open(last_path, 'r+') + last_checked = pickle.load(fh_last) + if last_checked < time.time() - 24*60*60: + return # stop here because it's been less than 24 hours + else: + pickle.dump(time.time(), fh_last)" +500,https://:@github.com/PmagPy/PmagPy.git,1c9dfb436532fcefcdf85913462eca89c4a05886,"@@ -3363,7 +3363,7 @@ def upload_magic3(concat=0, dir_path='.', dmodel=None, vocab="""", contribution=No + # otherwise create a new Contribution in dir_path + con = Contribution(dir_path, vocabulary=vocab) + +- dir_path = contribution.directory ++ dir_path = con.directory + # take out any extra added columns + con.remove_non_magic_cols() + # begin the upload process +",pmagpy/ipmag.py,"ReplaceText(target='con' @(3366,15)->(3366,27))","def upload_magic3(concat=0, dir_path='.', dmodel=None, vocab="""", contribution=No + # otherwise create a new Contribution in dir_path + con = Contribution(dir_path, vocabulary=vocab) + + dir_path = contribution.directory + # take out any extra added columns + con.remove_non_magic_cols() + # begin the upload process","def upload_magic3(concat=0, dir_path='.', dmodel=None, vocab="""", contribution=No + # otherwise create a new Contribution in dir_path + con = Contribution(dir_path, vocabulary=vocab) + + dir_path = con.directory + # take out any extra added columns + con.remove_non_magic_cols() + # begin the upload process" +501,https://:@github.com/PmagPy/PmagPy.git,8fd06aa1272e4a82082fc0a0b5641242e2f18154,"@@ -72,7 +72,7 @@ def main(): + pastTime=startTime + if d < commandLength: + pastTime=startTime-commandLength +- printout=""Due to long processing time the look-back time has been extended to "" +str(pastTime.total_seconds()) + "" seconds"" + ""\n"" ++ printout=""Due to long processing time the look-back time has been extended to "" +str(commandLength.total_seconds()) + "" seconds"" + ""\n"" + f.write(printout) + else: + pastTime=startTime-d +",programs/createNewPlots.py,"ReplaceText(target='commandLength' @(75,97)->(75,105))","def main(): + pastTime=startTime + if d < commandLength: + pastTime=startTime-commandLength + printout=""Due to long processing time the look-back time has been extended to "" +str(pastTime.total_seconds()) + "" seconds"" + ""\n"" + f.write(printout) + else: + pastTime=startTime-d","def main(): + pastTime=startTime + if d < commandLength: + pastTime=startTime-commandLength + printout=""Due to long processing time the look-back time has been extended to "" +str(commandLength.total_seconds()) + "" seconds"" + ""\n"" + f.write(printout) + else: + pastTime=startTime-d" +502,https://:@github.com/PmagPy/PmagPy.git,de14e55e58558ac9d6980bdaf309fe17496a8f44,"@@ -3524,7 +3524,7 @@ def iodp_kly4s_lore(kly4s_file, meas_out='measurements.txt', + tau3=in_df['Kmin susceptibility (SI)']/3 + v3_dec=in_df['Kmin dec (deg)'] + v3_inc=in_df['Kmin inc (deg)'] +- specimens_df['aniso_v3']=tau1.astype('str')+"":""+v3_dec.astype('str')+"":""+v3_inc.astype('str') ++ specimens_df['aniso_v3']=tau3.astype('str')+"":""+v3_dec.astype('str')+"":""+v3_inc.astype('str') + + + # output data files +",pmagpy/convert_2_magic.py,"ReplaceText(target='tau3' @(3527,29)->(3527,33))","def iodp_kly4s_lore(kly4s_file, meas_out='measurements.txt', + tau3=in_df['Kmin susceptibility (SI)']/3 + v3_dec=in_df['Kmin dec (deg)'] + v3_inc=in_df['Kmin inc (deg)'] + specimens_df['aniso_v3']=tau1.astype('str')+"":""+v3_dec.astype('str')+"":""+v3_inc.astype('str') + + + # output data files","def iodp_kly4s_lore(kly4s_file, meas_out='measurements.txt', + tau3=in_df['Kmin susceptibility (SI)']/3 + v3_dec=in_df['Kmin dec (deg)'] + v3_inc=in_df['Kmin inc (deg)'] + specimens_df['aniso_v3']=tau3.astype('str')+"":""+v3_dec.astype('str')+"":""+v3_inc.astype('str') + + + # output data files" +503,https://:@github.com/efficios/pytsdl.git,1b6d994aa14340af28ed903692ff0fde598ebaeb,"@@ -1671,7 +1671,7 @@ class _DocCreatorVisitor: + # assign tag to copy now + variant_copy.tag = self._decode_unary(t.tag.value) + +- return variant ++ return variant_copy + + def _type_to_obj(self, t): + return self._type_to_obj_map[type(t)](t) +",pytsdl/parser.py,"ReplaceText(target='variant_copy' @(1674,15)->(1674,22))","class _DocCreatorVisitor: + # assign tag to copy now + variant_copy.tag = self._decode_unary(t.tag.value) + + return variant + + def _type_to_obj(self, t): + return self._type_to_obj_map[type(t)](t)","class _DocCreatorVisitor: + # assign tag to copy now + variant_copy.tag = self._decode_unary(t.tag.value) + + return variant_copy + + def _type_to_obj(self, t): + return self._type_to_obj_map[type(t)](t)" +504,https://:@github.com/mabrownnyu/youtube-data-api.git,07d71d5668d1dbeec28d84ce1cf8982fbd71be36,"@@ -585,7 +585,7 @@ class YoutubeDataApi: + else: + captions = [] + for v_id in video_id: +- captions.append(_get_captions(video_id, lang_code=lang_code, parser=parser, **kwargs)) ++ captions.append(_get_captions(v_id, lang_code=lang_code, parser=parser, **kwargs)) + return captions + + +",youtube_api/youtube_api.py,"ReplaceText(target='v_id' @(588,46)->(588,54))","class YoutubeDataApi: + else: + captions = [] + for v_id in video_id: + captions.append(_get_captions(video_id, lang_code=lang_code, parser=parser, **kwargs)) + return captions + + ","class YoutubeDataApi: + else: + captions = [] + for v_id in video_id: + captions.append(_get_captions(v_id, lang_code=lang_code, parser=parser, **kwargs)) + return captions + + " +505,https://:@github.com/xhochy/conda-mirror-ng.git,e0b34555d779f9b440512f850da39aa5a0e29ece,"@@ -85,5 +85,5 @@ def test_handling_bad_package(tmpdir, repodata): + with bz2.BZ2File(bad_pkg_path, 'wb') as f: + f.write(""This is a fake package"".encode()) + assert bad_pkg_name in os.listdir(bad_pkg_root) +- conda_mirror._validate_packages(repodata, local_repo_root) ++ conda_mirror._validate_packages(repodata, bad_pkg_root) + assert bad_pkg_name not in os.listdir(bad_pkg_root) +\ No newline at end of file +",test/test_conda_mirror.py,"ReplaceText(target='bad_pkg_root' @(88,46)->(88,61))","def test_handling_bad_package(tmpdir, repodata): + with bz2.BZ2File(bad_pkg_path, 'wb') as f: + f.write(""This is a fake package"".encode()) + assert bad_pkg_name in os.listdir(bad_pkg_root) + conda_mirror._validate_packages(repodata, local_repo_root) + assert bad_pkg_name not in os.listdir(bad_pkg_root) +\ No newline at end of file","def test_handling_bad_package(tmpdir, repodata): + with bz2.BZ2File(bad_pkg_path, 'wb') as f: + f.write(""This is a fake package"".encode()) + assert bad_pkg_name in os.listdir(bad_pkg_root) + conda_mirror._validate_packages(repodata, bad_pkg_root) + assert bad_pkg_name not in os.listdir(bad_pkg_root) +\ No newline at end of file" +506,https://:@github.com/kelsoncm/sc4.git,8c4e8ac8358668aaa6c32b73af44178e6e9db3ab,"@@ -45,6 +45,6 @@ def others_months(): + + def daterange(start, end, step=datetime.timedelta(1)): + curr = start +- while curr < end: ++ while curr <= end: + yield curr + curr += step +",sc4py/sc4py/datetime.py,"ReplaceText(target='<=' @(48,15)->(48,16))","def others_months(): + + def daterange(start, end, step=datetime.timedelta(1)): + curr = start + while curr < end: + yield curr + curr += step","def others_months(): + + def daterange(start, end, step=datetime.timedelta(1)): + curr = start + while curr <= end: + yield curr + curr += step" +507,https://:@github.com/makingspace/pubsubpy.git,bd6903e8ea6e7069712d7cf17cb725aa7f821d1a,"@@ -5,7 +5,7 @@ MODEL_EXCHANGE = 'model_exchange' + + __REQUIRED_INIT_KWARGS = {AMQP_URL, MODEL_EXCHANGE} + __OPTIONAL_INIT_KWARGS = set() +-__ALLOWED_INIT_KWARGS = __REQUIRED_INIT_KWARGS & __OPTIONAL_INIT_KWARGS ++__ALLOWED_INIT_KWARGS = __REQUIRED_INIT_KWARGS | __OPTIONAL_INIT_KWARGS + + + def init(**kwargs): +",pubsub/__init__.py,"ReplaceText(target='|' @(8,47)->(8,48))","MODEL_EXCHANGE = 'model_exchange' + + __REQUIRED_INIT_KWARGS = {AMQP_URL, MODEL_EXCHANGE} + __OPTIONAL_INIT_KWARGS = set() + __ALLOWED_INIT_KWARGS = __REQUIRED_INIT_KWARGS & __OPTIONAL_INIT_KWARGS + + + def init(**kwargs):","MODEL_EXCHANGE = 'model_exchange' + + __REQUIRED_INIT_KWARGS = {AMQP_URL, MODEL_EXCHANGE} + __OPTIONAL_INIT_KWARGS = set() + __ALLOWED_INIT_KWARGS = __REQUIRED_INIT_KWARGS | __OPTIONAL_INIT_KWARGS + + + def init(**kwargs):" +508,https://:@github.com/moff4/kframe.git,01c644e825136b2b86d9b6f7dd6a34e4997c128c,"@@ -310,7 +310,7 @@ class Parent: + kwargs (dict) - dict of arg that will be passed to init() as **kwargs (plugins only) + """""" + from kframe.base.plugin import Plugin +- if issubclass(target, Plugin): ++ if not issubclass(target, Plugin): + raise ValueError('target ({}) bust be isinstance of kframe.Plugin'.format(str(target))) + self.plugin_t[kw.get('key', target.name)] = { + 'target': target, +",kframe/base/parent.py,"ReplaceText(target='not ' @(313,11)->(313,11))","class Parent: + kwargs (dict) - dict of arg that will be passed to init() as **kwargs (plugins only) + """""" + from kframe.base.plugin import Plugin + if issubclass(target, Plugin): + raise ValueError('target ({}) bust be isinstance of kframe.Plugin'.format(str(target))) + self.plugin_t[kw.get('key', target.name)] = { + 'target': target,","class Parent: + kwargs (dict) - dict of arg that will be passed to init() as **kwargs (plugins only) + """""" + from kframe.base.plugin import Plugin + if not issubclass(target, Plugin): + raise ValueError('target ({}) bust be isinstance of kframe.Plugin'.format(str(target))) + self.plugin_t[kw.get('key', target.name)] = { + 'target': target," +509,https://:@github.com/moff4/kframe.git,85c41d1f13cb2c7d79787bbe35de661aa6c6b824,"@@ -329,7 +329,7 @@ class Task: + cfg.update(kwargs) + if 'shedule' in cfg: + cfg['shedule'] = self._convert_shedule(cfg['shedule']) +- self.cfg.update(kwargs) ++ self.cfg.update(cfg) + + def ready_for_run(self, t, tm): + """""" +",kframe/plugins/planner/task.py,"ReplaceText(target='cfg' @(332,24)->(332,30))","class Task: + cfg.update(kwargs) + if 'shedule' in cfg: + cfg['shedule'] = self._convert_shedule(cfg['shedule']) + self.cfg.update(kwargs) + + def ready_for_run(self, t, tm): + """"""","class Task: + cfg.update(kwargs) + if 'shedule' in cfg: + cfg['shedule'] = self._convert_shedule(cfg['shedule']) + self.cfg.update(cfg) + + def ready_for_run(self, t, tm): + """"""" +510,https://:@github.com/qaviton/qaviton_package_manager.git,0498c2b71479109db949e369a0b7189d75dded65,"@@ -63,7 +63,7 @@ class Build(Prep): + def update_version(self, version): + version = self.versioning(version) + content = self.get_pkg_init() +- if b'\n__version__' not in content or not content.startswith(b'__version__'): ++ if b'\n__version__' not in content and not content.startswith(b'__version__'): + raise IOError(""missing __version__ in the package __init__.py file"") + lines = content.splitlines() + for i, line in enumerate(lines): +",qaviton_package_manager/manager_methods/distribute_to_git.py,"ReplaceText(target='and' @(66,43)->(66,45))","class Build(Prep): + def update_version(self, version): + version = self.versioning(version) + content = self.get_pkg_init() + if b'\n__version__' not in content or not content.startswith(b'__version__'): + raise IOError(""missing __version__ in the package __init__.py file"") + lines = content.splitlines() + for i, line in enumerate(lines):","class Build(Prep): + def update_version(self, version): + version = self.versioning(version) + content = self.get_pkg_init() + if b'\n__version__' not in content and not content.startswith(b'__version__'): + raise IOError(""missing __version__ in the package __init__.py file"") + lines = content.splitlines() + for i, line in enumerate(lines):" +511,https://:@github.com/morganthrapp/pyACH.git,516f347fa832237e2868544c078f86f80c7c2a1c,"@@ -256,7 +256,7 @@ class BatchHeader: + def _get_effective_entry_date(effective_entry_date): + _date = datetime.datetime.today() + _date += datetime.timedelta(days=effective_entry_date) +- while _date.isoweekday() not in WEEKEND: ++ while _date.isoweekday() in WEEKEND: + _date += datetime.timedelta(days=1) + return _date.strftime(day_format_string) + +",pyach/ACHRecordTypes.py,"ReplaceText(target=' in ' @(259,32)->(259,40))","class BatchHeader: + def _get_effective_entry_date(effective_entry_date): + _date = datetime.datetime.today() + _date += datetime.timedelta(days=effective_entry_date) + while _date.isoweekday() not in WEEKEND: + _date += datetime.timedelta(days=1) + return _date.strftime(day_format_string) + ","class BatchHeader: + def _get_effective_entry_date(effective_entry_date): + _date = datetime.datetime.today() + _date += datetime.timedelta(days=effective_entry_date) + while _date.isoweekday() in WEEKEND: + _date += datetime.timedelta(days=1) + return _date.strftime(day_format_string) + " +512,https://:@github.com/eldarion/agon-ratings.git,99a317f1ead850e948cf08123fef8ea60b30060e,"@@ -72,7 +72,7 @@ class Rating(models.Model): + rating_obj = None + + if rating_obj and rating == 0: +- return rating.clear() ++ return rating_obj.clear() + + if rating_obj is None: + rating_obj = cls.objects.create( +",pinax/ratings/models.py,"ReplaceText(target='rating_obj' @(75,19)->(75,25))","class Rating(models.Model): + rating_obj = None + + if rating_obj and rating == 0: + return rating.clear() + + if rating_obj is None: + rating_obj = cls.objects.create(","class Rating(models.Model): + rating_obj = None + + if rating_obj and rating == 0: + return rating_obj.clear() + + if rating_obj is None: + rating_obj = cls.objects.create(" +513,https://:@github.com/sraashis/ature.git,caee2ab19dc6b73ab1916156ad80c5732957803f,"@@ -94,7 +94,7 @@ class PatchesGenerator(Dataset): + img_tensor = self.transform(img_tensor) + + if self.segment_mode: +- return self.data[ID], img_tensor, self.labels[index] ++ return self.data[index], img_tensor, self.labels[index] + + return img_tensor, self.labels[index] + +",neuralnet/utils/datasets.py,"ReplaceText(target='index' @(97,29)->(97,31))","class PatchesGenerator(Dataset): + img_tensor = self.transform(img_tensor) + + if self.segment_mode: + return self.data[ID], img_tensor, self.labels[index] + + return img_tensor, self.labels[index] + ","class PatchesGenerator(Dataset): + img_tensor = self.transform(img_tensor) + + if self.segment_mode: + return self.data[index], img_tensor, self.labels[index] + + return img_tensor, self.labels[index] + " +514,https://:@github.com/sraashis/ature.git,e192de63324d8472c331bd06ab36ea710ee93d2a,"@@ -96,7 +96,7 @@ class ThrnetTrainer(NNTrainer): + img_loss += current_loss + + thr = thr_map[..., None][..., None] +- segmented = (prob_map >= thr.byte()) ++ segmented = (prob_map > thr.byte()) + + # batch_score = ScoreAccumulator().add_tensor(segmented, truth) + print('Loss: ', current_loss, end='\r') +",neuralnet/thrnet/thrnet_trainer.py,"ReplaceText(target='>' @(99,42)->(99,44))","class ThrnetTrainer(NNTrainer): + img_loss += current_loss + + thr = thr_map[..., None][..., None] + segmented = (prob_map >= thr.byte()) + + # batch_score = ScoreAccumulator().add_tensor(segmented, truth) + print('Loss: ', current_loss, end='\r')","class ThrnetTrainer(NNTrainer): + img_loss += current_loss + + thr = thr_map[..., None][..., None] + segmented = (prob_map > thr.byte()) + + # batch_score = ScoreAccumulator().add_tensor(segmented, truth) + print('Loss: ', current_loss, end='\r')" +515,https://:@github.com/sraashis/ature.git,934f9ff3b34b487614e4f2653c153cd78d716b57,"@@ -50,7 +50,7 @@ class ThrnetTrainer(NNTrainer): + + if gen_images: + img = segmented_img.clone().cpu().numpy() +- img_score.add_array(img_obj.ground_truth, img) ++ img_score.add_array(img, img_obj.ground_truth) + # img = iu.remove_connected_comp(np.array(segmented_img, dtype=np.uint8), + # connected_comp_diam_limit=10) + IMG.fromarray(np.array(img, dtype=np.uint8)).save( +",neuralnet/mapnet/mapnet_trainer.py,"ArgSwap(idxs=0<->1 @(53,20)->(53,39))","class ThrnetTrainer(NNTrainer): + + if gen_images: + img = segmented_img.clone().cpu().numpy() + img_score.add_array(img_obj.ground_truth, img) + # img = iu.remove_connected_comp(np.array(segmented_img, dtype=np.uint8), + # connected_comp_diam_limit=10) + IMG.fromarray(np.array(img, dtype=np.uint8)).save(","class ThrnetTrainer(NNTrainer): + + if gen_images: + img = segmented_img.clone().cpu().numpy() + img_score.add_array(img, img_obj.ground_truth) + # img = iu.remove_connected_comp(np.array(segmented_img, dtype=np.uint8), + # connected_comp_diam_limit=10) + IMG.fromarray(np.array(img, dtype=np.uint8)).save(" +516,https://:@github.com/sraashis/ature.git,934f9ff3b34b487614e4f2653c153cd78d716b57,"@@ -59,7 +59,7 @@ class UNetNNTrainer(NNTrainer): + if gen_images: + map_img = map_img.cpu().numpy() + predicted_img = predicted_img.cpu().numpy() +- img_score.add_array(img_obj.ground_truth, predicted_img) ++ img_score.add_array(predicted_img, img_obj.ground_truth) + IMG.fromarray(np.array(predicted_img, dtype=np.uint8)).save( + os.path.join(self.log_dir, 'pred_' + img_obj.file_name.split('.')[0] + '.png')) + IMG.fromarray(np.array(map_img, dtype=np.uint8)).save( +",neuralnet/unet/unet_trainer.py,"ArgSwap(idxs=0<->1 @(62,20)->(62,39))","class UNetNNTrainer(NNTrainer): + if gen_images: + map_img = map_img.cpu().numpy() + predicted_img = predicted_img.cpu().numpy() + img_score.add_array(img_obj.ground_truth, predicted_img) + IMG.fromarray(np.array(predicted_img, dtype=np.uint8)).save( + os.path.join(self.log_dir, 'pred_' + img_obj.file_name.split('.')[0] + '.png')) + IMG.fromarray(np.array(map_img, dtype=np.uint8)).save(","class UNetNNTrainer(NNTrainer): + if gen_images: + map_img = map_img.cpu().numpy() + predicted_img = predicted_img.cpu().numpy() + img_score.add_array(predicted_img, img_obj.ground_truth) + IMG.fromarray(np.array(predicted_img, dtype=np.uint8)).save( + os.path.join(self.log_dir, 'pred_' + img_obj.file_name.split('.')[0] + '.png')) + IMG.fromarray(np.array(map_img, dtype=np.uint8)).save(" +517,https://:@github.com/tessgi/ticgen.git,9350670fed545226d33c16432802990b6ddd7274,"@@ -144,7 +144,7 @@ class Star(object): + E * self.Tmag**4 + F * self.Tmag**5) + + def get_oneSigmaNoise(self): +- return (np.exp(self.get_oneHourNoiseLnsigma()) * ++ return (np.exp(self.get_oneHourNoiseLnsigma()) / + np.sqrt(self.integration / 60.)) + + def TESS_Mag_VJKs(self): +",ticgen/ticgen.py,"ReplaceText(target='/' @(147,55)->(147,56))","class Star(object): + E * self.Tmag**4 + F * self.Tmag**5) + + def get_oneSigmaNoise(self): + return (np.exp(self.get_oneHourNoiseLnsigma()) * + np.sqrt(self.integration / 60.)) + + def TESS_Mag_VJKs(self):","class Star(object): + E * self.Tmag**4 + F * self.Tmag**5) + + def get_oneSigmaNoise(self): + return (np.exp(self.get_oneHourNoiseLnsigma()) / + np.sqrt(self.integration / 60.)) + + def TESS_Mag_VJKs(self):" +518,https://:@github.com/aki-nishimura/bayes-bridge.git,728164889880a793dd156bafeeaaec2da93c4706,"@@ -94,7 +94,7 @@ class SparseRegressionCoefficientSampler(): + )) + precond_hessian_matvec = lambda beta: \ + precond_prior_prec * beta \ +- + precond_scale * loglik_hessian_matvec(precond_scale * beta) ++ - precond_scale * loglik_hessian_matvec(precond_scale * beta) + precond_hessian_op = sp.sparse.linalg.LinearOperator( + (X.shape[1], X.shape[1]), precond_hessian_matvec + ) +",bayesbridge/reg_coef_sampler/reg_coef_sampler.py,"ReplaceText(target='-' @(97,12)->(97,13))","class SparseRegressionCoefficientSampler(): + )) + precond_hessian_matvec = lambda beta: \ + precond_prior_prec * beta \ + + precond_scale * loglik_hessian_matvec(precond_scale * beta) + precond_hessian_op = sp.sparse.linalg.LinearOperator( + (X.shape[1], X.shape[1]), precond_hessian_matvec + )","class SparseRegressionCoefficientSampler(): + )) + precond_hessian_matvec = lambda beta: \ + precond_prior_prec * beta \ + - precond_scale * loglik_hessian_matvec(precond_scale * beta) + precond_hessian_op = sp.sparse.linalg.LinearOperator( + (X.shape[1], X.shape[1]), precond_hessian_matvec + )" +519,https://:@github.com/aki-nishimura/bayes-bridge.git,8558d665b0d07e1565d88b4d477a67c576c7ffbd,"@@ -70,7 +70,7 @@ class BayesBridge(): + self.model = LinearModel(outcome, X) + elif model == 'logit': + n_success, n_trial = outcome +- self.model = LogisticModel(n_success, X, n_trial) ++ self.model = LogisticModel(n_success, n_trial, X) + elif model == 'cox': + self.model = CoxModel(event_time, censoring_time, X) + else: +",bayesbridge/bayesbridge.py,"ArgSwap(idxs=1<->2 @(73,25)->(73,38))","class BayesBridge(): + self.model = LinearModel(outcome, X) + elif model == 'logit': + n_success, n_trial = outcome + self.model = LogisticModel(n_success, X, n_trial) + elif model == 'cox': + self.model = CoxModel(event_time, censoring_time, X) + else:","class BayesBridge(): + self.model = LinearModel(outcome, X) + elif model == 'logit': + n_success, n_trial = outcome + self.model = LogisticModel(n_success, n_trial, X) + elif model == 'cox': + self.model = CoxModel(event_time, censoring_time, X) + else:" +520,https://:@github.com/BTrDB/btrdb4-python.git,68f67274b6c2a6bb4a9206cfb00e7c3747cab1fa,"@@ -36,7 +36,7 @@ from btrdb4.endpoint import Endpoint + from btrdb4.utils import * + + MIN_TIME = -(16 << 56) +-MAX_TIME = 48 >> 56 ++MAX_TIME = 48 << 56 + MAX_POINTWIDTH = 63 + + class Connection(object): +",btrdb4/__init__.py,"ReplaceText(target='<<' @(39,14)->(39,16))","from btrdb4.endpoint import Endpoint + from btrdb4.utils import * + + MIN_TIME = -(16 << 56) + MAX_TIME = 48 >> 56 + MAX_POINTWIDTH = 63 + + class Connection(object):","from btrdb4.endpoint import Endpoint + from btrdb4.utils import * + + MIN_TIME = -(16 << 56) + MAX_TIME = 48 << 56 + MAX_POINTWIDTH = 63 + + class Connection(object):" +521,https://:@github.com/mahaoyang/newspaper.git,ac1d4c7346ddd0e035f9c7968e7e712340723934,"@@ -62,7 +62,7 @@ def prepare_url(url, source_url=None): + """"""operations that purify a url, removes arguments, + redirects, and merges relatives with absolutes"""""" + +- if source_url is None: ++ if source_url is not None: + source_domain = urlparse(source_url).netloc + proper_url = urljoin(source_url, url) + proper_url = redirect_back(proper_url, source_domain) +",newspaper/urls.py,"ReplaceText(target=' is not ' @(65,17)->(65,21))","def prepare_url(url, source_url=None): + """"""operations that purify a url, removes arguments, + redirects, and merges relatives with absolutes"""""" + + if source_url is None: + source_domain = urlparse(source_url).netloc + proper_url = urljoin(source_url, url) + proper_url = redirect_back(proper_url, source_domain)","def prepare_url(url, source_url=None): + """"""operations that purify a url, removes arguments, + redirects, and merges relatives with absolutes"""""" + + if source_url is not None: + source_domain = urlparse(source_url).netloc + proper_url = urljoin(source_url, url) + proper_url = redirect_back(proper_url, source_domain)" +522,https://:@github.com/tmconsulting/onelya-railway-sdk.git,059265060ae8f9828ae6f5d7a143988cd9c5da4c,"@@ -28,7 +28,7 @@ class Session(object): + + if 'Code' in response: + raise OnelyaAPIError(method, response, data) +- return data ++ return response + + def __send_api_request(self, method, data): + url = '{}{}'.format(Session.API_URL, method) +",onelya_railway_sdk/session.py,"ReplaceText(target='response' @(31,15)->(31,19))","class Session(object): + + if 'Code' in response: + raise OnelyaAPIError(method, response, data) + return data + + def __send_api_request(self, method, data): + url = '{}{}'.format(Session.API_URL, method)","class Session(object): + + if 'Code' in response: + raise OnelyaAPIError(method, response, data) + return response + + def __send_api_request(self, method, data): + url = '{}{}'.format(Session.API_URL, method)" +523,https://:@github.com/rafalp/misago-social-app-django.git,d1d23e7e3cf4364c0d35289290b27787b84f5211,"@@ -50,7 +50,7 @@ def sanitize_redirect(host, redirect_to): + """""" + # Quick sanity check. + if not redirect_to or \ +- not isinstance(redirect_to, six.string_types) and \ ++ not isinstance(redirect_to, six.string_types) or \ + getattr(redirect_to, 'decode', None) and \ + not isinstance(redirect_to.decode(), six.string_types): + return None +",social/utils.py,"ReplaceText(target='or' @(53,53)->(53,56))","def sanitize_redirect(host, redirect_to): + """""" + # Quick sanity check. + if not redirect_to or \ + not isinstance(redirect_to, six.string_types) and \ + getattr(redirect_to, 'decode', None) and \ + not isinstance(redirect_to.decode(), six.string_types): + return None","def sanitize_redirect(host, redirect_to): + """""" + # Quick sanity check. + if not redirect_to or \ + not isinstance(redirect_to, six.string_types) or \ + getattr(redirect_to, 'decode', None) and \ + not isinstance(redirect_to.decode(), six.string_types): + return None" +524,https://:@github.com/rafalp/misago-social-app-django.git,7d0628e7a756526b50449435eb02b2806e815755,"@@ -132,7 +132,7 @@ def partial_pipeline_data(strategy, user, *args, **kwargs): + kwargs.setdefault('user', user) + kwargs.setdefault('request', strategy.request) + kwargs.update(xkwargs) +- return idx, backend, xargs, xkwargs ++ return idx, backend, xargs, kwargs + + + def build_absolute_uri(host_url, path=None): +",social/utils.py,"ReplaceText(target='kwargs' @(135,36)->(135,43))","def partial_pipeline_data(strategy, user, *args, **kwargs): + kwargs.setdefault('user', user) + kwargs.setdefault('request', strategy.request) + kwargs.update(xkwargs) + return idx, backend, xargs, xkwargs + + + def build_absolute_uri(host_url, path=None):","def partial_pipeline_data(strategy, user, *args, **kwargs): + kwargs.setdefault('user', user) + kwargs.setdefault('request', strategy.request) + kwargs.update(xkwargs) + return idx, backend, xargs, kwargs + + + def build_absolute_uri(host_url, path=None):" +525,https://:@github.com/rafalp/misago-social-app-django.git,d53529b57f0a4992889ad490e5314a2244155afa,"@@ -27,7 +27,7 @@ class SocialAuthExceptionMiddleware(object): + return + + if isinstance(exception, SocialAuthBaseException): +- backend_name = strategy.backend.name ++ backend_name = request.backend.name + message = self.get_message(request, exception) + url = self.get_redirect_uri(request, exception) + try: +",social/apps/django_app/middleware.py,"ReplaceText(target='request' @(30,27)->(30,35))","class SocialAuthExceptionMiddleware(object): + return + + if isinstance(exception, SocialAuthBaseException): + backend_name = strategy.backend.name + message = self.get_message(request, exception) + url = self.get_redirect_uri(request, exception) + try:","class SocialAuthExceptionMiddleware(object): + return + + if isinstance(exception, SocialAuthBaseException): + backend_name = request.backend.name + message = self.get_message(request, exception) + url = self.get_redirect_uri(request, exception) + try:" +526,https://:@github.com/c137digital/unv_app.git,d217fa0d780bc6f2acbbf4ea307630c78a695653,"@@ -34,7 +34,7 @@ class ComponentSettings: + """"""Create app settings, overrided by env."""""" + settings = settings or {} + if base_settings: +- settings = update_dict_recur(settings, base_settings) ++ settings = update_dict_recur(base_settings, settings) + for key, value in os.environ.items(): + if 'SETTINGS_' not in key: + continue +",src/unv/app/settings.py,"ArgSwap(idxs=0<->1 @(37,23)->(37,40))","class ComponentSettings: + """"""Create app settings, overrided by env."""""" + settings = settings or {} + if base_settings: + settings = update_dict_recur(settings, base_settings) + for key, value in os.environ.items(): + if 'SETTINGS_' not in key: + continue","class ComponentSettings: + """"""Create app settings, overrided by env."""""" + settings = settings or {} + if base_settings: + settings = update_dict_recur(base_settings, settings) + for key, value in os.environ.items(): + if 'SETTINGS_' not in key: + continue" +527,https://:@github.com/timothycrosley/blox.git,fdc21c5be25dd5452075748e4027e067bfb28e1e,"@@ -141,7 +141,7 @@ class TagAttributes(type): + full_attribute_map = dict(parents[0].attribute_map) + full_attribute_map.update(attribute_map) + attribute_map = full_attribute_map +- class_dict['attribute_map'] = full_attributes ++ class_dict['attribute_map'] = attribute_map + + class_dict['attribute_descriptors'] = attributes + attribute_signals = (attribute.signal for attribute in attributes.values() if getattr(attribute, 'signal')) +",blox/base.py,"ReplaceText(target='attribute_map' @(144,46)->(144,61))","class TagAttributes(type): + full_attribute_map = dict(parents[0].attribute_map) + full_attribute_map.update(attribute_map) + attribute_map = full_attribute_map + class_dict['attribute_map'] = full_attributes + + class_dict['attribute_descriptors'] = attributes + attribute_signals = (attribute.signal for attribute in attributes.values() if getattr(attribute, 'signal'))","class TagAttributes(type): + full_attribute_map = dict(parents[0].attribute_map) + full_attribute_map.update(attribute_map) + attribute_map = full_attribute_map + class_dict['attribute_map'] = attribute_map + + class_dict['attribute_descriptors'] = attributes + attribute_signals = (attribute.signal for attribute in attributes.values() if getattr(attribute, 'signal'))" +528,https://:@github.com/Vizzuality/LMIPy.git,abd7e5a3a0d4e6f5fdaf2798647adb88c490cd6b,"@@ -557,5 +557,5 @@ class Layer: + # confirm update + + # update other layer +- target_layer.update(update_params=payload, token=token) ++ target_layer.update(update_params=filtered_payload, token=token) + +",LMIPy/layer.py,"ReplaceText(target='filtered_payload' @(560,42)->(560,49))","class Layer: + # confirm update + + # update other layer + target_layer.update(update_params=payload, token=token) + ","class Layer: + # confirm update + + # update other layer + target_layer.update(update_params=filtered_payload, token=token) + " +529,https://:@github.com/collective/mr.cabot.git,9c955abc239fcdff9bd12db236142387bce61f21,"@@ -7,7 +7,7 @@ def html_snippet(obj): + else: + lat, lon = loc + content = IListing(obj).summary +- if lat < 0: ++ if lat > 0: + hemi = ""west"" + else: + hemi = ""east"" +",src/mr/cabot/html.py,"ReplaceText(target='>' @(10,11)->(10,12))","def html_snippet(obj): + else: + lat, lon = loc + content = IListing(obj).summary + if lat < 0: + hemi = ""west"" + else: + hemi = ""east""","def html_snippet(obj): + else: + lat, lon = loc + content = IListing(obj).summary + if lat > 0: + hemi = ""west"" + else: + hemi = ""east""" +530,https://:@github.com/TeamSpen210/srctools.git,079e1c394836a6daecc3e4c996514286937a98dc,"@@ -392,7 +392,7 @@ class ModelManager: + with open(qc.ref_smd, 'rb') as fb: + child_ref = Mesh.parse_smd(fb) + +- if prop.skin != 0 and prop.skin <= len(mdl.skins): ++ if prop.skin != 0 and prop.skin < len(mdl.skins): + # We need to rename the materials to match the skin. + swap_skins = dict(zip( + mdl.skins[0], +",srctools/compiler/propcombine.py,"ReplaceText(target='<' @(395,48)->(395,50))","class ModelManager: + with open(qc.ref_smd, 'rb') as fb: + child_ref = Mesh.parse_smd(fb) + + if prop.skin != 0 and prop.skin <= len(mdl.skins): + # We need to rename the materials to match the skin. + swap_skins = dict(zip( + mdl.skins[0],","class ModelManager: + with open(qc.ref_smd, 'rb') as fb: + child_ref = Mesh.parse_smd(fb) + + if prop.skin != 0 and prop.skin < len(mdl.skins): + # We need to rename the materials to match the skin. + swap_skins = dict(zip( + mdl.skins[0]," +531,https://:@github.com/TeamSpen210/srctools.git,ef4510d1517525251ae2f62f8be714b068e4d909,"@@ -1799,7 +1799,7 @@ class Entity: + + base_name = orig_name.rstrip('0123456789') + +- if self.map.by_target[orig_name]: ++ if self.map.by_target[base_name]: + # Check every index in order. + for i in itertools.count(start=1): + name = base_name + str(i) +",srctools/vmf.py,"ReplaceText(target='base_name' @(1802,30)->(1802,39))","class Entity: + + base_name = orig_name.rstrip('0123456789') + + if self.map.by_target[orig_name]: + # Check every index in order. + for i in itertools.count(start=1): + name = base_name + str(i)","class Entity: + + base_name = orig_name.rstrip('0123456789') + + if self.map.by_target[base_name]: + # Check every index in order. + for i in itertools.count(start=1): + name = base_name + str(i)" +532,https://:@github.com/TeamSpen210/srctools.git,3954c99aa7922609c5c90a40b239ef57d747c5cc,"@@ -88,7 +88,7 @@ def main(argv: List[str]) -> None: + LOGGER.warning('No studiomdl path provided.') + studiomdl_loc = None + +- run_transformations(vmf, fsys, packlist, path, game_info, studiomdl_loc) ++ run_transformations(vmf, fsys, packlist, bsp_file, game_info, studiomdl_loc) + + if studiomdl_loc is not None and args.propcombine: + LOGGER.info('Combining props...') +",srctools/scripts/postcompiler.py,"ReplaceText(target='bsp_file' @(91,45)->(91,49))","def main(argv: List[str]) -> None: + LOGGER.warning('No studiomdl path provided.') + studiomdl_loc = None + + run_transformations(vmf, fsys, packlist, path, game_info, studiomdl_loc) + + if studiomdl_loc is not None and args.propcombine: + LOGGER.info('Combining props...')","def main(argv: List[str]) -> None: + LOGGER.warning('No studiomdl path provided.') + studiomdl_loc = None + + run_transformations(vmf, fsys, packlist, bsp_file, game_info, studiomdl_loc) + + if studiomdl_loc is not None and args.propcombine: + LOGGER.info('Combining props...')" +533,https://:@github.com/garicchi/pyassistant.git,46494b523af213c34a755bfee77fdc0ff00525b1,"@@ -31,4 +31,4 @@ class Assistant(): + with open(self.setting_file, 'w') as f: + json.dump(self.setting,f) + +- return True +\ No newline at end of file ++ return False +\ No newline at end of file +",assistant/util/assistant.py,"ReplaceText(target='False' @(34,15)->(34,19))","class Assistant(): + with open(self.setting_file, 'w') as f: + json.dump(self.setting,f) + + return True +\ No newline at end of file +\ No newline at end of file","class Assistant(): + with open(self.setting_file, 'w') as f: + json.dump(self.setting,f) + +\ No newline at end of file + return False +\ No newline at end of file" +534,https://:@github.com/u0078867/PyBiomech.git,b817b7617d9d57c39c72d8288d8cdb5748b9755c,"@@ -272,7 +272,7 @@ def evalPolynomialDerivative(poly, u, der=1): + tck, dummy = interpolate.splprep([x.tolist(),x.tolist()], s=0, k=1) + xU = np.array(interpolate.splev(u, tck)[1]) + out = f2(xU) +- p = np.array([np.ones((x.shape[0],)), out]).T ++ p = np.array([np.ones((xU.shape[0],)), out]).T + return p + + +",src/PyBiomech/vtkh.py,"ReplaceText(target='xU' @(275,27)->(275,28))","def evalPolynomialDerivative(poly, u, der=1): + tck, dummy = interpolate.splprep([x.tolist(),x.tolist()], s=0, k=1) + xU = np.array(interpolate.splev(u, tck)[1]) + out = f2(xU) + p = np.array([np.ones((x.shape[0],)), out]).T + return p + + ","def evalPolynomialDerivative(poly, u, der=1): + tck, dummy = interpolate.splprep([x.tolist(),x.tolist()], s=0, k=1) + xU = np.array(interpolate.splev(u, tck)[1]) + out = f2(xU) + p = np.array([np.ones((xU.shape[0],)), out]).T + return p + + " +535,https://:@github.com/mardix/gokku.git,c44093fc8d160748f4c6902e590ecd2193fdeb90,"@@ -509,7 +509,7 @@ def deploy_node(app, deltas={}): + first_time = False + if not exists(virtualenv_path): + echo(""-----> Creating virtualenv_path for '{}'"".format(app), fg='green') +- makedirs(node_path) ++ makedirs(virtualenv_path) + first_time = True + if not exists(node_path): + echo(""-----> Creating node_modules for '{}'"".format(app), fg='green') +",gokku.py,"ReplaceText(target='virtualenv_path' @(512,17)->(512,26))","def deploy_node(app, deltas={}): + first_time = False + if not exists(virtualenv_path): + echo(""-----> Creating virtualenv_path for '{}'"".format(app), fg='green') + makedirs(node_path) + first_time = True + if not exists(node_path): + echo(""-----> Creating node_modules for '{}'"".format(app), fg='green')","def deploy_node(app, deltas={}): + first_time = False + if not exists(virtualenv_path): + echo(""-----> Creating virtualenv_path for '{}'"".format(app), fg='green') + makedirs(virtualenv_path) + first_time = True + if not exists(node_path): + echo(""-----> Creating node_modules for '{}'"".format(app), fg='green')" +536,https://:@github.com/sophacles/pyCLiFF.git,35bf4ff2714329a786c093d7e24a63e6fc1555b9,"@@ -16,7 +16,7 @@ def handle_opts(opts): + + def datahandler(line): + global n +- if n > clmax: ++ if n >= clmax: + raise StopIteration + + n += 1 +",examples/head.py,"ReplaceText(target='>=' @(19,9)->(19,10))","def handle_opts(opts): + + def datahandler(line): + global n + if n > clmax: + raise StopIteration + + n += 1","def handle_opts(opts): + + def datahandler(line): + global n + if n >= clmax: + raise StopIteration + + n += 1" +537,https://:@github.com/pilt/flask-versioned.git,2dd47374531a9426845a2b3b10fa5f2dc2418bf2,"@@ -45,7 +45,7 @@ class FileChangedDriver(Driver): + mods = time.strftime('%Y%m%dT%H%M%S', modt) + return self.format % { + 'version': mods, +- 'path': path, ++ 'path': stream, + } + + +",flaskext/versioned/__init__.py,"ReplaceText(target='stream' @(48,20)->(48,24))","class FileChangedDriver(Driver): + mods = time.strftime('%Y%m%dT%H%M%S', modt) + return self.format % { + 'version': mods, + 'path': path, + } + + ","class FileChangedDriver(Driver): + mods = time.strftime('%Y%m%dT%H%M%S', modt) + return self.format % { + 'version': mods, + 'path': stream, + } + + " +538,https://:@github.com/lantunes/netomaton.git,7d73976ac295f05911b9b67e495bd54021f97644,"@@ -7,7 +7,7 @@ if __name__ == '__main__': + + initial_conditions = [0] * 100 + [1] + [0] * 99 + +- activities, connectivities = evolve(adjacencies, initial_conditions, timesteps=100, ++ activities, connectivities = evolve(initial_conditions, adjacencies, timesteps=100, + activity_rule=lambda n, c, t: ActivityRule.nks_ca_rule(n, c, 30)) + + plot_grid(activities) +",demos/elementary_ca/elementary_ca_demo.py,"ArgSwap(idxs=0<->1 @(10,33)->(10,39))","if __name__ == '__main__': + + initial_conditions = [0] * 100 + [1] + [0] * 99 + + activities, connectivities = evolve(adjacencies, initial_conditions, timesteps=100, + activity_rule=lambda n, c, t: ActivityRule.nks_ca_rule(n, c, 30)) + + plot_grid(activities)","if __name__ == '__main__': + + initial_conditions = [0] * 100 + [1] + [0] * 99 + + activities, connectivities = evolve(initial_conditions, adjacencies, timesteps=100, + activity_rule=lambda n, c, t: ActivityRule.nks_ca_rule(n, c, 30)) + + plot_grid(activities)" +539,https://:@github.com/lantunes/netomaton.git,7d73976ac295f05911b9b67e495bd54021f97644,"@@ -61,7 +61,7 @@ if __name__ == '__main__': + + initial_conditions = half_two + +- activities, connectivities = evolve(hopfield_net.adjacency_matrix, initial_conditions, timesteps=155, ++ activities, connectivities = evolve(initial_conditions, hopfield_net.adjacency_matrix, timesteps=155, + activity_rule=hopfield_net.activity_rule) + + # view the weights, stored in the adjacency matrix +",demos/hopfield_net/hopfield_net_demo.py,"ArgSwap(idxs=0<->1 @(64,33)->(64,39))","if __name__ == '__main__': + + initial_conditions = half_two + + activities, connectivities = evolve(hopfield_net.adjacency_matrix, initial_conditions, timesteps=155, + activity_rule=hopfield_net.activity_rule) + + # view the weights, stored in the adjacency matrix","if __name__ == '__main__': + + initial_conditions = half_two + + activities, connectivities = evolve(initial_conditions, hopfield_net.adjacency_matrix, timesteps=155, + activity_rule=hopfield_net.activity_rule) + + # view the weights, stored in the adjacency matrix" +540,https://:@github.com/orionw/tuningDEAP.git,7e7a40a386832fd386dfb8f67ff10e27ade0421e,"@@ -96,7 +96,7 @@ class TestConfigMapping(unittest.TestCase): + assert value == bool(new_value) and type(value) == bool, ""did not set the correct value from the map, expected {} but got {} (which is not the original {})"".format(""bool"", bool(new_value), type(value), value) + set_by_path(test_config, path, new_value, is_bool=False) + int_value = get_by_path(test_config, path) +- assert new_value == int_value and type(int_value) == int, ""did not set the correct value from the map, expected type {} = {} but got type {} = {})"".format(""int"", int_value, type(int_value), new_value) ++ assert value == int_value and type(int_value) == int, ""did not set the correct value from the map, expected type {} = {} but got type {} = {})"".format(""int"", int_value, type(int_value), new_value) + + def test_set_from_map_invalid(self): + test_value = ""three_levels"" +",test/test_config_mapping.py,"ReplaceText(target='value' @(99,15)->(99,24))","class TestConfigMapping(unittest.TestCase): + assert value == bool(new_value) and type(value) == bool, ""did not set the correct value from the map, expected {} but got {} (which is not the original {})"".format(""bool"", bool(new_value), type(value), value) + set_by_path(test_config, path, new_value, is_bool=False) + int_value = get_by_path(test_config, path) + assert new_value == int_value and type(int_value) == int, ""did not set the correct value from the map, expected type {} = {} but got type {} = {})"".format(""int"", int_value, type(int_value), new_value) + + def test_set_from_map_invalid(self): + test_value = ""three_levels""","class TestConfigMapping(unittest.TestCase): + assert value == bool(new_value) and type(value) == bool, ""did not set the correct value from the map, expected {} but got {} (which is not the original {})"".format(""bool"", bool(new_value), type(value), value) + set_by_path(test_config, path, new_value, is_bool=False) + int_value = get_by_path(test_config, path) + assert value == int_value and type(int_value) == int, ""did not set the correct value from the map, expected type {} = {} but got type {} = {})"".format(""int"", int_value, type(int_value), new_value) + + def test_set_from_map_invalid(self): + test_value = ""three_levels""" +541,https://:@github.com/benjamincrom/scrabble.git,59d26971b75475d0a66aeb03902fda6bfa57a048,"@@ -188,7 +188,7 @@ def move_does_not_stack_tiles(letter_list, location_set): + # return False + + def move_is_rack_size_or_less(location_set): +- return len(location_set) > config.PLAYER_RACK_SIZE ++ return len(location_set) <= config.PLAYER_RACK_SIZE + # print('Move places greater than seven tiles.') + # return False + # else: +",scrabble_game.py,"ReplaceText(target='<=' @(191,29)->(191,30))","def move_does_not_stack_tiles(letter_list, location_set): + # return False + + def move_is_rack_size_or_less(location_set): + return len(location_set) > config.PLAYER_RACK_SIZE + # print('Move places greater than seven tiles.') + # return False + # else:","def move_does_not_stack_tiles(letter_list, location_set): + # return False + + def move_is_rack_size_or_less(location_set): + return len(location_set) <= config.PLAYER_RACK_SIZE + # print('Move places greater than seven tiles.') + # return False + # else:" +542,https://:@bitbucket.org/norok2/pytk.git,934113ff8273afe9c2737a1bdee6f5f298217986,"@@ -179,7 +179,7 @@ def center(target, reference=None): + geometry = reference.winfo_geometry() + else: + geometry = reference +- if isinstance(reference, str): ++ if isinstance(geometry, str): + geometry = Geometry(geometry) + target_geometry = Geometry(target.winfo_geometry()) + target.geometry(str(target_geometry.set_to_center(geometry))) +",pytk/util.py,"ReplaceText(target='geometry' @(182,18)->(182,27))","def center(target, reference=None): + geometry = reference.winfo_geometry() + else: + geometry = reference + if isinstance(reference, str): + geometry = Geometry(geometry) + target_geometry = Geometry(target.winfo_geometry()) + target.geometry(str(target_geometry.set_to_center(geometry)))","def center(target, reference=None): + geometry = reference.winfo_geometry() + else: + geometry = reference + if isinstance(geometry, str): + geometry = Geometry(geometry) + target_geometry = Geometry(target.winfo_geometry()) + target.geometry(str(target_geometry.set_to_center(geometry)))" +543,https://:@github.com/ds4dm/ecole.git,90d17acf7796734b64299619474a60519b19db59,"@@ -13,7 +13,7 @@ def test_IsDone(state): + def test_NLPIterations(state): + reward_func = R.NLPIterations() + reward_func.reset(state) +- assert reward_func.get(state) >= 0 ++ assert reward_func.get(state) <= 0 + assert reward_func.get(state, done=True) == 0 + + +",python/tests/test_reward.py,"ReplaceText(target='<=' @(16,34)->(16,36))","def test_IsDone(state): + def test_NLPIterations(state): + reward_func = R.NLPIterations() + reward_func.reset(state) + assert reward_func.get(state) >= 0 + assert reward_func.get(state, done=True) == 0 + + ","def test_IsDone(state): + def test_NLPIterations(state): + reward_func = R.NLPIterations() + reward_func.reset(state) + assert reward_func.get(state) <= 0 + assert reward_func.get(state, done=True) == 0 + + " +544,https://:@github.com/ds4dm/ecole.git,6bc408253cbea5c8cb6740412601d13eb6772039,"@@ -101,4 +101,4 @@ def test_LpIterations(model): + def test_NNodes(model): + reward_func = R.NNodes() + reward_func.reset(model) +- assert reward_func.obtain_reward(model) <= 0 ++ assert reward_func.obtain_reward(model) >= 0 +",python/tests/test_reward.py,"ReplaceText(target='>=' @(104,44)->(104,46))","def test_LpIterations(model): + def test_NNodes(model): + reward_func = R.NNodes() + reward_func.reset(model) + assert reward_func.obtain_reward(model) <= 0","def test_LpIterations(model): + def test_NNodes(model): + reward_func = R.NNodes() + reward_func.reset(model) + assert reward_func.obtain_reward(model) >= 0" +545,https://:@github.com/nodedge/nodedge.git,b610ea8a12132e143aafe2824a83a9c032a973f7,"@@ -313,7 +313,7 @@ class GraphicsView(QGraphicsView): + event.localPos(), + event.screenPos(), + Qt.LeftButton, +- event.buttons() & -Qt.LeftButton, ++ event.buttons() | -Qt.LeftButton, + event.modifiers(), + ) + super().mouseReleaseEvent(fake_event) +",nodedge/graphics_view.py,"ReplaceText(target='|' @(316,28)->(316,29))","class GraphicsView(QGraphicsView): + event.localPos(), + event.screenPos(), + Qt.LeftButton, + event.buttons() & -Qt.LeftButton, + event.modifiers(), + ) + super().mouseReleaseEvent(fake_event)","class GraphicsView(QGraphicsView): + event.localPos(), + event.screenPos(), + Qt.LeftButton, + event.buttons() | -Qt.LeftButton, + event.modifiers(), + ) + super().mouseReleaseEvent(fake_event)" +546,https://:@github.com/ovnicraft/suds2.git,b5d1aa94c6c825f717bf41f687ca687241aeae43,"@@ -130,7 +130,7 @@ class UMBase: + return content.data + lang = attributes.lang() + if not len(node.children) and content.text is None: +- if self.nillable(content.data) and content.node.isnil(): ++ if self.nillable(content.data) or content.node.isnil(): + return None + else: + return xlstr.string('', lang) +",suds/bindings/unmarshaller.py,"ReplaceText(target='or' @(133,43)->(133,46))","class UMBase: + return content.data + lang = attributes.lang() + if not len(node.children) and content.text is None: + if self.nillable(content.data) and content.node.isnil(): + return None + else: + return xlstr.string('', lang)","class UMBase: + return content.data + lang = attributes.lang() + if not len(node.children) and content.text is None: + if self.nillable(content.data) or content.node.isnil(): + return None + else: + return xlstr.string('', lang)" +547,https://:@github.com/ovnicraft/suds2.git,e54498f49a9973bc9a385885b5a220026503f22b,"@@ -113,6 +113,6 @@ class Options(Skin): + Definition('retxml', bool, False), + Definition('autoblend', bool, False), + Definition('cachingpolicy', int, 0), +- Definition('plugins', [], (list, tuple)), ++ Definition('plugins', (list, tuple), []), + ] + Skin.__init__(self, domain, definitions, kwargs) +",suds/options.py,"ArgSwap(idxs=1<->2 @(116,12)->(116,22))","class Options(Skin): + Definition('retxml', bool, False), + Definition('autoblend', bool, False), + Definition('cachingpolicy', int, 0), + Definition('plugins', [], (list, tuple)), + ] + Skin.__init__(self, domain, definitions, kwargs)","class Options(Skin): + Definition('retxml', bool, False), + Definition('autoblend', bool, False), + Definition('cachingpolicy', int, 0), + Definition('plugins', (list, tuple), []), + ] + Skin.__init__(self, domain, definitions, kwargs)" +548,https://:@github.com/lukegb/ticketml.git,99c13a8e34a4397470564a355d639a4fbd5c72c4,"@@ -122,7 +122,7 @@ class BaseBackend(object): + self._serial.write(h2b('1d21' + hex)) + + def get_characters_per_line(self, font_width): +- return self.BASE_CHARS_PER_LINE / font_width ++ return self.BASE_CHARS_PER_LINE // font_width + + class Ibm4610Backend(BaseBackend): + BARCODE_MAP = { +",ticketml/ticketml.py,"ReplaceText(target='//' @(125,40)->(125,41))","class BaseBackend(object): + self._serial.write(h2b('1d21' + hex)) + + def get_characters_per_line(self, font_width): + return self.BASE_CHARS_PER_LINE / font_width + + class Ibm4610Backend(BaseBackend): + BARCODE_MAP = {","class BaseBackend(object): + self._serial.write(h2b('1d21' + hex)) + + def get_characters_per_line(self, font_width): + return self.BASE_CHARS_PER_LINE // font_width + + class Ibm4610Backend(BaseBackend): + BARCODE_MAP = {" +549,https://:@github.com/EmanuelGoncalves/crispy.git,2a029a350d328a65b32b5434a6b555dcc94a562c,"@@ -60,7 +60,7 @@ def iterate_correction(crispr_file, crispr_lib_file, cnv_file, output_folder, bs + assert len(overlap_genes) > 0, 'No genes (rows) overlap between CRISPR and Copy-number matrices' + + # run correction for each cell line +- for sample in overlap_genes: ++ for sample in overlap_samples: + if bsub_flag: + print('[{}] Crispy: bsub {}'.format(dt.now().strftime('%Y-%m-%d %H:%M:%S'), sample)) + +",scripts/crispy/processing/correct_cnv_bias.py,"ReplaceText(target='overlap_samples' @(63,18)->(63,31))","def iterate_correction(crispr_file, crispr_lib_file, cnv_file, output_folder, bs + assert len(overlap_genes) > 0, 'No genes (rows) overlap between CRISPR and Copy-number matrices' + + # run correction for each cell line + for sample in overlap_genes: + if bsub_flag: + print('[{}] Crispy: bsub {}'.format(dt.now().strftime('%Y-%m-%d %H:%M:%S'), sample)) + ","def iterate_correction(crispr_file, crispr_lib_file, cnv_file, output_folder, bs + assert len(overlap_genes) > 0, 'No genes (rows) overlap between CRISPR and Copy-number matrices' + + # run correction for each cell line + for sample in overlap_samples: + if bsub_flag: + print('[{}] Crispy: bsub {}'.format(dt.now().strftime('%Y-%m-%d %H:%M:%S'), sample)) + " +550,https://:@github.com/ninapavlich/sitecomber-article-tests.git,a053bd33aa15bf1c6e4a2dded9e5e1a71511e9bc,"@@ -159,4 +159,4 @@ def check_spelling(page, settings): + message = ""No misspellings found"" if not found_misspellings else u'Found %s misspelling(s): ""%s""' % (len(misspelled), '"", ""'.join(misspelled)) + return found_misspellings, message + +- return True, 'No article found' ++ return False, 'No article found' +",sitecomber_article_tests/utils.py,"ReplaceText(target='False' @(162,11)->(162,15))","def check_spelling(page, settings): + message = ""No misspellings found"" if not found_misspellings else u'Found %s misspelling(s): ""%s""' % (len(misspelled), '"", ""'.join(misspelled)) + return found_misspellings, message + + return True, 'No article found'","def check_spelling(page, settings): + message = ""No misspellings found"" if not found_misspellings else u'Found %s misspelling(s): ""%s""' % (len(misspelled), '"", ""'.join(misspelled)) + return found_misspellings, message + + return False, 'No article found'" +551,https://:@github.com/salpreh/tablat.git,fef6e07276bced6e885653ef760884a0ee5e0606,"@@ -132,7 +132,7 @@ class Table(object): + end = row_lenght + filt_data = [] + +- while end < len(self._table_data): ++ while end <= len(self._table_data): + filt_data.extend(self._filter_list(self._table_data[start:end], mask)) + start = end + end += row_lenght +",tablat/Table.py,"ReplaceText(target='<=' @(135,18)->(135,19))","class Table(object): + end = row_lenght + filt_data = [] + + while end < len(self._table_data): + filt_data.extend(self._filter_list(self._table_data[start:end], mask)) + start = end + end += row_lenght","class Table(object): + end = row_lenght + filt_data = [] + + while end <= len(self._table_data): + filt_data.extend(self._filter_list(self._table_data[start:end], mask)) + start = end + end += row_lenght" +552,https://:@github.com/cloudshare/cloudshare-py-sdk.git,1363279f77267f5e18ec26f2d1bd345b3adea08e,"@@ -156,7 +156,7 @@ def request(method, path, queryParams=None, content=None): + path=path, + queryParams=queryParams, + content=content) +- if res.status / 100 != 2: ++ if res.status // 100 != 2: + raise Exception('{} {}'.format(res.status, res.content['message'])) + return res.content + +",example.py,"ReplaceText(target='//' @(159,18)->(159,19))","def request(method, path, queryParams=None, content=None): + path=path, + queryParams=queryParams, + content=content) + if res.status / 100 != 2: + raise Exception('{} {}'.format(res.status, res.content['message'])) + return res.content + ","def request(method, path, queryParams=None, content=None): + path=path, + queryParams=queryParams, + content=content) + if res.status // 100 != 2: + raise Exception('{} {}'.format(res.status, res.content['message'])) + return res.content + " +553,https://:@github.com/Oslandia/deeposlandia.git,529dd916303d712ea3c51bb8454349812537e506,"@@ -111,7 +111,7 @@ if __name__ == '__main__': + testing_dataset.load(testing_filename, args.nb_testing_image) + else: + input_image_dir = os.path.join(input_repo, ""testing"") +- testing_dataset.populate(input_image_dir, preprocessed_testing_path, ++ testing_dataset.populate(preprocessed_testing_path, input_image_dir, + nb_images=args.nb_testing_image, labelling=False) + testing_dataset.save(testing_filename) + +",sources/test.py,"ArgSwap(idxs=0<->1 @(114,8)->(114,32))","if __name__ == '__main__': + testing_dataset.load(testing_filename, args.nb_testing_image) + else: + input_image_dir = os.path.join(input_repo, ""testing"") + testing_dataset.populate(input_image_dir, preprocessed_testing_path, + nb_images=args.nb_testing_image, labelling=False) + testing_dataset.save(testing_filename) + ","if __name__ == '__main__': + testing_dataset.load(testing_filename, args.nb_testing_image) + else: + input_image_dir = os.path.join(input_repo, ""testing"") + testing_dataset.populate(preprocessed_testing_path, input_image_dir, + nb_images=args.nb_testing_image, labelling=False) + testing_dataset.save(testing_filename) + " +554,https://:@github.com/Oslandia/deeposlandia.git,2bc626291e2f069c68e4a5a43e6ef5bfc3059d6a,"@@ -158,7 +158,7 @@ class SemanticSegmentationModel(ConvolutionalNeuralNetwork): + name=dataset_type+""_images"") + label_filepaths = [dataset.image_info[i][""label_filename""] + for i in range(dataset.get_nb_images())] +- label_tensors = ops.convert_to_tensor(image_filepaths, dtype=tf.string, ++ label_tensors = ops.convert_to_tensor(label_filepaths, dtype=tf.string, + name=dataset_type+""_labels"") + input_queue = tf.train.slice_input_producer([image_tensors, + label_tensors], +",sources/semantic_segmentation.py,"ReplaceText(target='label_filepaths' @(161,50)->(161,65))","class SemanticSegmentationModel(ConvolutionalNeuralNetwork): + name=dataset_type+""_images"") + label_filepaths = [dataset.image_info[i][""label_filename""] + for i in range(dataset.get_nb_images())] + label_tensors = ops.convert_to_tensor(image_filepaths, dtype=tf.string, + name=dataset_type+""_labels"") + input_queue = tf.train.slice_input_producer([image_tensors, + label_tensors],","class SemanticSegmentationModel(ConvolutionalNeuralNetwork): + name=dataset_type+""_images"") + label_filepaths = [dataset.image_info[i][""label_filename""] + for i in range(dataset.get_nb_images())] + label_tensors = ops.convert_to_tensor(label_filepaths, dtype=tf.string, + name=dataset_type+""_labels"") + input_queue = tf.train.slice_input_producer([image_tensors, + label_tensors]," +555,https://:@github.com/Oslandia/deeposlandia.git,09e5206460eae73b533e9007ca5241bd5baee7f6,"@@ -449,7 +449,7 @@ def main(args): + ""semseg"", + ""predicted_geometries"", + ) +- os.makedirs(predicted_label_folder, exist_ok=True) ++ os.makedirs(predicted_geom_folder, exist_ok=True) + predicted_geom_file = os.path.join( + predicted_geom_folder, + args.image_basename + ""_"" + str(args.image_size) + "".geojson"", +",deeposlandia/postprocess.py,"ReplaceText(target='predicted_geom_folder' @(452,16)->(452,38))","def main(args): + ""semseg"", + ""predicted_geometries"", + ) + os.makedirs(predicted_label_folder, exist_ok=True) + predicted_geom_file = os.path.join( + predicted_geom_folder, + args.image_basename + ""_"" + str(args.image_size) + "".geojson"",","def main(args): + ""semseg"", + ""predicted_geometries"", + ) + os.makedirs(predicted_geom_folder, exist_ok=True) + predicted_geom_file = os.path.join( + predicted_geom_folder, + args.image_basename + ""_"" + str(args.image_size) + "".geojson""," +556,https://:@github.com/metal3d/keras-video-generators.git,7313aa497a80147714dda3581ce34d4821130ae1,"@@ -72,7 +72,7 @@ class VideoFrameGenerator(Sequence): + + # split factor should be a propoer value + if split is not None: +- assert 0.0 > split < 1.0 ++ assert 0.0 < split < 1.0 + + # be sure that classes are well ordered + classes.sort() +",src/keras_video/generator.py,"ReplaceText(target='<' @(75,23)->(75,24))","class VideoFrameGenerator(Sequence): + + # split factor should be a propoer value + if split is not None: + assert 0.0 > split < 1.0 + + # be sure that classes are well ordered + classes.sort()","class VideoFrameGenerator(Sequence): + + # split factor should be a propoer value + if split is not None: + assert 0.0 < split < 1.0 + + # be sure that classes are well ordered + classes.sort()" +557,https://:@github.com/yongzhuo/Macropodus.git,11789503e9122303464bf6f02df1122397c0ca97,"@@ -142,7 +142,7 @@ class RandomEmbedding(BaseEmbedding): + else: + raise RuntimeError(""your input level_type is wrong, it must be 'word', 'char', 'ngram'"") + for text_one in text: +- if term_one not in token2idx: ++ if text_one not in token2idx: + token2idx[text_one] = len(token2idx) + else: + raise RuntimeError(""your input corpus_path is wrong, it must be 'dict' or 'corpus'"") +",macropodus/network/base/embedding.py,"ReplaceText(target='text_one' @(145,27)->(145,35))","class RandomEmbedding(BaseEmbedding): + else: + raise RuntimeError(""your input level_type is wrong, it must be 'word', 'char', 'ngram'"") + for text_one in text: + if term_one not in token2idx: + token2idx[text_one] = len(token2idx) + else: + raise RuntimeError(""your input corpus_path is wrong, it must be 'dict' or 'corpus'"")","class RandomEmbedding(BaseEmbedding): + else: + raise RuntimeError(""your input level_type is wrong, it must be 'word', 'char', 'ngram'"") + for text_one in text: + if text_one not in token2idx: + token2idx[text_one] = len(token2idx) + else: + raise RuntimeError(""your input corpus_path is wrong, it must be 'dict' or 'corpus'"")" +558,https://:@github.com/foxkit-us/PyIRC.git,c0bcbffa66f6fe1ddb7f3002e85fa38bfaafa103,"@@ -156,7 +156,7 @@ class IRCString(UserString): + + def convert(self, case): + """"""Convert string into another caseform"""""" +- return IRCString(self, case) ++ return IRCString(case, self) + + def ascii_lower(self): + """"""Return a copy of the string S converted to lowercase, using ASCII +",PyIRC/casemapping.py,"ArgSwap(idxs=0<->1 @(159,15)->(159,24))","class IRCString(UserString): + + def convert(self, case): + """"""Convert string into another caseform"""""" + return IRCString(self, case) + + def ascii_lower(self): + """"""Return a copy of the string S converted to lowercase, using ASCII","class IRCString(UserString): + + def convert(self, case): + """"""Convert string into another caseform"""""" + return IRCString(case, self) + + def ascii_lower(self): + """"""Return a copy of the string S converted to lowercase, using ASCII" +559,https://:@github.com/foxkit-us/PyIRC.git,b262e84b066a39cd911a37c5f3ab517413ed707f,"@@ -332,7 +332,7 @@ class UserTrack(BaseExtension): + + basicrfc = self.get_extension(""BasicRFC"") + +- if self.casecmp(user.nick, basicrfc.nick): ++ if self.casecmp(target.nick, basicrfc.nick): + # It's us! + isupport = self.get_extension(""ISupport"") + +",PyIRC/extensions/usertrack.py,"ReplaceText(target='target' @(335,24)->(335,28))","class UserTrack(BaseExtension): + + basicrfc = self.get_extension(""BasicRFC"") + + if self.casecmp(user.nick, basicrfc.nick): + # It's us! + isupport = self.get_extension(""ISupport"") + ","class UserTrack(BaseExtension): + + basicrfc = self.get_extension(""BasicRFC"") + + if self.casecmp(target.nick, basicrfc.nick): + # It's us! + isupport = self.get_extension(""ISupport"") + " +560,https://:@github.com/foxkit-us/PyIRC.git,71fa54a10227f629b88a2345a1da19b7db02b862,"@@ -48,7 +48,7 @@ class NullSocket(IRCBase): + + def inject_line(self, line): + """"""Inject a Line into the recvq for the client."""""" +- assert isinstance(Line, line) ++ assert isinstance(line, Line) + self.recvq.put(line) + + def loop(self): +",PyIRC/io/null.py,"ArgSwap(idxs=0<->1 @(51,15)->(51,25))","class NullSocket(IRCBase): + + def inject_line(self, line): + """"""Inject a Line into the recvq for the client."""""" + assert isinstance(Line, line) + self.recvq.put(line) + + def loop(self):","class NullSocket(IRCBase): + + def inject_line(self, line): + """"""Inject a Line into the recvq for the client."""""" + assert isinstance(line, Line) + self.recvq.put(line) + + def loop(self):" +561,https://:@github.com/foxkit-us/PyIRC.git,bf102eab33bde57ba3ae1b240a84ee2d161103f0,"@@ -362,7 +362,7 @@ class XTerm16ColourFormatter(ANSIFormatter): + + if self.background is not None: + bgc = ColoursANSI[self.background.name].value +- ret.append(str(fgc.background_16)) ++ ret.append(str(bgc.background_16)) + else: + # Reset background just in case + ret.append(self.fmt_resetbackground) +",PyIRC/formatting/formatters.py,"ReplaceText(target='bgc' @(365,31)->(365,34))","class XTerm16ColourFormatter(ANSIFormatter): + + if self.background is not None: + bgc = ColoursANSI[self.background.name].value + ret.append(str(fgc.background_16)) + else: + # Reset background just in case + ret.append(self.fmt_resetbackground)","class XTerm16ColourFormatter(ANSIFormatter): + + if self.background is not None: + bgc = ColoursANSI[self.background.name].value + ret.append(str(bgc.background_16)) + else: + # Reset background just in case + ret.append(self.fmt_resetbackground)" +562,https://:@bitbucket.org/pixelforest/pixelforest_drf.git,71155a01605838be2123eae28b650ceae32d7c2c,"@@ -14,7 +14,7 @@ from ..permissions import FullDjangoModelPermissions + + User = get_user_model() + +-if User is PFUser: ++if User is not PFUser: + raise ImproperlyConfigured(""Pf User is not the User model"") + + +",pixelforest_drf/rest/users/api_views.py,"ReplaceText(target=' is not ' @(17,7)->(17,11))","from ..permissions import FullDjangoModelPermissions + + User = get_user_model() + + if User is PFUser: + raise ImproperlyConfigured(""Pf User is not the User model"") + + ","from ..permissions import FullDjangoModelPermissions + + User = get_user_model() + + if User is not PFUser: + raise ImproperlyConfigured(""Pf User is not the User model"") + + " +563,https://:@github.com/sphemakh/meerkathi.git,b6220f225f989604f184d10863e5012f215ed639,"@@ -65,7 +65,7 @@ class worker_administrator(object): + else: + worker = name + '_worker' + +- self.workers.append((name, worker, order)) ++ self.workers.append((name, worker, i)) + + self.workers = sorted(self.workers, key=lambda a: a[2]) + +",meerkathi/workers/worker_administrator.py,"ReplaceText(target='i' @(68,47)->(68,52))","class worker_administrator(object): + else: + worker = name + '_worker' + + self.workers.append((name, worker, order)) + + self.workers = sorted(self.workers, key=lambda a: a[2]) + ","class worker_administrator(object): + else: + worker = name + '_worker' + + self.workers.append((name, worker, i)) + + self.workers = sorted(self.workers, key=lambda a: a[2]) + " +564,https://:@github.com/sphemakh/meerkathi.git,8bb75b04fe481c06cf0e7987e0072ed58fea1bc3,"@@ -528,7 +528,7 @@ found in our database or in the CASA NRAO database'.format(field)) + step = 'plot_fluxscale_{0:d}'.format(i) + table = prefix+"".F0"" + fieldtoplot = [] +- fieldtoplot.append(utils.get_field_id(msinfo, ref)[0]) ++ fieldtoplot.append(utils.get_field_id(msinfo, trans)[0]) + recipe.add('cab/ragavi', step, + { + ""table"" : '{0:s}/{1:s}:{2:s}'.format(get_dir_path(pipeline.caltables, pipeline), table, 'output'), +",meerkathi/workers/cross_cal_worker.py,"ReplaceText(target='trans' @(531,62)->(531,65))","found in our database or in the CASA NRAO database'.format(field)) + step = 'plot_fluxscale_{0:d}'.format(i) + table = prefix+"".F0"" + fieldtoplot = [] + fieldtoplot.append(utils.get_field_id(msinfo, ref)[0]) + recipe.add('cab/ragavi', step, + { + ""table"" : '{0:s}/{1:s}:{2:s}'.format(get_dir_path(pipeline.caltables, pipeline), table, 'output'),","found in our database or in the CASA NRAO database'.format(field)) + step = 'plot_fluxscale_{0:d}'.format(i) + table = prefix+"".F0"" + fieldtoplot = [] + fieldtoplot.append(utils.get_field_id(msinfo, trans)[0]) + recipe.add('cab/ragavi', step, + { + ""table"" : '{0:s}/{1:s}:{2:s}'.format(get_dir_path(pipeline.caltables, pipeline), table, 'output')," +565,https://:@github.com/sphemakh/meerkathi.git,67485769492da55875da1fea491a7a32ce82d16a,"@@ -176,7 +176,7 @@ def worker(pipeline, recipe, config): + substep = 'delete_flag_versions_after_{0:s}_ms{1:d}'.format(version, target_iter) + manflags.delete_cflags(pipeline, recipe, + available_flagversions[available_flagversions.index(version)+1], +- msname, cab_name=substep) ++ fms, cab_name=substep) + + flagv = tms+'.flagversions' + +",caracal/workers/transform_worker.py,"ReplaceText(target='fms' @(179,24)->(179,30))","def worker(pipeline, recipe, config): + substep = 'delete_flag_versions_after_{0:s}_ms{1:d}'.format(version, target_iter) + manflags.delete_cflags(pipeline, recipe, + available_flagversions[available_flagversions.index(version)+1], + msname, cab_name=substep) + + flagv = tms+'.flagversions' + ","def worker(pipeline, recipe, config): + substep = 'delete_flag_versions_after_{0:s}_ms{1:d}'.format(version, target_iter) + manflags.delete_cflags(pipeline, recipe, + available_flagversions[available_flagversions.index(version)+1], + fms, cab_name=substep) + + flagv = tms+'.flagversions' + " +566,https://:@gitlab.com/nekokatt/hikari.git,0b4d26aa20ddbf580ad84581bc5eeea34c687896,"@@ -48,4 +48,4 @@ class TestReaction: + + assert re.count == 420 + assert re.me is True +- test_state.parse_emoji.assert_called_with(None, emoji_dict) ++ test_state.parse_emoji.assert_called_with(emoji_dict, None) +",tests/hikari/core/model/test_reaction.py,"ArgSwap(idxs=0<->1 @(51,8)->(51,49))","class TestReaction: + + assert re.count == 420 + assert re.me is True + test_state.parse_emoji.assert_called_with(None, emoji_dict)","class TestReaction: + + assert re.count == 420 + assert re.me is True + test_state.parse_emoji.assert_called_with(emoji_dict, None)" +567,https://:@gitlab.com/nekokatt/hikari.git,b40bd61096cbd597d0f2863351ebddebf571867d,"@@ -286,7 +286,7 @@ class DispatchingEventAdapterImpl(dispatching_event_adapter.DispatchingEventAdap + + for role_id in role_ids: + role_obj = self.fabric.state_registry.get_role_by_id(guild_id, role_id) +- if role_objs is not None: ++ if role_obj is not None: + role_objs.append(role_obj) + else: + self.logger.warning( +",hikari/orm/dispatching_event_adapter_impl.py,"ReplaceText(target='role_obj' @(289,19)->(289,28))","class DispatchingEventAdapterImpl(dispatching_event_adapter.DispatchingEventAdap + + for role_id in role_ids: + role_obj = self.fabric.state_registry.get_role_by_id(guild_id, role_id) + if role_objs is not None: + role_objs.append(role_obj) + else: + self.logger.warning(","class DispatchingEventAdapterImpl(dispatching_event_adapter.DispatchingEventAdap + + for role_id in role_ids: + role_obj = self.fabric.state_registry.get_role_by_id(guild_id, role_id) + if role_obj is not None: + role_objs.append(role_obj) + else: + self.logger.warning(" +568,https://:@gitlab.com/nekokatt/hikari.git,89f2070c7a2135162e4852a8b778490b4695bc78,"@@ -699,7 +699,7 @@ class BotAppImpl(bot.IBotApp): + if plat == ""win32"": + supports_color |= os.getenv(""TERM_PROGRAM"", None) == ""mintty"" + supports_color |= ""ANSICON"" in os.environ +- supports_color |= is_a_tty ++ supports_color &= is_a_tty + else: + supports_color = is_a_tty + +",hikari/impl/bot.py,"ReplaceText(target='&=' @(702,31)->(702,33))","class BotAppImpl(bot.IBotApp): + if plat == ""win32"": + supports_color |= os.getenv(""TERM_PROGRAM"", None) == ""mintty"" + supports_color |= ""ANSICON"" in os.environ + supports_color |= is_a_tty + else: + supports_color = is_a_tty + ","class BotAppImpl(bot.IBotApp): + if plat == ""win32"": + supports_color |= os.getenv(""TERM_PROGRAM"", None) == ""mintty"" + supports_color |= ""ANSICON"" in os.environ + supports_color &= is_a_tty + else: + supports_color = is_a_tty + " +569,https://:@github.com/matthewhanson/boto3-utils.git,23390e1f08fda449451266dc7136a89914e00b4e,"@@ -33,7 +33,7 @@ class s3(object): + _url = deepcopy(url) + if url[0:5] == 'https': + _url = cls.https_to_s3(url) +- if url[0:5] != 's3://': ++ if _url[0:5] != 's3://': + raise Exception('Invalid S3 url %s' % _url) + + url_obj = _url.replace('s3://', '').split('/') +",boto3utils/s3.py,"ReplaceText(target='_url' @(36,11)->(36,14))","class s3(object): + _url = deepcopy(url) + if url[0:5] == 'https': + _url = cls.https_to_s3(url) + if url[0:5] != 's3://': + raise Exception('Invalid S3 url %s' % _url) + + url_obj = _url.replace('s3://', '').split('/')","class s3(object): + _url = deepcopy(url) + if url[0:5] == 'https': + _url = cls.https_to_s3(url) + if _url[0:5] != 's3://': + raise Exception('Invalid S3 url %s' % _url) + + url_obj = _url.replace('s3://', '').split('/')" +570,https://:@github.com/spex-xray/pyspextools.git,c68beb5206e3525010e0265f2c18f8f5fc4bebc3,"@@ -131,7 +131,7 @@ class OGIPRegion(Region): + if isinstance(corr, Pha): + self.corr = corr + self.input_corr = True +- elif back is None: ++ elif corr is None: + self.input_corr = False + else: + self.input_corr = False +",pyspextools/io/ogip.py,"ReplaceText(target='corr' @(134,13)->(134,17))","class OGIPRegion(Region): + if isinstance(corr, Pha): + self.corr = corr + self.input_corr = True + elif back is None: + self.input_corr = False + else: + self.input_corr = False","class OGIPRegion(Region): + if isinstance(corr, Pha): + self.corr = corr + self.input_corr = True + elif corr is None: + self.input_corr = False + else: + self.input_corr = False" +571,https://:@github.com/djerbic/xlrd-ignore-writeaccess-corruption.git,8ce449208ac3a8a1f4ec9c72954c11afcd40d3a8,"@@ -1975,7 +1975,7 @@ class Sheet(BaseObject): + nchars = data2_len - 1 + if nb: + assert nchars % 2 == 0 +- nchars /= 2 ++ nchars //= 2 + utext, endpos = unpack_unicode_update_pos(data2, 0, known_len=nchars) + assert endpos == data2_len + o.text += utext +",xlrd/sheet.py,"ReplaceText(target='//=' @(1978,23)->(1978,25))","class Sheet(BaseObject): + nchars = data2_len - 1 + if nb: + assert nchars % 2 == 0 + nchars /= 2 + utext, endpos = unpack_unicode_update_pos(data2, 0, known_len=nchars) + assert endpos == data2_len + o.text += utext","class Sheet(BaseObject): + nchars = data2_len - 1 + if nb: + assert nchars % 2 == 0 + nchars //= 2 + utext, endpos = unpack_unicode_update_pos(data2, 0, known_len=nchars) + assert endpos == data2_len + o.text += utext" +572,https://:@github.com/ijiraq/daomop.git,2b9c4af87e1b899b7589cfb04aa272540d2e8a04,"@@ -61,7 +61,7 @@ class GeneralModelTest(FileReadingTestCase, DirectoryCleaningTestCase): + # Put a real fits image on the first source, first observation + apcor_str = ""4 15 0.19 0.01"" + with open(self.get_abs_path(path), ""rb"") as fh: +- self.first_image = DownloadedFitsImage(fh.read(), apcor_str, Mock(), in_memory=True) ++ self.first_image = DownloadedFitsImage(fh.read(), Mock(), apcor_str, in_memory=True) + first_reading = self.model.get_current_workunit().get_sources()[0].get_readings()[0] + self.model._on_image_loaded(first_reading, self.first_image) + +",src/ossos-pipeline/tests/test_integration/test_models.py,"ArgSwap(idxs=1<->2 @(64,31)->(64,50))","class GeneralModelTest(FileReadingTestCase, DirectoryCleaningTestCase): + # Put a real fits image on the first source, first observation + apcor_str = ""4 15 0.19 0.01"" + with open(self.get_abs_path(path), ""rb"") as fh: + self.first_image = DownloadedFitsImage(fh.read(), apcor_str, Mock(), in_memory=True) + first_reading = self.model.get_current_workunit().get_sources()[0].get_readings()[0] + self.model._on_image_loaded(first_reading, self.first_image) + ","class GeneralModelTest(FileReadingTestCase, DirectoryCleaningTestCase): + # Put a real fits image on the first source, first observation + apcor_str = ""4 15 0.19 0.01"" + with open(self.get_abs_path(path), ""rb"") as fh: + self.first_image = DownloadedFitsImage(fh.read(), Mock(), apcor_str, in_memory=True) + first_reading = self.model.get_current_workunit().get_sources()[0].get_readings()[0] + self.model._on_image_loaded(first_reading, self.first_image) + " +573,https://:@github.com/iamsteadman/bambu-buffer.git,5704abdda5297d6cde2ccac7f91ded4108e1f616,"@@ -12,7 +12,7 @@ def post_save_receiver(sender, instance, **kwargs): + + name = m.pop(0) + app, model = name.lower().split('.') +- if app != instance._meta.app_label and model != instance._meta.module_name: ++ if app != instance._meta.app_label or model != instance._meta.module_name: + continue + + if any(m): +",bambu_buffer/receivers.py,"ReplaceText(target='or' @(15,43)->(15,46))","def post_save_receiver(sender, instance, **kwargs): + + name = m.pop(0) + app, model = name.lower().split('.') + if app != instance._meta.app_label and model != instance._meta.module_name: + continue + + if any(m):","def post_save_receiver(sender, instance, **kwargs): + + name = m.pop(0) + app, model = name.lower().split('.') + if app != instance._meta.app_label or model != instance._meta.module_name: + continue + + if any(m):" +574,https://:@github.com/khllkcm/templot.git,d4b329d16f94e3808e54b05116a8545e987a5e7b,"@@ -95,7 +95,7 @@ def plot_aggregated_map( + + if aggregation_method not in aggregates: + raise ValueError( +- f""{group} is not a valid aggregation method. Possible values are: {', '.join([k for k in aggregates])}"" ++ f""{aggregation_method} is not a valid aggregation method. Possible values are: {', '.join([k for k in aggregates])}"" + ) + + map_data = aggregates[aggregation_method][variables] +",templot/plot_aggregated_map.py,"ReplaceText(target='aggregation_method' @(98,15)->(98,20))","def plot_aggregated_map( + + if aggregation_method not in aggregates: + raise ValueError( + f""{group} is not a valid aggregation method. Possible values are: {', '.join([k for k in aggregates])}"" + ) + + map_data = aggregates[aggregation_method][variables]","def plot_aggregated_map( + + if aggregation_method not in aggregates: + raise ValueError( + f""{aggregation_method} is not a valid aggregation method. Possible values are: {', '.join([k for k in aggregates])}"" + ) + + map_data = aggregates[aggregation_method][variables]" +575,https://:@github.com/cjneely10/BioMetaDB.git,71352d2e75c038af886007c7b82591896aa23e1c,"@@ -146,4 +146,4 @@ def create_database(db_name, table_name, directory_name, data_file, alias, silen + if not silent: + _initialization_display_message_epilogue() + if not integrity_cancel: +- integrity_check(directory_name, table_name, ""None"", silent) ++ integrity_check(db_name, table_name, ""None"", silent) +",BioMetaDB/DBOperations/create_database.py,"ReplaceText(target='db_name' @(149,24)->(149,38))","def create_database(db_name, table_name, directory_name, data_file, alias, silen + if not silent: + _initialization_display_message_epilogue() + if not integrity_cancel: + integrity_check(directory_name, table_name, ""None"", silent)","def create_database(db_name, table_name, directory_name, data_file, alias, silen + if not silent: + _initialization_display_message_epilogue() + if not integrity_cancel: + integrity_check(db_name, table_name, ""None"", silent)" +576,https://:@github.com/lsst-sqre/kubespawner.git,5f0ca5f9734552b4c40563828899316d2b69156c,"@@ -361,7 +361,7 @@ class KubeSpawner(Spawner): + # shut down to complete + while True: + data = yield self.get_pod_info(self.pod_name) +- if data is not None: ++ if data is None: + break + time.sleep(5) + +",kubespawner/spawner.py,"ReplaceText(target=' is ' @(364,23)->(364,31))","class KubeSpawner(Spawner): + # shut down to complete + while True: + data = yield self.get_pod_info(self.pod_name) + if data is not None: + break + time.sleep(5) + ","class KubeSpawner(Spawner): + # shut down to complete + while True: + data = yield self.get_pod_info(self.pod_name) + if data is None: + break + time.sleep(5) + " +577,https://:@github.com/lsst-sqre/kubespawner.git,df9936a785e34c898ffd065f17697a0035cf310c,"@@ -404,7 +404,7 @@ class KubeSpawner(Spawner): + @gen.coroutine + def start(self): + pvc_data = get_pvc_info(self.pvc_name) +- if pvc_data is not None: ++ if pvc_data is None: + pvc_manifest = self.get_pvc_manifest() + yield self.httpclient.fetch(self.request( + url=k8s_url(self.namespace, 'persistentvolumeclaims'), +",kubespawner/spawner.py,"ReplaceText(target=' is ' @(407,19)->(407,27))","class KubeSpawner(Spawner): + @gen.coroutine + def start(self): + pvc_data = get_pvc_info(self.pvc_name) + if pvc_data is not None: + pvc_manifest = self.get_pvc_manifest() + yield self.httpclient.fetch(self.request( + url=k8s_url(self.namespace, 'persistentvolumeclaims'),","class KubeSpawner(Spawner): + @gen.coroutine + def start(self): + pvc_data = get_pvc_info(self.pvc_name) + if pvc_data is None: + pvc_manifest = self.get_pvc_manifest() + yield self.httpclient.fetch(self.request( + url=k8s_url(self.namespace, 'persistentvolumeclaims')," +578,https://:@github.com/d-meiser/cold-atoms.git,8235e3bc1d9cc9b1bbfe27948d24adc48db33f06,"@@ -48,5 +48,5 @@ def bend_kick(dt, Bz, ensemble, forces, reference_impl=False): + f = np.zeros_like(ensemble.v) + for force in forces: + force.force(dt, ensemble, f) +- ensemble.v *= f / m ++ ensemble.v += f / m + updater(0.5 * dt, omegaB, ensemble.x, ensemble.v) +",src/coldatoms/bend_kick.py,"ReplaceText(target='+=' @(51,19)->(51,21))","def bend_kick(dt, Bz, ensemble, forces, reference_impl=False): + f = np.zeros_like(ensemble.v) + for force in forces: + force.force(dt, ensemble, f) + ensemble.v *= f / m + updater(0.5 * dt, omegaB, ensemble.x, ensemble.v)","def bend_kick(dt, Bz, ensemble, forces, reference_impl=False): + f = np.zeros_like(ensemble.v) + for force in forces: + force.force(dt, ensemble, f) + ensemble.v += f / m + updater(0.5 * dt, omegaB, ensemble.x, ensemble.v)" +579,https://:@github.com/silvacms/silva.pas.base.git,d0e1b5196420a6a1359fc5f45d220d172f7a1e01,"@@ -41,7 +41,7 @@ class SilvaCascadingPASPlugin(SearchPrincipalsPlugin): + for authenticator_id, auth in authenticators: + try: + info = auth.authenticateCredentials(credentials) +- if info is not None and info[0] is None: ++ if info is not None and info[0] is not None: + # Failed login can be None OR (None, None) + return info + except _SWALLOWABLE_PLUGIN_EXCEPTIONS: +",src/silva/pas/base/plugins/cascading.py,"ReplaceText(target=' is not ' @(44,47)->(44,51))","class SilvaCascadingPASPlugin(SearchPrincipalsPlugin): + for authenticator_id, auth in authenticators: + try: + info = auth.authenticateCredentials(credentials) + if info is not None and info[0] is None: + # Failed login can be None OR (None, None) + return info + except _SWALLOWABLE_PLUGIN_EXCEPTIONS:","class SilvaCascadingPASPlugin(SearchPrincipalsPlugin): + for authenticator_id, auth in authenticators: + try: + info = auth.authenticateCredentials(credentials) + if info is not None and info[0] is not None: + # Failed login can be None OR (None, None) + return info + except _SWALLOWABLE_PLUGIN_EXCEPTIONS:" +580,https://:@github.com/jgolob/maliampi.git,dd0a5bf78106e083005db0e7bd21f1122e63f162,"@@ -239,7 +239,7 @@ class Workflow_Placement(sl.WorkflowTask): + lpca = self.new_task( + 'calculate_lpca', + Jplace_PCA, +- containerinfo=long_containerinfo, ++ containerinfo=highmem_containerinfo, + path=os.path.join( + self.destination_dir, + 'placement', +",maliampi/subcommands/placement.py,"ReplaceText(target='highmem_containerinfo' @(242,26)->(242,44))","class Workflow_Placement(sl.WorkflowTask): + lpca = self.new_task( + 'calculate_lpca', + Jplace_PCA, + containerinfo=long_containerinfo, + path=os.path.join( + self.destination_dir, + 'placement',","class Workflow_Placement(sl.WorkflowTask): + lpca = self.new_task( + 'calculate_lpca', + Jplace_PCA, + containerinfo=highmem_containerinfo, + path=os.path.join( + self.destination_dir, + 'placement'," +581,https://:@github.com/jgolob/maliampi.git,cdea28dbb12093af0165e983149da396b69fe33a,"@@ -115,7 +115,7 @@ class Workflow_DADA2(sl.WorkflowTask): + batch_errModels[batch] = self.new_task( + 'dada2_learn_error_batch_{}'.format(batch), + DADA2_LearnError, +- containerinfo=heavy_containerinfo, ++ containerinfo=midcpu_containerinfo, + batch=batch, + tar_reads=False, + path=os.path.join( +",maliampi/subcommands/sv_dada2.py,"ReplaceText(target='midcpu_containerinfo' @(118,30)->(118,49))","class Workflow_DADA2(sl.WorkflowTask): + batch_errModels[batch] = self.new_task( + 'dada2_learn_error_batch_{}'.format(batch), + DADA2_LearnError, + containerinfo=heavy_containerinfo, + batch=batch, + tar_reads=False, + path=os.path.join(","class Workflow_DADA2(sl.WorkflowTask): + batch_errModels[batch] = self.new_task( + 'dada2_learn_error_batch_{}'.format(batch), + DADA2_LearnError, + containerinfo=midcpu_containerinfo, + batch=batch, + tar_reads=False, + path=os.path.join(" +582,https://:@github.com/jgolob/maliampi.git,3cde81cdd2b908b7edd44a000986744301092fae,"@@ -203,7 +203,7 @@ class Workflow_Classify(sl.WorkflowTask): + placement_db_classified = self.new_task( + 'classify_into_placement_db', + PlacementDB_Classify_SV, +- containerinfo=heavy_containerinfo, ++ containerinfo=midcpu_containerinfo, + ) + placement_db_classified.in_placement_db = placement_db_w_si.out_placement_db + placement_db_classified.in_refpkg_tgz = refpkg_tgz.out_refpkg_tgz +",maliampi/subcommands/classify.py,"ReplaceText(target='midcpu_containerinfo' @(206,26)->(206,45))","class Workflow_Classify(sl.WorkflowTask): + placement_db_classified = self.new_task( + 'classify_into_placement_db', + PlacementDB_Classify_SV, + containerinfo=heavy_containerinfo, + ) + placement_db_classified.in_placement_db = placement_db_w_si.out_placement_db + placement_db_classified.in_refpkg_tgz = refpkg_tgz.out_refpkg_tgz","class Workflow_Classify(sl.WorkflowTask): + placement_db_classified = self.new_task( + 'classify_into_placement_db', + PlacementDB_Classify_SV, + containerinfo=midcpu_containerinfo, + ) + placement_db_classified.in_placement_db = placement_db_w_si.out_placement_db + placement_db_classified.in_refpkg_tgz = refpkg_tgz.out_refpkg_tgz" +583,https://:@github.com/jgolob/maliampi.git,f50cfcea1e390ae5eb05de0c116c2251a09f4864,"@@ -203,7 +203,7 @@ class Workflow_Classify(sl.WorkflowTask): + placement_db_classified = self.new_task( + 'classify_into_placement_db', + PlacementDB_Classify_SV, +- containerinfo=midcpu_containerinfo, ++ containerinfo=highmem_containerinfo, + ) + placement_db_classified.in_placement_db = placement_db_w_si.out_placement_db + placement_db_classified.in_refpkg_tgz = refpkg_tgz.out_refpkg_tgz +",maliampi/subcommands/classify.py,"ReplaceText(target='highmem_containerinfo' @(206,26)->(206,46))","class Workflow_Classify(sl.WorkflowTask): + placement_db_classified = self.new_task( + 'classify_into_placement_db', + PlacementDB_Classify_SV, + containerinfo=midcpu_containerinfo, + ) + placement_db_classified.in_placement_db = placement_db_w_si.out_placement_db + placement_db_classified.in_refpkg_tgz = refpkg_tgz.out_refpkg_tgz","class Workflow_Classify(sl.WorkflowTask): + placement_db_classified = self.new_task( + 'classify_into_placement_db', + PlacementDB_Classify_SV, + containerinfo=highmem_containerinfo, + ) + placement_db_classified.in_placement_db = placement_db_w_si.out_placement_db + placement_db_classified.in_refpkg_tgz = refpkg_tgz.out_refpkg_tgz" +584,https://:@github.com/d3rp/clima.git,92eced31f43fd49f87e6af8582066a25fc0ba726,"@@ -46,7 +46,7 @@ def SeparateFlagArgs(args: list): + Returns: + A tuple with the Fire args (a list), followed by the Flag args (a list). + """""" +- if len(args) > 1 and (args[-1] == '-h' or args[-1] == '--help') and '--' not in args: ++ if len(args) > 0 and (args[-1] == '-h' or args[-1] == '--help') and '--' not in args: + args.pop() + args.append('--') + args.append('-h') +",clima/fire/parser.py,"ReplaceText(target='0' @(49,17)->(49,18))","def SeparateFlagArgs(args: list): + Returns: + A tuple with the Fire args (a list), followed by the Flag args (a list). + """""" + if len(args) > 1 and (args[-1] == '-h' or args[-1] == '--help') and '--' not in args: + args.pop() + args.append('--') + args.append('-h')","def SeparateFlagArgs(args: list): + Returns: + A tuple with the Fire args (a list), followed by the Flag args (a list). + """""" + if len(args) > 0 and (args[-1] == '-h' or args[-1] == '--help') and '--' not in args: + args.pop() + args.append('--') + args.append('-h')" +585,https://:@github.com/jeffkinnison/pyrameter.git,306c95b1e0643fc47e0206281cd12c714849782d,"@@ -47,7 +47,7 @@ def backend_factory(path, *args, **kwargs): + if os.path.isfile(path) or os.path.isdir(path): + from pyrameter.db.local import JsonStorage + return JsonStorage(path, *args, **kwargs) +- elif path.find('mongodb://') >= 0: ++ elif path.find('mongodb://') == 0: + from pyrameter.db.mongo import MongoStorage + return MongoStorage(path, *args, **kwargs) + else: +",pyrameter/db/backend_factory.py,"ReplaceText(target='==' @(50,33)->(50,35))","def backend_factory(path, *args, **kwargs): + if os.path.isfile(path) or os.path.isdir(path): + from pyrameter.db.local import JsonStorage + return JsonStorage(path, *args, **kwargs) + elif path.find('mongodb://') >= 0: + from pyrameter.db.mongo import MongoStorage + return MongoStorage(path, *args, **kwargs) + else:","def backend_factory(path, *args, **kwargs): + if os.path.isfile(path) or os.path.isdir(path): + from pyrameter.db.local import JsonStorage + return JsonStorage(path, *args, **kwargs) + elif path.find('mongodb://') == 0: + from pyrameter.db.mongo import MongoStorage + return MongoStorage(path, *args, **kwargs) + else:" +586,https://:@github.com/RADAR-base/pyRADAR-processing.git,2c6ea694e1d40b9c16d6a10e10c0af9afd5a3d0d,"@@ -115,7 +115,7 @@ class Project(RadarObject): + self.ptcs_update_info(info) + + labels = kwargs.get('labels', False) +- if info: ++ if labels: + for ptc in labels: + if ptc not in self.participants: + self.add_participant(ptc) +",radar/wrappers.py,"ReplaceText(target='labels' @(118,11)->(118,15))","class Project(RadarObject): + self.ptcs_update_info(info) + + labels = kwargs.get('labels', False) + if info: + for ptc in labels: + if ptc not in self.participants: + self.add_participant(ptc)","class Project(RadarObject): + self.ptcs_update_info(info) + + labels = kwargs.get('labels', False) + if labels: + for ptc in labels: + if ptc not in self.participants: + self.add_participant(ptc)" +587,https://:@github.com/marshallward/ropes.git,b8fd70b68d2ec157c7f2397aab3931e50c5a16ae,"@@ -145,7 +145,7 @@ class Rope(object): + else: + if start is None: + offset = index.step + (head.length - 1) % (-index.step) +- elif start > 0: ++ elif start >= 0: + offset = index.step + min(start, head.length - 1) % (-index.step) + else: + offset = index.step + (start + head.length) % (-index.step) +",ropes.py,"ReplaceText(target='>=' @(148,35)->(148,36))","class Rope(object): + else: + if start is None: + offset = index.step + (head.length - 1) % (-index.step) + elif start > 0: + offset = index.step + min(start, head.length - 1) % (-index.step) + else: + offset = index.step + (start + head.length) % (-index.step)","class Rope(object): + else: + if start is None: + offset = index.step + (head.length - 1) % (-index.step) + elif start >= 0: + offset = index.step + min(start, head.length - 1) % (-index.step) + else: + offset = index.step + (start + head.length) % (-index.step)" +588,https://:@github.com/pkgw/bibtools.git,2273ff1a94f4f6952026c5ab1d3ddffa042f2158,"@@ -204,7 +204,7 @@ class Dump (multitool.Command): + help_if_no_args = False + + def invoke (self, args, app=None, **kwargs): +- if len (args) != 1: ++ if len (args) != 0: + raise multitool.UsageError ('expected no arguments') + + app.export_all (sys.stdout, 72) +",bibtools/cli.py,"ReplaceText(target='0' @(207,25)->(207,26))","class Dump (multitool.Command): + help_if_no_args = False + + def invoke (self, args, app=None, **kwargs): + if len (args) != 1: + raise multitool.UsageError ('expected no arguments') + + app.export_all (sys.stdout, 72)","class Dump (multitool.Command): + help_if_no_args = False + + def invoke (self, args, app=None, **kwargs): + if len (args) != 0: + raise multitool.UsageError ('expected no arguments') + + app.export_all (sys.stdout, 72)" +589,https://:@github.com/cooper-software/hammock.git,ed682f4d33be53d7d2f2b21b384a36a2770c6cf5,"@@ -20,7 +20,7 @@ class Hammock(object): + entities = set() + self.collections_by_class_name = {} + +- for collection_cls in collections: ++ for collection_cls in collection_classes: + entities.add(collection_cls.entity) + collection = collection_cls(storage) + self.collections_by_class_name[collection_cls.__name__] = collection +",hammock/__init__.py,"ReplaceText(target='collection_classes' @(23,24)->(23,35))","class Hammock(object): + entities = set() + self.collections_by_class_name = {} + + for collection_cls in collections: + entities.add(collection_cls.entity) + collection = collection_cls(storage) + self.collections_by_class_name[collection_cls.__name__] = collection","class Hammock(object): + entities = set() + self.collections_by_class_name = {} + + for collection_cls in collection_classes: + entities.add(collection_cls.entity) + collection = collection_cls(storage) + self.collections_by_class_name[collection_cls.__name__] = collection" +590,https://:@github.com/bempp/bempp-cl.git,7ab5546ce89b626e146cb29433ed1113a3c72c9c,"@@ -97,7 +97,7 @@ def visualize_with_jupyter_notebook(obj, mode=""element"", transformation=None): + for element in grid.entity_iterator(0): + index = element.index + local_values = np.real( +- transformation(obj.evaluate(element, local_coordinates)) ++ transformation(obj.evaluate(index, local_coordinates)) + ) + values[index] = local_values.flatten() + +",bempp/api/external/viewers.py,"ReplaceText(target='index' @(100,44)->(100,51))","def visualize_with_jupyter_notebook(obj, mode=""element"", transformation=None): + for element in grid.entity_iterator(0): + index = element.index + local_values = np.real( + transformation(obj.evaluate(element, local_coordinates)) + ) + values[index] = local_values.flatten() + ","def visualize_with_jupyter_notebook(obj, mode=""element"", transformation=None): + for element in grid.entity_iterator(0): + index = element.index + local_values = np.real( + transformation(obj.evaluate(index, local_coordinates)) + ) + values[index] = local_values.flatten() + " +591,https://:@github.com/bempp/bempp-cl.git,094eb06f36e837f3a17d2abe23f4bb78d1a32dc0,"@@ -91,7 +91,7 @@ def assemble_dense( + cols = domain.global_dof_count + + nshape_test = dual_to_range.number_of_shape_functions +- nshape_trial = dual_to_range.number_of_shape_functions ++ nshape_trial = domain.number_of_shape_functions + + precision = operator_descriptor.precision + +",bempp/core/numba/dense_assembler.py,"ReplaceText(target='domain' @(94,19)->(94,32))","def assemble_dense( + cols = domain.global_dof_count + + nshape_test = dual_to_range.number_of_shape_functions + nshape_trial = dual_to_range.number_of_shape_functions + + precision = operator_descriptor.precision + ","def assemble_dense( + cols = domain.global_dof_count + + nshape_test = dual_to_range.number_of_shape_functions + nshape_trial = domain.number_of_shape_functions + + precision = operator_descriptor.precision + " +592,https://:@github.com/bempp/bempp-cl.git,242da1c08304423e6ef6ead60e691928426dab1b,"@@ -1035,9 +1035,9 @@ def helmholtz_hypersingular_regular( + ] * ( + curl_product[test_fun_index, trial_fun_index] + - wavenumber +- * wavenumber ++ * wavenumber + * local_test_fun_values[ +- 0, test_fun_index, quad_point_index ++ 0, test_fun_index, test_point_index + ] + * local_trial_fun_values[ + 0, trial_fun_index, quad_point_index +",bempp/core/numba/kernels.py,"ReplaceText(target='test_point_index' @(1040,55)->(1040,71))","def helmholtz_hypersingular_regular( + ] * ( + curl_product[test_fun_index, trial_fun_index] + - wavenumber + * wavenumber + * local_test_fun_values[ + 0, test_fun_index, quad_point_index + ] + * local_trial_fun_values[ + 0, trial_fun_index, quad_point_index","def helmholtz_hypersingular_regular( + ] * ( + curl_product[test_fun_index, trial_fun_index] + - wavenumber + * wavenumber + * local_test_fun_values[ + 0, test_fun_index, test_point_index + ] + * local_trial_fun_values[ + 0, trial_fun_index, quad_point_index" +593,https://:@github.com/bempp/bempp-cl.git,1bb4a1c097e4e3e87ed328f37cde5abd9c0c24b9,"@@ -33,7 +33,7 @@ class DensePotentialAssembler(object): + x_transformed = self.space.map_to_full_grid @ ( + self.space.dof_transformation @ x + ) +- result = implementation(x) ++ result = implementation(x_transformed) + return result.reshape([kernel_dimension, -1], order=""F"") + + self._evaluator = potential_evaluator +",bempp/core/dense_potential_assembler.py,"ReplaceText(target='x_transformed' @(36,36)->(36,37))","class DensePotentialAssembler(object): + x_transformed = self.space.map_to_full_grid @ ( + self.space.dof_transformation @ x + ) + result = implementation(x) + return result.reshape([kernel_dimension, -1], order=""F"") + + self._evaluator = potential_evaluator","class DensePotentialAssembler(object): + x_transformed = self.space.map_to_full_grid @ ( + self.space.dof_transformation @ x + ) + result = implementation(x_transformed) + return result.reshape([kernel_dimension, -1], order=""F"") + + self._evaluator = potential_evaluator" +594,https://:@bitbucket.org/agaveapi/agaveflask.git,17f24e257b275fe1bf64afcf6a5b09d87ab05b79,"@@ -34,7 +34,7 @@ def read_config(conf_file='service.conf'): + raise RuntimeError('No config file found.') + if not parser.parser.read(place): + raise RuntimeError(""couldn't read config file from {0}"" +- .format(', '.join(place))) ++ .format(', '.join(places))) + return parser + + Config = read_config() +\ No newline at end of file +",agaveflask/config.py,"ReplaceText(target='places' @(37,45)->(37,50))","def read_config(conf_file='service.conf'): + raise RuntimeError('No config file found.') + if not parser.parser.read(place): + raise RuntimeError(""couldn't read config file from {0}"" + .format(', '.join(place))) + return parser + + Config = read_config() +\ No newline at end of file","def read_config(conf_file='service.conf'): + raise RuntimeError('No config file found.') + if not parser.parser.read(place): + raise RuntimeError(""couldn't read config file from {0}"" + .format(', '.join(places))) + return parser + + Config = read_config() +\ No newline at end of file" +595,https://:@github.com/llazzaro/jarvispatrick.git,05457d04a6982a47c39d5109b6e91efa6441bd93,"@@ -27,7 +27,7 @@ class JarvisPatrick(object): + def __call__(self, number_of_neighbors, number_of_common_neighbors): + """""" + """""" +- if number_of_common_neighbors >= number_of_neighbors: ++ if number_of_common_neighbors > number_of_neighbors: + raise ValueError('Asked for more common neighbors than number of neighbors') + neighbors_list = {} + for element in self.dataset_elements: +",jarvispatrick/__init__.py,"ReplaceText(target='>' @(30,38)->(30,40))","class JarvisPatrick(object): + def __call__(self, number_of_neighbors, number_of_common_neighbors): + """""" + """""" + if number_of_common_neighbors >= number_of_neighbors: + raise ValueError('Asked for more common neighbors than number of neighbors') + neighbors_list = {} + for element in self.dataset_elements:","class JarvisPatrick(object): + def __call__(self, number_of_neighbors, number_of_common_neighbors): + """""" + """""" + if number_of_common_neighbors > number_of_neighbors: + raise ValueError('Asked for more common neighbors than number of neighbors') + neighbors_list = {} + for element in self.dataset_elements:" +596,https://:@github.com/kennydo/oauthlib.git,1f292e6923aa9419d28e3700e22102dffd447886,"@@ -112,7 +112,7 @@ def collect_parameters(uri_query='', body='', headers=None, + if isinstance(k, str): + k = k.decode('utf-8') + if isinstance(v, str): +- if v.startswith('oauth_'): ++ if k.startswith('oauth_'): + v = utils.unescape(v) + else: + v = v.decode('utf-8') +",oauthlib/oauth1/rfc5849/signature.py,"ReplaceText(target='k' @(115,15)->(115,16))","def collect_parameters(uri_query='', body='', headers=None, + if isinstance(k, str): + k = k.decode('utf-8') + if isinstance(v, str): + if v.startswith('oauth_'): + v = utils.unescape(v) + else: + v = v.decode('utf-8')","def collect_parameters(uri_query='', body='', headers=None, + if isinstance(k, str): + k = k.decode('utf-8') + if isinstance(v, str): + if k.startswith('oauth_'): + v = utils.unescape(v) + else: + v = v.decode('utf-8')" +597,https://:@github.com/kennydo/oauthlib.git,8f57459fbbab1f317d5475f31f90b1a75016a2a8,"@@ -281,7 +281,7 @@ def add_params_to_uri(uri, params, fragment=False): + """"""Add a list of two-tuples to the uri query components."""""" + sch, net, path, par, query, fra = urlparse.urlparse(uri) + if fragment: +- fra = add_params_to_qs(query, params) ++ fra = add_params_to_qs(fra, params) + else: + query = add_params_to_qs(query, params) + return urlparse.urlunparse((sch, net, path, par, query, fra)) +",oauthlib/common.py,"ReplaceText(target='fra' @(284,31)->(284,36))","def add_params_to_uri(uri, params, fragment=False): + """"""Add a list of two-tuples to the uri query components."""""" + sch, net, path, par, query, fra = urlparse.urlparse(uri) + if fragment: + fra = add_params_to_qs(query, params) + else: + query = add_params_to_qs(query, params) + return urlparse.urlunparse((sch, net, path, par, query, fra))","def add_params_to_uri(uri, params, fragment=False): + """"""Add a list of two-tuples to the uri query components."""""" + sch, net, path, par, query, fra = urlparse.urlparse(uri) + if fragment: + fra = add_params_to_qs(fra, params) + else: + query = add_params_to_qs(query, params) + return urlparse.urlunparse((sch, net, path, par, query, fra))" +598,https://:@github.com/jakobrunge/tigramite.git,2011867b0f0cc4c3ca6bb3317b2a3a37d828116b,"@@ -236,7 +236,7 @@ def time_bin_with_mask(data, time_bin_length, sample_selector=None): + sample_selector.shape = (T, 1) + + bindata = numpy.zeros( +- (T / time_bin_length,) + data.shape[1:], dtype=""float32"") ++ (T // time_bin_length,) + data.shape[1:], dtype=""float32"") + for index, i in enumerate(range(0, T - time_bin_length + 1, + time_bin_length)): + # print weighted_avg_and_std(fulldata[i:i+time_bin_length], axis=0, +",tigramite/data_processing.py,"ReplaceText(target='//' @(239,11)->(239,12))","def time_bin_with_mask(data, time_bin_length, sample_selector=None): + sample_selector.shape = (T, 1) + + bindata = numpy.zeros( + (T / time_bin_length,) + data.shape[1:], dtype=""float32"") + for index, i in enumerate(range(0, T - time_bin_length + 1, + time_bin_length)): + # print weighted_avg_and_std(fulldata[i:i+time_bin_length], axis=0,","def time_bin_with_mask(data, time_bin_length, sample_selector=None): + sample_selector.shape = (T, 1) + + bindata = numpy.zeros( + (T // time_bin_length,) + data.shape[1:], dtype=""float32"") + for index, i in enumerate(range(0, T - time_bin_length + 1, + time_bin_length)): + # print weighted_avg_and_std(fulldata[i:i+time_bin_length], axis=0," +599,https://:@github.com/jakobrunge/tigramite.git,2011867b0f0cc4c3ca6bb3317b2a3a37d828116b,"@@ -528,7 +528,7 @@ class LinearMediation(Models): + + def tsg_to_net(self, node, max_lag): + """"""Helper function to translate from time series graph to network."""""" +- row = node / max_lag ++ row = node // max_lag + lag = node % max_lag + return (row, -lag) + +",tigramite/models.py,"ReplaceText(target='//' @(531,19)->(531,20))","class LinearMediation(Models): + + def tsg_to_net(self, node, max_lag): + """"""Helper function to translate from time series graph to network."""""" + row = node / max_lag + lag = node % max_lag + return (row, -lag) + ","class LinearMediation(Models): + + def tsg_to_net(self, node, max_lag): + """"""Helper function to translate from time series graph to network."""""" + row = node // max_lag + lag = node % max_lag + return (row, -lag) + " +600,https://:@github.com/jakobrunge/tigramite.git,ebf5ae6ad58a416f2097bc7453df96b6ff584b17,"@@ -2577,7 +2577,7 @@ class CMIsymb(CondIndTest): + dim, T = symb_array.shape + + # Needed because np.bincount cannot process longs +- if isinstance(self.n_symbs ** dim, int): ++ if not isinstance(self.n_symbs ** dim, int): + raise ValueError(""Too many n_symbs and/or dimensions, "" + ""numpy.bincount cannot process longs"") + if self.n_symbs ** dim * 16. / 8. / 1024. ** 3 > 3.: +",tigramite/independence_tests.py,"ReplaceText(target='not ' @(2580,11)->(2580,11))","class CMIsymb(CondIndTest): + dim, T = symb_array.shape + + # Needed because np.bincount cannot process longs + if isinstance(self.n_symbs ** dim, int): + raise ValueError(""Too many n_symbs and/or dimensions, "" + ""numpy.bincount cannot process longs"") + if self.n_symbs ** dim * 16. / 8. / 1024. ** 3 > 3.:","class CMIsymb(CondIndTest): + dim, T = symb_array.shape + + # Needed because np.bincount cannot process longs + if not isinstance(self.n_symbs ** dim, int): + raise ValueError(""Too many n_symbs and/or dimensions, "" + ""numpy.bincount cannot process longs"") + if self.n_symbs ** dim * 16. / 8. / 1024. ** 3 > 3.:" +601,https://:@github.com/ontio/neo-boa.git,07ac051d44eb38ac612effd14b57af0a5b65c90e,"@@ -8,7 +8,7 @@ class SCTest(FunctionCode): + @staticmethod + def Main(a, b): + +- if a > b: ++ if a == b: + + return True + +",tests/src/CompareTest2.py,"ReplaceText(target='==' @(11,13)->(11,14))","class SCTest(FunctionCode): + @staticmethod + def Main(a, b): + + if a > b: + + return True + ","class SCTest(FunctionCode): + @staticmethod + def Main(a, b): + + if a == b: + + return True + " +602,https://:@github.com/ggventurini/python-deltasigma.git,3dd6127dc022234c4433d4e4a018942927fa417f,"@@ -59,7 +59,7 @@ def cancelPZ(arg1, tol=1e-6): + z = copy.copy(arg1.zeros) + p = copy.copy(arg1.poles) + k = arg1.gain +- for i in range(max(z.shape) - 1, 0, -1): ++ for i in range(max(z.shape) - 1, -1, -1): + d = z[i] - p + cancel = np.nonzero(np.abs(d) < tol)[0] + if cancel.size: +",deltasigma/_cancelPZ.py,"ReplaceText(target='-1' @(62,37)->(62,38))","def cancelPZ(arg1, tol=1e-6): + z = copy.copy(arg1.zeros) + p = copy.copy(arg1.poles) + k = arg1.gain + for i in range(max(z.shape) - 1, 0, -1): + d = z[i] - p + cancel = np.nonzero(np.abs(d) < tol)[0] + if cancel.size:","def cancelPZ(arg1, tol=1e-6): + z = copy.copy(arg1.zeros) + p = copy.copy(arg1.poles) + k = arg1.gain + for i in range(max(z.shape) - 1, -1, -1): + d = z[i] - p + cancel = np.nonzero(np.abs(d) < tol)[0] + if cancel.size:" +603,https://:@github.com/jordens/rayopt.git,3bc56650b966e2c34d25d47af76d3b7f63110c4f,"@@ -199,7 +199,7 @@ class Analysis(object): + axp, axm, axsm, axss, axo = axi + axp.add_patch(mpl.patches.Circle((0, 0), r, edgecolor=""black"", + facecolor=""none"")) +- axp.text(-.1, .5, ""OY=%s"" % hi, rotation=""vertical"", ++ axo.text(-.1, .5, ""OY=%s"" % hi, rotation=""vertical"", + transform=axp.transAxes, + verticalalignment=""center"") + for i, (wi, ci) in enumerate(zip(wavelengths, colors)): +",rayopt/analysis.py,"ReplaceText(target='axo' @(202,12)->(202,15))","class Analysis(object): + axp, axm, axsm, axss, axo = axi + axp.add_patch(mpl.patches.Circle((0, 0), r, edgecolor=""black"", + facecolor=""none"")) + axp.text(-.1, .5, ""OY=%s"" % hi, rotation=""vertical"", + transform=axp.transAxes, + verticalalignment=""center"") + for i, (wi, ci) in enumerate(zip(wavelengths, colors)):","class Analysis(object): + axp, axm, axsm, axss, axo = axi + axp.add_patch(mpl.patches.Circle((0, 0), r, edgecolor=""black"", + facecolor=""none"")) + axo.text(-.1, .5, ""OY=%s"" % hi, rotation=""vertical"", + transform=axp.transAxes, + verticalalignment=""center"") + for i, (wi, ci) in enumerate(zip(wavelengths, colors)):" +604,https://:@github.com/jordens/rayopt.git,0d5689d0c36fa3aec836c7869e169f4bc4b1a72f,"@@ -333,7 +333,7 @@ class System(list): + c = getattr(el, ""curvature"", 0) + if pending is not None: + r = max(el.radius, pending.radius) +- if c < 0: ++ if c <= 0: + el.radius = r + if c0 > 0: + pending.radius = r +",rayopt/system.py,"ReplaceText(target='<=' @(336,21)->(336,22))","class System(list): + c = getattr(el, ""curvature"", 0) + if pending is not None: + r = max(el.radius, pending.radius) + if c < 0: + el.radius = r + if c0 > 0: + pending.radius = r","class System(list): + c = getattr(el, ""curvature"", 0) + if pending is not None: + r = max(el.radius, pending.radius) + if c <= 0: + el.radius = r + if c0 > 0: + pending.radius = r" +605,https://:@github.com/pantherlab/v2d-cli.git,fe2f6fe46f14778cfcb74852d817d1876d171352,"@@ -92,7 +92,7 @@ def main(): + print('Similar domains to {}'.format(dom)) + domains.difference_update(set(dom)) + for d in domains: +- print_diff(d, args.domain) ++ print_diff(args.domain, d) + if write: + f.write(d + ""\n"") + if (args.check): +",v2d/main.py,"ArgSwap(idxs=0<->1 @(95,16)->(95,26))","def main(): + print('Similar domains to {}'.format(dom)) + domains.difference_update(set(dom)) + for d in domains: + print_diff(d, args.domain) + if write: + f.write(d + ""\n"") + if (args.check):","def main(): + print('Similar domains to {}'.format(dom)) + domains.difference_update(set(dom)) + for d in domains: + print_diff(args.domain, d) + if write: + f.write(d + ""\n"") + if (args.check):" +606,https://:@github.com/xtimon/inipgdump.git,47c9bf35a256ee9c6caa0aeb6913a5e80cc15d23,"@@ -92,7 +92,7 @@ def main(): + if not os.path.isdir(dump_dir): + print('Folder \'%s\' not found' % dump_dir) + sys.exit(1) +- if keep_count <= 0: ++ if keep_count < 0: + print('keep_count must be greater than 0') + sys.exit(1) + make_dump(conf_file, dump_dir, keep_count) +",inipgdump/core.py,"ReplaceText(target='<' @(95,18)->(95,20))","def main(): + if not os.path.isdir(dump_dir): + print('Folder \'%s\' not found' % dump_dir) + sys.exit(1) + if keep_count <= 0: + print('keep_count must be greater than 0') + sys.exit(1) + make_dump(conf_file, dump_dir, keep_count)","def main(): + if not os.path.isdir(dump_dir): + print('Folder \'%s\' not found' % dump_dir) + sys.exit(1) + if keep_count < 0: + print('keep_count must be greater than 0') + sys.exit(1) + make_dump(conf_file, dump_dir, keep_count)" +607,https://:@github.com/dogebuild/dogebuild.git,5fbc92cbf6aceb4a99374e5e19208b3889c36628,"@@ -14,7 +14,7 @@ class Doge: + plugin_full_name = self.contrib_name + '-' + plugin_name + plugin_package = self.contrib_name + '_' + plugin_name + +- if not self.check_plugin_installed(plugin_full_name): ++ if not self.check_plugin_installed(plugin_package): + self.pip.install(plugin_full_name) # ??? + + file, path, desc = self.find_dotted_module(plugin_package + '.loader') +",dogebuild/Doge.py,"ReplaceText(target='plugin_package' @(17,43)->(17,59))","class Doge: + plugin_full_name = self.contrib_name + '-' + plugin_name + plugin_package = self.contrib_name + '_' + plugin_name + + if not self.check_plugin_installed(plugin_full_name): + self.pip.install(plugin_full_name) # ??? + + file, path, desc = self.find_dotted_module(plugin_package + '.loader')","class Doge: + plugin_full_name = self.contrib_name + '-' + plugin_name + plugin_package = self.contrib_name + '_' + plugin_name + + if not self.check_plugin_installed(plugin_package): + self.pip.install(plugin_full_name) # ??? + + file, path, desc = self.find_dotted_module(plugin_package + '.loader')" +608,https://:@github.com/jiosue/qubovert.git,11782cc691038742a250ee53b863c413f28b6455,"@@ -329,7 +329,7 @@ class DictArithmetic(dict): + for k, v in other.items(): + self[k] -= v + else: +- self[()] -= v ++ self[()] -= other + return self + + def __mul__(self, other): +",qubovert/utils/_dict_arithmetic.py,"ReplaceText(target='other' @(332,24)->(332,25))","class DictArithmetic(dict): + for k, v in other.items(): + self[k] -= v + else: + self[()] -= v + return self + + def __mul__(self, other):","class DictArithmetic(dict): + for k, v in other.items(): + self[k] -= v + else: + self[()] -= other + return self + + def __mul__(self, other):" +609,https://:@github.com/jiosue/qubovert.git,ad39ad11cea1cd2ca8f82a23b21990cd0e758915,"@@ -323,7 +323,7 @@ class SpinSimulation: + # the change in energy from flipping variable i is equal to + # -2 * (the energy of the subgraph depending on i) + dE = -2 * puso_value(self._state, self._subgraphs[i]) +- if dE < 0 or (T and random.random() < exp(-dE / T)): ++ if dE <= 0 or (T and random.random() < exp(-dE / T)): + self._flip_bit(i) + + +",qubovert/sim/_simulations.py,"ReplaceText(target='<=' @(326,22)->(326,23))","class SpinSimulation: + # the change in energy from flipping variable i is equal to + # -2 * (the energy of the subgraph depending on i) + dE = -2 * puso_value(self._state, self._subgraphs[i]) + if dE < 0 or (T and random.random() < exp(-dE / T)): + self._flip_bit(i) + + ","class SpinSimulation: + # the change in energy from flipping variable i is equal to + # -2 * (the energy of the subgraph depending on i) + dE = -2 * puso_value(self._state, self._subgraphs[i]) + if dE <= 0 or (T and random.random() < exp(-dE / T)): + self._flip_bit(i) + + " +610,https://:@github.com/gjo/colander_jsonschema.git,14d7446b85b8faf56705047146a62f10981c0bf7,"@@ -124,7 +124,7 @@ class ValidatorConversionDispatcher(object): + if isinstance(validator, colander.All): + converted = {} + for v in validator.validators: +- ret = self(schema_node, validator) ++ ret = self(schema_node, v) + converted.update(ret) + return converted + +",colander_jsonschema/__init__.py,"ReplaceText(target='v' @(127,40)->(127,49))","class ValidatorConversionDispatcher(object): + if isinstance(validator, colander.All): + converted = {} + for v in validator.validators: + ret = self(schema_node, validator) + converted.update(ret) + return converted + ","class ValidatorConversionDispatcher(object): + if isinstance(validator, colander.All): + converted = {} + for v in validator.validators: + ret = self(schema_node, v) + converted.update(ret) + return converted + " +611,https://:@github.com/ucl-exoplanets/TauREx3_public.git,fdfa8c4e1d29dc715c7f42d55c21c0d911390a83,"@@ -127,7 +127,7 @@ def main(): + + wlgrid = np.log10(10000/bindown_wngrid) + if args.plot: +- if get_rank()==0 and nprocs()==1: ++ if get_rank()==0 and nprocs()<=1: + import matplotlib.pyplot as plt + if args.contrib: + for name,value in contrib: +",taurex/taurex.py,"ReplaceText(target='<=' @(130,38)->(130,40))","def main(): + + wlgrid = np.log10(10000/bindown_wngrid) + if args.plot: + if get_rank()==0 and nprocs()==1: + import matplotlib.pyplot as plt + if args.contrib: + for name,value in contrib:","def main(): + + wlgrid = np.log10(10000/bindown_wngrid) + if args.plot: + if get_rank()==0 and nprocs()<=1: + import matplotlib.pyplot as plt + if args.contrib: + for name,value in contrib:" +612,https://:@github.com/ucl-exoplanets/TauREx3_public.git,b159dcc22b3e753aaea101031b3c8df14e5affdc,"@@ -135,7 +135,7 @@ def main(): + priors = {} + priors['Profiles'] = profiles + priors['Spectra'] = spectrum +- out.store_dictionary(solution,group_name='Priors') ++ out.store_dictionary(priors,group_name='Priors') + else: + out.store_dictionary(profiles,group_name='Profiles') + out.store_dictionary(spectrum,group_name='Spectra') +",taurex/taurex.py,"ReplaceText(target='priors' @(138,37)->(138,45))","def main(): + priors = {} + priors['Profiles'] = profiles + priors['Spectra'] = spectrum + out.store_dictionary(solution,group_name='Priors') + else: + out.store_dictionary(profiles,group_name='Profiles') + out.store_dictionary(spectrum,group_name='Spectra')","def main(): + priors = {} + priors['Profiles'] = profiles + priors['Spectra'] = spectrum + out.store_dictionary(priors,group_name='Priors') + else: + out.store_dictionary(profiles,group_name='Profiles') + out.store_dictionary(spectrum,group_name='Spectra')" +613,https://:@github.com/ucl-exoplanets/TauREx3_public.git,1aa67f68d7086afcf2390add80728193d7a9024e,"@@ -13,7 +13,7 @@ def nprocs(): + try: + from mpi4py import MPI + except ImportError: +- return 0 ++ return 1 + + comm = MPI.COMM_WORLD + +",taurex/mpi.py,"ReplaceText(target='1' @(16,15)->(16,16))","def nprocs(): + try: + from mpi4py import MPI + except ImportError: + return 0 + + comm = MPI.COMM_WORLD + ","def nprocs(): + try: + from mpi4py import MPI + except ImportError: + return 1 + + comm = MPI.COMM_WORLD + " +614,https://:@github.com/sjoerdk/yeahyeah.git,11a1a12a02c9fea724f0dc4072b5e86e688e33fd,"@@ -66,7 +66,7 @@ def add(context: ClockifyPluginContext, message, project, time): + project_obj = None + + log_start = time +- click.echo(f""Adding {message} at {as_local(log_start)} to project {project}"") ++ click.echo(f""Adding {message} at {as_local(log_start)} to project {project_obj}"") + context.session.add_time_entry( + start_time=time, description=message, project=project_obj + ) +",plugins/clockify_plugin/cli.py,"ReplaceText(target='project_obj' @(69,71)->(69,78))","def add(context: ClockifyPluginContext, message, project, time): + project_obj = None + + log_start = time + click.echo(f""Adding {message} at {as_local(log_start)} to project {project}"") + context.session.add_time_entry( + start_time=time, description=message, project=project_obj + )","def add(context: ClockifyPluginContext, message, project, time): + project_obj = None + + log_start = time + click.echo(f""Adding {message} at {as_local(log_start)} to project {project_obj}"") + context.session.add_time_entry( + start_time=time, description=message, project=project_obj + )" +615,https://:@bitbucket.org/synerty/peek-plugin-graphdb.git,c47b1c7df8ba01b9a47a9afda0f1c1f829517990,"@@ -58,7 +58,7 @@ class PackedSegmentTupleProvider(TuplesProviderABC): + + # Create the new object + foundDocuments.append(GraphDbPackedSegmentTuple( +- key=key, ++ key=subKey, + packedJson=segmentsByKey[subKey] + )) + +",peek_plugin_graphdb/_private/client/tuple_providers/PackedSegmentTupleProvider.py,"ReplaceText(target='subKey' @(61,24)->(61,27))","class PackedSegmentTupleProvider(TuplesProviderABC): + + # Create the new object + foundDocuments.append(GraphDbPackedSegmentTuple( + key=key, + packedJson=segmentsByKey[subKey] + )) + ","class PackedSegmentTupleProvider(TuplesProviderABC): + + # Create the new object + foundDocuments.append(GraphDbPackedSegmentTuple( + key=subKey, + packedJson=segmentsByKey[subKey] + )) + " +616,https://:@github.com/ihgazni2/ematmap.git,d6f160d8c7b85fdca2d552ca6de1c1c3c75b3245,"@@ -50,7 +50,7 @@ def get_matsize(m): + size = 0 + depth = len(m) + for i in range(depth): +- layer = m[depth] ++ layer = m[i] + lngth = len(layer) + for j in range(lngth): + size = size + 1 +",ematmap/utils.py,"ReplaceText(target='i' @(53,18)->(53,23))","def get_matsize(m): + size = 0 + depth = len(m) + for i in range(depth): + layer = m[depth] + lngth = len(layer) + for j in range(lngth): + size = size + 1","def get_matsize(m): + size = 0 + depth = len(m) + for i in range(depth): + layer = m[i] + lngth = len(layer) + for j in range(lngth): + size = size + 1" +617,https://:@github.com/ndawe/goodruns.git,fa5a7a24b6ebaa80141a0fd5b887e61eeb60d0d0,"@@ -258,7 +258,7 @@ class GRL(object): + version = root.find('NamedLumiRange/Version') + if version is not None: + self.version = version.text +- self.metadata = root.findall('NamedLumiRange/Metadata') ++ self.metadata += root.findall('NamedLumiRange/Metadata') + lbcols = root.findall( + 'NamedLumiRange/LumiBlockCollection') + for lbcol in lbcols: +",goodruns/grl.py,"ReplaceText(target='+=' @(261,22)->(261,23))","class GRL(object): + version = root.find('NamedLumiRange/Version') + if version is not None: + self.version = version.text + self.metadata = root.findall('NamedLumiRange/Metadata') + lbcols = root.findall( + 'NamedLumiRange/LumiBlockCollection') + for lbcol in lbcols:","class GRL(object): + version = root.find('NamedLumiRange/Version') + if version is not None: + self.version = version.text + self.metadata += root.findall('NamedLumiRange/Metadata') + lbcols = root.findall( + 'NamedLumiRange/LumiBlockCollection') + for lbcol in lbcols:" +618,https://:@github.com/churchill-lab/scBASE.git,456bacc4227fd3ccb5a901a205b0add65f9d8dfc,"@@ -37,7 +37,7 @@ except NameError: + + def select(loomfile, min_read_count, min_cell_count, layer): + with loompy.connect(loomfile) as ds: +- gsurv = (ds.sparse(layer=layer) >= min_read_count).sum(axis=1) > min_cell_count ++ gsurv = (ds.sparse(layer=layer) >= min_read_count).sum(axis=1) >= min_cell_count + ds.ra.Selected = np.squeeze(np.asarray(gsurv)) + LOG.info('Total %d genes selected' % gsurv.sum()) + # totals = ds.map([np.sum], axis=1)[0] # Select based upon cell size? +",scbase/scbase.py,"ReplaceText(target='>=' @(40,71)->(40,72))","except NameError: + + def select(loomfile, min_read_count, min_cell_count, layer): + with loompy.connect(loomfile) as ds: + gsurv = (ds.sparse(layer=layer) >= min_read_count).sum(axis=1) > min_cell_count + ds.ra.Selected = np.squeeze(np.asarray(gsurv)) + LOG.info('Total %d genes selected' % gsurv.sum()) + # totals = ds.map([np.sum], axis=1)[0] # Select based upon cell size?","except NameError: + + def select(loomfile, min_read_count, min_cell_count, layer): + with loompy.connect(loomfile) as ds: + gsurv = (ds.sparse(layer=layer) >= min_read_count).sum(axis=1) >= min_cell_count + ds.ra.Selected = np.squeeze(np.asarray(gsurv)) + LOG.info('Total %d genes selected' % gsurv.sum()) + # totals = ds.map([np.sum], axis=1)[0] # Select based upon cell size?" +619,https://:@github.com/glottolog/treedb.git,af327b021d5aa5ee8c593903f663f5653181217d,"@@ -48,7 +48,7 @@ def iterrecords(bind=ENGINE, windowsize=WINDOWSIZE, skip_unknown=True): + with bind.connect() as conn: + select_files.bind = conn + select_values.bind = conn +- for in_slice in window_slices(File.id, size=windowsize, bind=bind): ++ for in_slice in window_slices(File.id, size=windowsize, bind=conn): + if log.level <= logging.DEBUG: + where = literal_compile(in_slice(File.id)) + log.debug('fetch rows %r', where.string) +",treedb/raw/records.py,"ReplaceText(target='conn' @(51,69)->(51,73))","def iterrecords(bind=ENGINE, windowsize=WINDOWSIZE, skip_unknown=True): + with bind.connect() as conn: + select_files.bind = conn + select_values.bind = conn + for in_slice in window_slices(File.id, size=windowsize, bind=bind): + if log.level <= logging.DEBUG: + where = literal_compile(in_slice(File.id)) + log.debug('fetch rows %r', where.string)","def iterrecords(bind=ENGINE, windowsize=WINDOWSIZE, skip_unknown=True): + with bind.connect() as conn: + select_files.bind = conn + select_values.bind = conn + for in_slice in window_slices(File.id, size=windowsize, bind=conn): + if log.level <= logging.DEBUG: + where = literal_compile(in_slice(File.id)) + log.debug('fetch rows %r', where.string)" +620,https://:@github.com/funkybob/django-rated.git,4c68393abfdbb42030e0211c8c99ac8f2fa251d0,"@@ -14,7 +14,7 @@ class RatedMiddleware(object): + def process_view(self, request, view_func, view_args, view_kwargs): + # Try to determine the realm for this view + try: +- realm = request._rated_realm ++ realm = view_func._rated_realm + except AttributeError: + try: + realm = settings.REALM_MAP[request.resolver_match.url_name] +",rated/middleware.py,"ReplaceText(target='view_func' @(17,20)->(17,27))","class RatedMiddleware(object): + def process_view(self, request, view_func, view_args, view_kwargs): + # Try to determine the realm for this view + try: + realm = request._rated_realm + except AttributeError: + try: + realm = settings.REALM_MAP[request.resolver_match.url_name]","class RatedMiddleware(object): + def process_view(self, request, view_func, view_args, view_kwargs): + # Try to determine the realm for this view + try: + realm = view_func._rated_realm + except AttributeError: + try: + realm = settings.REALM_MAP[request.resolver_match.url_name]" +621,https://:@github.com/StevenGolovkine/FDApy.git,f1768ccf93593162be890f8685027b9d9a1d3ad2,"@@ -25,7 +25,7 @@ def _check_argvals(argvals): + ------ + argvals : list of numpy.ndarray + """""" +- if isinstance(argvals, (np.ndarray, list)): ++ if not isinstance(argvals, (np.ndarray, list)): + raise ValueError( + 'argvals has to be a list of numpy.ndarray or a numpy.ndarray!') + # TODO: Modify the condition to accept multidimensional irregular +",FDApy/irregular_functional.py,"ReplaceText(target='not ' @(28,7)->(28,7))","def _check_argvals(argvals): + ------ + argvals : list of numpy.ndarray + """""" + if isinstance(argvals, (np.ndarray, list)): + raise ValueError( + 'argvals has to be a list of numpy.ndarray or a numpy.ndarray!') + # TODO: Modify the condition to accept multidimensional irregular","def _check_argvals(argvals): + ------ + argvals : list of numpy.ndarray + """""" + if not isinstance(argvals, (np.ndarray, list)): + raise ValueError( + 'argvals has to be a list of numpy.ndarray or a numpy.ndarray!') + # TODO: Modify the condition to accept multidimensional irregular" +622,https://:@github.com/StevenGolovkine/FDApy.git,f1768ccf93593162be890f8685027b9d9a1d3ad2,"@@ -30,7 +30,7 @@ def _check_argvals(argvals): + ------ + argvals : list of numpy.ndarray + """""" +- if isinstance(argvals, (np.ndarray, list)): ++ if not isinstance(argvals, (np.ndarray, list)): + raise ValueError( + 'argvals has to be a list of numpy.ndarray or a numpy.ndarray!') + if isinstance(argvals, list) and \ +",FDApy/univariate_functional.py,"ReplaceText(target='not ' @(33,7)->(33,7))","def _check_argvals(argvals): + ------ + argvals : list of numpy.ndarray + """""" + if isinstance(argvals, (np.ndarray, list)): + raise ValueError( + 'argvals has to be a list of numpy.ndarray or a numpy.ndarray!') + if isinstance(argvals, list) and \","def _check_argvals(argvals): + ------ + argvals : list of numpy.ndarray + """""" + if not isinstance(argvals, (np.ndarray, list)): + raise ValueError( + 'argvals has to be a list of numpy.ndarray or a numpy.ndarray!') + if isinstance(argvals, list) and \" +623,https://:@github.com/StevenGolovkine/FDApy.git,4fbe69f439588f469d858b25c3d063e02b45ed97,"@@ -24,9 +24,9 @@ def _check_data(data): + ------ + data : list of UnivariateFunctionalData ot IrregularFunctionalData + """""" +- if isinstance(data, (list, +- UnivariateFunctionalData, +- IrregularFunctionalData)): ++ if not isinstance(data, (list, ++ UnivariateFunctionalData, ++ IrregularFunctionalData)): + raise ValueError( + """"""Data has to be a list or elements of UnivariateFunctionalData + or IrregularFunctionalData!"""""") +",FDApy/multivariate_functional.py,"ReplaceText(target='not ' @(27,7)->(27,7))","def _check_data(data): + ------ + data : list of UnivariateFunctionalData ot IrregularFunctionalData + """""" + if isinstance(data, (list, + UnivariateFunctionalData, + IrregularFunctionalData)): + raise ValueError( + """"""Data has to be a list or elements of UnivariateFunctionalData + or IrregularFunctionalData!"""""")","def _check_data(data): + ------ + data : list of UnivariateFunctionalData ot IrregularFunctionalData + """""" + if not isinstance(data, (list, + UnivariateFunctionalData, + IrregularFunctionalData)): + raise ValueError( + """"""Data has to be a list or elements of UnivariateFunctionalData + or IrregularFunctionalData!"""""")" +624,https://:@github.com/StevenGolovkine/FDApy.git,a671e9da96d43a8cd21778b535374dce8942e7da,"@@ -1075,7 +1075,7 @@ class IrregularFunctionalData(FunctionalData): + bandwidth=b, + degree=degree) + pred = lp.fit_predict(arg, val, points_estim) +- smooth_argvals[i] = arg ++ smooth_argvals[i] = points_estim + smooth_values[i] = pred + return IrregularFunctionalData({'input_dim_0': smooth_argvals}, + smooth_values) +",FDApy/representation/functional_data.py,"ReplaceText(target='points_estim' @(1078,32)->(1078,35))","class IrregularFunctionalData(FunctionalData): + bandwidth=b, + degree=degree) + pred = lp.fit_predict(arg, val, points_estim) + smooth_argvals[i] = arg + smooth_values[i] = pred + return IrregularFunctionalData({'input_dim_0': smooth_argvals}, + smooth_values)","class IrregularFunctionalData(FunctionalData): + bandwidth=b, + degree=degree) + pred = lp.fit_predict(arg, val, points_estim) + smooth_argvals[i] = points_estim + smooth_values[i] = pred + return IrregularFunctionalData({'input_dim_0': smooth_argvals}, + smooth_values)" +625,https://:@github.com/Flowminder/pytest-airflow.git,47c128f0affa875e4baed2f7223fcd0747f3bb55,"@@ -138,7 +138,7 @@ def _task_gen(item, **kwds): + provide_context=True, + dag=dag, + ) +- dag.set_dependency(task_id, ""__pytest_branch"") ++ dag.set_dependency(""__pytest_branch"", task_id) + return task + + +",pytest_airflow/plugin.py,"ArgSwap(idxs=0<->1 @(141,4)->(141,22))","def _task_gen(item, **kwds): + provide_context=True, + dag=dag, + ) + dag.set_dependency(task_id, ""__pytest_branch"") + return task + + ","def _task_gen(item, **kwds): + provide_context=True, + dag=dag, + ) + dag.set_dependency(""__pytest_branch"", task_id) + return task + + " +626,https://:@github.com/datadrivencontrol/pyvrft.git,d21df29ac62c08e4de3bfbcc1c01a6943cfe78fe,"@@ -77,7 +77,7 @@ def design(u,y,y_iv,Td,C,L): + y_iv=y_iv[0:N,:] + # virtual error + ebar=rv-y +- ebar_iv=rv-y_iv ++ ebar_iv=rv_iv-y_iv + # remove the last samples of the input (to match the dimension of the virtual error) + uf=uf[0:N,:] + +",vrft/control.py,"ReplaceText(target='rv_iv' @(80,16)->(80,18))","def design(u,y,y_iv,Td,C,L): + y_iv=y_iv[0:N,:] + # virtual error + ebar=rv-y + ebar_iv=rv-y_iv + # remove the last samples of the input (to match the dimension of the virtual error) + uf=uf[0:N,:] + ","def design(u,y,y_iv,Td,C,L): + y_iv=y_iv[0:N,:] + # virtual error + ebar=rv-y + ebar_iv=rv_iv-y_iv + # remove the last samples of the input (to match the dimension of the virtual error) + uf=uf[0:N,:] + " +627,https://:@github.com/onecommons/unfurl.git,c7b04c15dc919919696f6d20fef4465c25fda6d3,"@@ -67,7 +67,7 @@ class Resource(object): + + @property + def root(self): +- return self.ancestors[0] ++ return self.ancestors[-1] + + def __getitem__(self, name): + if not name: +",giterop/resource.py,"ReplaceText(target='-1' @(70,26)->(70,27))","class Resource(object): + + @property + def root(self): + return self.ancestors[0] + + def __getitem__(self, name): + if not name:","class Resource(object): + + @property + def root(self): + return self.ancestors[-1] + + def __getitem__(self, name): + if not name:" +628,https://:@github.com/onecommons/unfurl.git,7b9fe40414b2646ba7ee98e1f7ab770feed1c80a,"@@ -336,7 +336,7 @@ Returns: + if not configSpec: + raise UnfurlError( + 'unable to find an implementation to ""%s"" ""%s"" on """"%s"": %s' +- % (action, resource.template.name, resource.template.name, reason) ++ % (action, resource.template.name, resource.template.name, notfoundmsg) + ) + logger.debug( + ""creating configuration %s with %s to run for %s: %s"", +",unfurl/plan.py,"ReplaceText(target='notfoundmsg' @(339,75)->(339,81))","Returns: + if not configSpec: + raise UnfurlError( + 'unable to find an implementation to ""%s"" ""%s"" on """"%s"": %s' + % (action, resource.template.name, resource.template.name, reason) + ) + logger.debug( + ""creating configuration %s with %s to run for %s: %s"",","Returns: + if not configSpec: + raise UnfurlError( + 'unable to find an implementation to ""%s"" ""%s"" on """"%s"": %s' + % (action, resource.template.name, resource.template.name, notfoundmsg) + ) + logger.debug( + ""creating configuration %s with %s to run for %s: %s""," +629,https://:@github.com/heartexlabs/label-studio-evalme.git,9b7f13ab32802d5ef602d1c4f9399e949b9f3df8,"@@ -35,7 +35,7 @@ class HTMLTagsEvalItem(EvalItem): + + + def _as_html_tags_eval_item(item): +- if not isinstance(HTMLTagsEvalItem, item): ++ if not isinstance(item, HTMLTagsEvalItem): + return HTMLTagsEvalItem(item) + return item + +",evalme/text/text.py,"ArgSwap(idxs=0<->1 @(38,11)->(38,21))","class HTMLTagsEvalItem(EvalItem): + + + def _as_html_tags_eval_item(item): + if not isinstance(HTMLTagsEvalItem, item): + return HTMLTagsEvalItem(item) + return item + ","class HTMLTagsEvalItem(EvalItem): + + + def _as_html_tags_eval_item(item): + if not isinstance(item, HTMLTagsEvalItem): + return HTMLTagsEvalItem(item) + return item + " +630,https://:@github.com/parlance/ctcdecode.git,1a35bb5fc07eee0c9939fdf824fa8158ec52499a,"@@ -20,7 +20,7 @@ class CTCBeamDecoder(object): + def decode(self, probs, seq_lens): + # We expect batch x seq x label_size + probs = probs.cpu().float() +- seq_lens = probs.cpu().int() ++ seq_lens = seq_lens.cpu().int() + batch_size, max_seq_len = probs.size(0), probs.size(1) + output = torch.IntTensor(batch_size, self._beam_width, max_seq_len).cpu().int() + timesteps = torch.IntTensor(batch_size, self._beam_width, max_seq_len).cpu().int() +",ctcdecode/__init__.py,"ReplaceText(target='seq_lens' @(23,19)->(23,24))","class CTCBeamDecoder(object): + def decode(self, probs, seq_lens): + # We expect batch x seq x label_size + probs = probs.cpu().float() + seq_lens = probs.cpu().int() + batch_size, max_seq_len = probs.size(0), probs.size(1) + output = torch.IntTensor(batch_size, self._beam_width, max_seq_len).cpu().int() + timesteps = torch.IntTensor(batch_size, self._beam_width, max_seq_len).cpu().int()","class CTCBeamDecoder(object): + def decode(self, probs, seq_lens): + # We expect batch x seq x label_size + probs = probs.cpu().float() + seq_lens = seq_lens.cpu().int() + batch_size, max_seq_len = probs.size(0), probs.size(1) + output = torch.IntTensor(batch_size, self._beam_width, max_seq_len).cpu().int() + timesteps = torch.IntTensor(batch_size, self._beam_width, max_seq_len).cpu().int()" +631,https://:@github.com/benmaier/binpacking.git,6ada2c62c319d56cd0f5918a2f01ff61d0e45348,"@@ -107,7 +107,7 @@ def to_constant_bin_number(d,N_bin,weight_pos=None,lower_bound=None,upper_bound= + while not found_bin: + + #if this weight fits in the bin +- if new_weight_sum < V_bin_max: ++ if new_weight_sum <= V_bin_max: + + #...put it in + if isdict: +",binpacking/to_constant_bin_number.py,"ReplaceText(target='<=' @(110,30)->(110,31))","def to_constant_bin_number(d,N_bin,weight_pos=None,lower_bound=None,upper_bound= + while not found_bin: + + #if this weight fits in the bin + if new_weight_sum < V_bin_max: + + #...put it in + if isdict:","def to_constant_bin_number(d,N_bin,weight_pos=None,lower_bound=None,upper_bound= + while not found_bin: + + #if this weight fits in the bin + if new_weight_sum <= V_bin_max: + + #...put it in + if isdict:" +632,https://:@github.com/amatino-code/nozomi.git,dc608f09a68fc8972f563e2b9974692581d40efc,"@@ -257,7 +257,7 @@ integers'.format( + min_value=min_value + )) + +- return values ++ return validated + + def optionally_parse_bool( + self, +",nozomi/http/parseable_data.py,"ReplaceText(target='validated' @(260,15)->(260,21))","integers'.format( + min_value=min_value + )) + + return values + + def optionally_parse_bool( + self,","integers'.format( + min_value=min_value + )) + + return validated + + def optionally_parse_bool( + self," +633,https://:@github.com/amatino-code/nozomi.git,b486a1109ac83dcabb4022d071644cadc4734769,"@@ -70,7 +70,7 @@ class Resource: + if not candidate.grants_read_to(unauthorised_agent): + raise NotAuthorised + continue +- return broadcast_candidate ++ return unauthorised_agent + + if not broadcast_candidate.grants_read_to(unauthorised_agent): + raise NotAuthorised +",nozomi/resources/resource.py,"ReplaceText(target='unauthorised_agent' @(73,19)->(73,38))","class Resource: + if not candidate.grants_read_to(unauthorised_agent): + raise NotAuthorised + continue + return broadcast_candidate + + if not broadcast_candidate.grants_read_to(unauthorised_agent): + raise NotAuthorised","class Resource: + if not candidate.grants_read_to(unauthorised_agent): + raise NotAuthorised + continue + return unauthorised_agent + + if not broadcast_candidate.grants_read_to(unauthorised_agent): + raise NotAuthorised" +634,https://:@github.com/Puumanamana/CoCoNet.git,5e966cbf19199b62e265f1320a5e60a0cdb2e26e,"@@ -54,7 +54,7 @@ def make_positive_pairs(label, frag_steps, contig_frags, fppc, encoding_len=128) + if k < fppc: + # print(""WARNING: cannot make {} unique pairs with genome of {} fragments"".format(fppc, contig_frags), end='\r') + pairs.sp = np.tile(label, [fppc, 2]) +- pairs.start = np.random.choice(frag_steps, [fppc, 2]) ++ pairs.start = np.random.choice(contig_frags, [fppc, 2]) + pairs.end = pairs.start + frag_steps + + return pairs +",coconet/fragmentation.py,"ReplaceText(target='contig_frags' @(57,39)->(57,49))","def make_positive_pairs(label, frag_steps, contig_frags, fppc, encoding_len=128) + if k < fppc: + # print(""WARNING: cannot make {} unique pairs with genome of {} fragments"".format(fppc, contig_frags), end='\r') + pairs.sp = np.tile(label, [fppc, 2]) + pairs.start = np.random.choice(frag_steps, [fppc, 2]) + pairs.end = pairs.start + frag_steps + + return pairs","def make_positive_pairs(label, frag_steps, contig_frags, fppc, encoding_len=128) + if k < fppc: + # print(""WARNING: cannot make {} unique pairs with genome of {} fragments"".format(fppc, contig_frags), end='\r') + pairs.sp = np.tile(label, [fppc, 2]) + pairs.start = np.random.choice(contig_frags, [fppc, 2]) + pairs.end = pairs.start + frag_steps + + return pairs" +635,https://:@github.com/struts2spring/sql-editor.git,92d594a22fc8cf532f18a445961615037bfa2685,"@@ -305,7 +305,7 @@ class FileBrowser(FileTree): + fileName=os.path.split(path)[-1] + + +- stc.SetText(FileOperations().readFile(filePath=fname)) ++ stc.SetText(FileOperations().readFile(filePath=path)) + centerPaneTab.window.addTab(name='openFileLoad'+fileName, worksheetPanel=stc) + + # win = wx.GetApp().GetActiveWindow() +",src/view/views/file/explorer/FileBrowserPanel.py,"ReplaceText(target='path' @(308,67)->(308,72))","class FileBrowser(FileTree): + fileName=os.path.split(path)[-1] + + + stc.SetText(FileOperations().readFile(filePath=fname)) + centerPaneTab.window.addTab(name='openFileLoad'+fileName, worksheetPanel=stc) + + # win = wx.GetApp().GetActiveWindow()","class FileBrowser(FileTree): + fileName=os.path.split(path)[-1] + + + stc.SetText(FileOperations().readFile(filePath=path)) + centerPaneTab.window.addTab(name='openFileLoad'+fileName, worksheetPanel=stc) + + # win = wx.GetApp().GetActiveWindow()" +636,https://:@github.com/struts2spring/sql-editor.git,3b18738cabd125bf7e4faeb0170edcc888f22c0b,"@@ -2306,7 +2306,7 @@ class ScrolledThumbnail(wx.ScrolledWindow): + logger.error(e, exc_info=True) + logger.error('selectedBookIndex: %s, len: %s', selectedBookIndex, len(self._items)) + # logger.debug(.0deleteBooks) +- if len(deleteBooks) > 0: ++ if len(deleteBooks) >= 0: + self.updateStatusBar(text=f'{len(deleteBooks)} books deleted') + self.GetParent().GetParent().loadingBook() + self.GetParent().GetParent().updatePangnation() +",src/view/views/calibre/book/browser/BookThumbCrtl.py,"ReplaceText(target='>=' @(2309,28)->(2309,29))","class ScrolledThumbnail(wx.ScrolledWindow): + logger.error(e, exc_info=True) + logger.error('selectedBookIndex: %s, len: %s', selectedBookIndex, len(self._items)) + # logger.debug(.0deleteBooks) + if len(deleteBooks) > 0: + self.updateStatusBar(text=f'{len(deleteBooks)} books deleted') + self.GetParent().GetParent().loadingBook() + self.GetParent().GetParent().updatePangnation()","class ScrolledThumbnail(wx.ScrolledWindow): + logger.error(e, exc_info=True) + logger.error('selectedBookIndex: %s, len: %s', selectedBookIndex, len(self._items)) + # logger.debug(.0deleteBooks) + if len(deleteBooks) >= 0: + self.updateStatusBar(text=f'{len(deleteBooks)} books deleted') + self.GetParent().GetParent().loadingBook() + self.GetParent().GetParent().updatePangnation()" +637,https://:@github.com/khaledghobashy/uraeus.git,d0011bf8d00b0212dd67ce4cd64b21719fbed709,"@@ -186,7 +186,7 @@ class internal_force(generic_force): + defflection = self.LF - distance + velocity = unit_vector.T*self.joint.dijd + +- self.Fi = unit_vector*(self.Fs(defflection) + self.Fd(velocity)) ++ self.Fi = unit_vector*(self.Fs(defflection) - self.Fd(velocity)) + Ti_e = 2*G(self.Pi).T*(self.Ti + Skew(self.ui).T*self.Fi) + + force_vector = sm.BlockMatrix([[self.Fi], [Ti_e]]) +",source/symbolic_classes/forces.py,"ReplaceText(target='-' @(189,52)->(189,53))","class internal_force(generic_force): + defflection = self.LF - distance + velocity = unit_vector.T*self.joint.dijd + + self.Fi = unit_vector*(self.Fs(defflection) + self.Fd(velocity)) + Ti_e = 2*G(self.Pi).T*(self.Ti + Skew(self.ui).T*self.Fi) + + force_vector = sm.BlockMatrix([[self.Fi], [Ti_e]])","class internal_force(generic_force): + defflection = self.LF - distance + velocity = unit_vector.T*self.joint.dijd + + self.Fi = unit_vector*(self.Fs(defflection) - self.Fd(velocity)) + Ti_e = 2*G(self.Pi).T*(self.Ti + Skew(self.ui).T*self.Fi) + + force_vector = sm.BlockMatrix([[self.Fi], [Ti_e]])" +638,https://:@github.com/naglis/odd-bunch.git,6e9e55c327eaa6bccd5a54a1da850db418fa3a3a,"@@ -74,7 +74,7 @@ class FieldAttrStringRedundant(Plugin): + f'for field ""{field.name}"". The same value will be computed ' + f""by Odoo automatically."", + addon, +- locations=[Location(path, [column_index_1(string_kwarg.start_pos)])], ++ locations=[Location(path, [column_index_1(field.start_pos)])], + confidence=Confidence.LOW, + categories=[""redundancy""], + sources=sources, +",odd_bunch/plugin/field_attr_string_redundant.py,"ReplaceText(target='field' @(77,58)->(77,70))","class FieldAttrStringRedundant(Plugin): + f'for field ""{field.name}"". The same value will be computed ' + f""by Odoo automatically."", + addon, + locations=[Location(path, [column_index_1(string_kwarg.start_pos)])], + confidence=Confidence.LOW, + categories=[""redundancy""], + sources=sources,","class FieldAttrStringRedundant(Plugin): + f'for field ""{field.name}"". The same value will be computed ' + f""by Odoo automatically."", + addon, + locations=[Location(path, [column_index_1(field.start_pos)])], + confidence=Confidence.LOW, + categories=[""redundancy""], + sources=sources," +639,https://:@github.com/naglis/odd-bunch.git,6e9e55c327eaa6bccd5a54a1da850db418fa3a3a,"@@ -23,7 +23,7 @@ class TrackVisibilityAlways(Plugin): + ""deprecated since version 12.0"", + addon, + locations=[ +- Location(field.model.path, [column_index_1(kwarg.start_pos)]) ++ Location(field.model.path, [column_index_1(field.start_pos)]) + ], + categories=[""deprecated""], + sources=[ +",odd_bunch/plugin/track_visibility_always.py,"ReplaceText(target='field' @(26,67)->(26,72))","class TrackVisibilityAlways(Plugin): + ""deprecated since version 12.0"", + addon, + locations=[ + Location(field.model.path, [column_index_1(kwarg.start_pos)]) + ], + categories=[""deprecated""], + sources=[","class TrackVisibilityAlways(Plugin): + ""deprecated since version 12.0"", + addon, + locations=[ + Location(field.model.path, [column_index_1(field.start_pos)]) + ], + categories=[""deprecated""], + sources=[" +640,https://:@github.com/haipdev/config.git,c81fb07972b62e9c51d47b7306ad0cb39b90025d,"@@ -115,7 +115,7 @@ def get(*paths, **options): + elif value is not MANDATORY: + result[key] = value + else: +- path = '/'.join(path) ++ path = '/'.join(paths) + raise HaipConfigException(f'option ""{key}"" not found in section ""{path}""') + return result + +",haip/config.py,"ReplaceText(target='paths' @(118,28)->(118,32))","def get(*paths, **options): + elif value is not MANDATORY: + result[key] = value + else: + path = '/'.join(path) + raise HaipConfigException(f'option ""{key}"" not found in section ""{path}""') + return result + ","def get(*paths, **options): + elif value is not MANDATORY: + result[key] = value + else: + path = '/'.join(paths) + raise HaipConfigException(f'option ""{key}"" not found in section ""{path}""') + return result + " +641,https://:@github.com/woblers/rightmove_webscraper.py.git,75bc8dc28e5a998582ddf86ae43a3160b5729a90,"@@ -37,7 +37,7 @@ class rightmove_data(object): + There are 24 results on each results page, but note that the + rightmove website limits results pages to a maximum of 42 pages."""""" + +- page_count = self.results_count() / 24 ++ page_count = self.results_count() // 24 + if self.results_count() % 24 > 0: + page_count += 1 + +",rightmove_webscraper.py,"ReplaceText(target='//' @(40,42)->(40,43))","class rightmove_data(object): + There are 24 results on each results page, but note that the + rightmove website limits results pages to a maximum of 42 pages."""""" + + page_count = self.results_count() / 24 + if self.results_count() % 24 > 0: + page_count += 1 + ","class rightmove_data(object): + There are 24 results on each results page, but note that the + rightmove website limits results pages to a maximum of 42 pages."""""" + + page_count = self.results_count() // 24 + if self.results_count() % 24 > 0: + page_count += 1 + " +642,https://:@github.com/DomBennett/MassPhylogenyEstimation.git,e72cb1554f059c77b45c8c74af96bd0b2fb140b9,"@@ -39,7 +39,7 @@ with open(os.path.join(working_dir, ""data"", ""test_alignment.p""), + # MOCK + def dummy_blast(query, subj, minoverlap): + # should return bools and positions +- bools = [True for e in subj] ++ bools = [True for e in query] + positions = [0 for e in subj] + max_positions = [len(e) for e in subj] + positions.extend(max_positions) +",tests/test_tools_alignment.py,"ReplaceText(target='query' @(42,27)->(42,31))","with open(os.path.join(working_dir, ""data"", ""test_alignment.p""), + # MOCK + def dummy_blast(query, subj, minoverlap): + # should return bools and positions + bools = [True for e in subj] + positions = [0 for e in subj] + max_positions = [len(e) for e in subj] + positions.extend(max_positions)","with open(os.path.join(working_dir, ""data"", ""test_alignment.p""), + # MOCK + def dummy_blast(query, subj, minoverlap): + # should return bools and positions + bools = [True for e in query] + positions = [0 for e in subj] + max_positions = [len(e) for e in subj] + positions.extend(max_positions)" +643,https://:@github.com/DomBennett/MassPhylogenyEstimation.git,832e9df9733c4e266c0583d4e1a329b5f72d4f4c,"@@ -159,7 +159,7 @@ class Stager(object): + @classmethod + def run_all(klass, wd, stages): + for s in stages: +- if check(stage=s, directory=wd): ++ if not check(stage=s, directory=wd): + Stager(wd, s).run() + + +",pglt/tools/system_tools.py,"ReplaceText(target='not ' @(162,15)->(162,15))","class Stager(object): + @classmethod + def run_all(klass, wd, stages): + for s in stages: + if check(stage=s, directory=wd): + Stager(wd, s).run() + + ","class Stager(object): + @classmethod + def run_all(klass, wd, stages): + for s in stages: + if not check(stage=s, directory=wd): + Stager(wd, s).run() + + " +644,https://:@bitbucket.org/bowaggonerpublic/bomail.git,383fe87f4b5a54ce110d33850ce10f19e088a001,"@@ -62,7 +62,7 @@ def main(): + exit(0) + + if sys.argv[1] == ""help"": +- if len(sys.argv) < 2: ++ if len(sys.argv) <= 2: + print(usage_str) + elif sys.argv[2] == ""datestr"": + print(bomail.util.datestr.datestr_str) +",bomail/bomail.py,"ReplaceText(target='<=' @(65,21)->(65,22))","def main(): + exit(0) + + if sys.argv[1] == ""help"": + if len(sys.argv) < 2: + print(usage_str) + elif sys.argv[2] == ""datestr"": + print(bomail.util.datestr.datestr_str)","def main(): + exit(0) + + if sys.argv[1] == ""help"": + if len(sys.argv) <= 2: + print(usage_str) + elif sys.argv[2] == ""datestr"": + print(bomail.util.datestr.datestr_str)" +645,https://:@bitbucket.org/bowaggonerpublic/bomail.git,6769b3f3dc022b9674b2f26d2ff842f74703da7e,"@@ -73,7 +73,7 @@ class TabNoThread: + new_fileset = set(new_filenames) + self.remove_files([t[0] for t in self.file_data if t[0] not in new_fileset], old_disp_info) + # assume, worst-case, that all matching files have changed/added +- self.update_for_change(new_fileset, old_disp_info) ++ self.update_for_change(new_filenames, old_disp_info) + + + # lazily load display data and return disp_data, is_unread, is_marked +",bomail/guistuff/tabnothread.py,"ReplaceText(target='new_filenames' @(76,27)->(76,38))","class TabNoThread: + new_fileset = set(new_filenames) + self.remove_files([t[0] for t in self.file_data if t[0] not in new_fileset], old_disp_info) + # assume, worst-case, that all matching files have changed/added + self.update_for_change(new_fileset, old_disp_info) + + + # lazily load display data and return disp_data, is_unread, is_marked","class TabNoThread: + new_fileset = set(new_filenames) + self.remove_files([t[0] for t in self.file_data if t[0] not in new_fileset], old_disp_info) + # assume, worst-case, that all matching files have changed/added + self.update_for_change(new_filenames, old_disp_info) + + + # lazily load display data and return disp_data, is_unread, is_marked" +646,https://:@github.com/GainCompliance/gain-requests-futures.git,2779819b9b7554d787280d5889878237ba1937b5,"@@ -69,7 +69,7 @@ class FuturesSession(Session): + func = super(FuturesSession, self).send + if isinstance(self.executor, ProcessPoolExecutor): + try: +- dumps(request) ++ dumps(func) + except (TypeError, PickleError): + raise RuntimeError(PICKLE_ERROR) + return self.executor.submit(func, request, **kwargs) +",requests_futures/sessions.py,"ReplaceText(target='func' @(72,22)->(72,29))","class FuturesSession(Session): + func = super(FuturesSession, self).send + if isinstance(self.executor, ProcessPoolExecutor): + try: + dumps(request) + except (TypeError, PickleError): + raise RuntimeError(PICKLE_ERROR) + return self.executor.submit(func, request, **kwargs)","class FuturesSession(Session): + func = super(FuturesSession, self).send + if isinstance(self.executor, ProcessPoolExecutor): + try: + dumps(func) + except (TypeError, PickleError): + raise RuntimeError(PICKLE_ERROR) + return self.executor.submit(func, request, **kwargs)" +647,https://:@github.com/praekelt/casepropods.family_connect_subscription.git,9f04ceacb29a64763e11de6c8fd3008faf9eddb2,"@@ -95,7 +95,7 @@ class SubscriptionPod(Pod): + 'subscription_ids': active_sub_ids + } + }) +- if len(active_sub_ids) > 0: ++ if len(active_sub_ids) > 1: + actions.append(self.get_cancel_action(active_sub_ids)) + + content['actions'] = actions +",casepropods/family_connect_subscription/plugin.py,"ReplaceText(target='1' @(98,33)->(98,34))","class SubscriptionPod(Pod): + 'subscription_ids': active_sub_ids + } + }) + if len(active_sub_ids) > 0: + actions.append(self.get_cancel_action(active_sub_ids)) + + content['actions'] = actions","class SubscriptionPod(Pod): + 'subscription_ids': active_sub_ids + } + }) + if len(active_sub_ids) > 1: + actions.append(self.get_cancel_action(active_sub_ids)) + + content['actions'] = actions" +648,https://:@github.com/fmilthaler/FinQuant.git,075430f74799040aa1d46c722e16a52a82637c63,"@@ -783,7 +783,7 @@ def _yfinance_request(names, start_date=None, end_date=None): + try: + import datetime + if isinstance(start_date, str): +- start_date = datetime.datetime.strptime(end_date, ""%Y-%m-%d"") ++ start_date = datetime.datetime.strptime(start_date, ""%Y-%m-%d"") + if isinstance(end_date, str): + end_date = datetime.datetime.strptime(end_date, ""%Y-%m-%d"") + except ImportError: +",finquant/portfolio.py,"ReplaceText(target='start_date' @(786,52)->(786,60))","def _yfinance_request(names, start_date=None, end_date=None): + try: + import datetime + if isinstance(start_date, str): + start_date = datetime.datetime.strptime(end_date, ""%Y-%m-%d"") + if isinstance(end_date, str): + end_date = datetime.datetime.strptime(end_date, ""%Y-%m-%d"") + except ImportError:","def _yfinance_request(names, start_date=None, end_date=None): + try: + import datetime + if isinstance(start_date, str): + start_date = datetime.datetime.strptime(start_date, ""%Y-%m-%d"") + if isinstance(end_date, str): + end_date = datetime.datetime.strptime(end_date, ""%Y-%m-%d"") + except ImportError:" +649,https://:@github.com/MrTango/click.git,a6af25df9c2e82e94c3aa15d579f9347881e5efb,"@@ -1173,7 +1173,7 @@ class Argument(Parameter): + if attrs.get('default') is not None: + required = False + else: +- required = attrs.get('nargs', 0) > 0 ++ required = attrs.get('nargs', 1) > 0 + Parameter.__init__(self, param_decls, required=required, **attrs) + + def make_metavar(self): +",click/core.py,"ReplaceText(target='1' @(1176,46)->(1176,47))","class Argument(Parameter): + if attrs.get('default') is not None: + required = False + else: + required = attrs.get('nargs', 0) > 0 + Parameter.__init__(self, param_decls, required=required, **attrs) + + def make_metavar(self):","class Argument(Parameter): + if attrs.get('default') is not None: + required = False + else: + required = attrs.get('nargs', 1) > 0 + Parameter.__init__(self, param_decls, required=required, **attrs) + + def make_metavar(self):" +650,https://:@github.com/MrTango/click.git,336e5e08acf98a4033e5aa4c6fcef118d4f469ec,"@@ -224,7 +224,7 @@ def version_option(version=None, *param_decls, **attrs): + message = attrs.pop('message', '%(prog)s, version %(version)s') + + def callback(ctx, param, value): +- if value or ctx.resilient_parsing: ++ if not value or ctx.resilient_parsing: + return + prog = prog_name + if prog is None: +",click/decorators.py,"ReplaceText(target='not ' @(227,15)->(227,15))","def version_option(version=None, *param_decls, **attrs): + message = attrs.pop('message', '%(prog)s, version %(version)s') + + def callback(ctx, param, value): + if value or ctx.resilient_parsing: + return + prog = prog_name + if prog is None:","def version_option(version=None, *param_decls, **attrs): + message = attrs.pop('message', '%(prog)s, version %(version)s') + + def callback(ctx, param, value): + if not value or ctx.resilient_parsing: + return + prog = prog_name + if prog is None:" +651,https://:@github.com/MrTango/click.git,598c6d76fbc036fb3219d9f09948a682cda66601,"@@ -213,7 +213,7 @@ class CliRunner(object): + old_env = {} + try: + for key, value in iteritems(env): +- old_env[key] = os.environ.get(value) ++ old_env[key] = os.environ.get(key) + if value is None: + try: + del os.environ[key] +",click/testing.py,"ReplaceText(target='key' @(216,46)->(216,51))","class CliRunner(object): + old_env = {} + try: + for key, value in iteritems(env): + old_env[key] = os.environ.get(value) + if value is None: + try: + del os.environ[key]","class CliRunner(object): + old_env = {} + try: + for key, value in iteritems(env): + old_env[key] = os.environ.get(key) + if value is None: + try: + del os.environ[key]" +652,https://:@github.com/epeios-q37/atlas-python.git,c310fd7273b7ec139c0eca6be43506cb611d5bfc,"@@ -69,7 +69,7 @@ class Chatroom: + def displayMessages(this, dom): + global messages + +- if len(messages) >= this.lastMessage: ++ if len(messages) > this.lastMessage: + id = dom.createElement(""span"") + dom.setLayoutXSL(id, this.buildXML(), ""Messages.xsl"") + dom.insertChild(id, ""Board"") +",Chatroom/main.py,"ReplaceText(target='>' @(72,19)->(72,21))","class Chatroom: + def displayMessages(this, dom): + global messages + + if len(messages) >= this.lastMessage: + id = dom.createElement(""span"") + dom.setLayoutXSL(id, this.buildXML(), ""Messages.xsl"") + dom.insertChild(id, ""Board"")","class Chatroom: + def displayMessages(this, dom): + global messages + + if len(messages) > this.lastMessage: + id = dom.createElement(""span"") + dom.setLayoutXSL(id, this.buildXML(), ""Messages.xsl"") + dom.insertChild(id, ""Board"")" +653,https://:@github.com/herrersystem/apize.git,3f4ce76b32fdc1cddc66cde54f0d7552b2ab2101,"@@ -15,7 +15,7 @@ def send_request(url, method, + """""" + ## Parse url args + for p in args: +- url = url.replace(':'+p, str(params[p])) ++ url = url.replace(':' + p, str(args[p])) + + try: + if data: +",apize/decorators.py,"ReplaceText(target='args' @(18,31)->(18,37))","def send_request(url, method, + """""" + ## Parse url args + for p in args: + url = url.replace(':'+p, str(params[p])) + + try: + if data:","def send_request(url, method, + """""" + ## Parse url args + for p in args: + url = url.replace(':' + p, str(args[p])) + + try: + if data:" +654,https://:@github.com/silvacms/silva.core.services.git,a674128c54bb10f2abdda32808285fabc985e363,"@@ -39,7 +39,7 @@ class SecretService(SilvaService): + assert len(args) > 1, u'Too few arguments' + challenge = hmac.new(self.__key, str(args[0]), hashlib.sha1) + for arg in args[1:]: +- challenge.update(str(args)) ++ challenge.update(str(arg)) + return challenge.hexdigest() + + InitializeClass(SecretService) +",src/silva/core/services/secret.py,"ReplaceText(target='arg' @(42,33)->(42,37))","class SecretService(SilvaService): + assert len(args) > 1, u'Too few arguments' + challenge = hmac.new(self.__key, str(args[0]), hashlib.sha1) + for arg in args[1:]: + challenge.update(str(args)) + return challenge.hexdigest() + + InitializeClass(SecretService)","class SecretService(SilvaService): + assert len(args) > 1, u'Too few arguments' + challenge = hmac.new(self.__key, str(args[0]), hashlib.sha1) + for arg in args[1:]: + challenge.update(str(arg)) + return challenge.hexdigest() + + InitializeClass(SecretService)" +655,https://:@github.com/SatelliteApplicationsCatapult/sedas_pyapi.git,db1d3308de5180dd9a26e8bc73b82c97d2f07507,"@@ -225,7 +225,7 @@ class SeDASAPI: + req = Request(url, headers=self.headers) + try: + decoded = json.load(urlopen(req)) +- if len(decoded) > 1 and 'downloadUrl' in decoded[0]: ++ if len(decoded) >= 1 and 'downloadUrl' in decoded[0]: + return decoded[0]['downloadUrl'] + return None + except HTTPError as e: +",getthestuff/sedas_api.py,"ReplaceText(target='>=' @(228,28)->(228,29))","class SeDASAPI: + req = Request(url, headers=self.headers) + try: + decoded = json.load(urlopen(req)) + if len(decoded) > 1 and 'downloadUrl' in decoded[0]: + return decoded[0]['downloadUrl'] + return None + except HTTPError as e:","class SeDASAPI: + req = Request(url, headers=self.headers) + try: + decoded = json.load(urlopen(req)) + if len(decoded) >= 1 and 'downloadUrl' in decoded[0]: + return decoded[0]['downloadUrl'] + return None + except HTTPError as e:" +656,https://:@github.com/gigaquads/pybiz.git,9431e28a54c7a64f4fabcd861239a9651a75dde5,"@@ -91,7 +91,7 @@ class YamlDao(Dao): + cur_data = self.fetch(_id) + new_data = DictUtils.merge(cur_data, data) + Yaml.to_file(file_path=file_path, data=new_data) +- return data ++ return new_data + + def delete(self, _id) -> None: + """""" +",pybiz/dao/yaml_dao.py,"ReplaceText(target='new_data' @(94,15)->(94,19))","class YamlDao(Dao): + cur_data = self.fetch(_id) + new_data = DictUtils.merge(cur_data, data) + Yaml.to_file(file_path=file_path, data=new_data) + return data + + def delete(self, _id) -> None: + """"""","class YamlDao(Dao): + cur_data = self.fetch(_id) + new_data = DictUtils.merge(cur_data, data) + Yaml.to_file(file_path=file_path, data=new_data) + return new_data + + def delete(self, _id) -> None: + """"""" +657,https://:@github.com/gigaquads/pybiz.git,cc4bc8499bdffbf4bef4704afb722fa55c7ccc1d,"@@ -790,7 +790,7 @@ class BizObject( + related_bizobj_list.append(obj) + else: + related_bizobj_list.append( +- rel.target(related_data) ++ rel.target(obj) + ) + + self._related_bizobjs[rel.name] = related_bizobj_list +",pybiz/biz.py,"ReplaceText(target='obj' @(793,39)->(793,51))","class BizObject( + related_bizobj_list.append(obj) + else: + related_bizobj_list.append( + rel.target(related_data) + ) + + self._related_bizobjs[rel.name] = related_bizobj_list","class BizObject( + related_bizobj_list.append(obj) + else: + related_bizobj_list.append( + rel.target(obj) + ) + + self._related_bizobjs[rel.name] = related_bizobj_list" +658,https://:@github.com/gigaquads/pybiz.git,4bfdaf78df6eec9213f65df0656d346cfd4a45f2,"@@ -79,6 +79,6 @@ class BreadthFirstSaver(Saver): + v_type = v.__class__ + if v._id is None: + to_create[v_type].append(v) +- elif x.dirty: ++ elif v.dirty: + to_update[v_type].append(x) + self._aggregate_related(v, to_create, to_update) +",pybiz/biz/internal/save.py,"ReplaceText(target='v' @(82,21)->(82,22))","class BreadthFirstSaver(Saver): + v_type = v.__class__ + if v._id is None: + to_create[v_type].append(v) + elif x.dirty: + to_update[v_type].append(x) + self._aggregate_related(v, to_create, to_update)","class BreadthFirstSaver(Saver): + v_type = v.__class__ + if v._id is None: + to_create[v_type].append(v) + elif v.dirty: + to_update[v_type].append(x) + self._aggregate_related(v, to_create, to_update)" +659,https://:@github.com/gigaquads/pybiz.git,9ccaa42fdf4677090e93c27b2326c5d935d568f9,"@@ -80,5 +80,5 @@ class BreadthFirstSaver(Saver): + if v._id is None: + to_create[v_type].append(v) + elif v.dirty: +- to_update[v_type].append(x) ++ to_update[v_type].append(v) + self._aggregate_related(v, to_create, to_update) +",pybiz/biz/internal/save.py,"ReplaceText(target='v' @(83,45)->(83,46))","class BreadthFirstSaver(Saver): + if v._id is None: + to_create[v_type].append(v) + elif v.dirty: + to_update[v_type].append(x) + self._aggregate_related(v, to_create, to_update)","class BreadthFirstSaver(Saver): + if v._id is None: + to_create[v_type].append(v) + elif v.dirty: + to_update[v_type].append(v) + self._aggregate_related(v, to_create, to_update)" +660,https://:@github.com/gigaquads/pybiz.git,c042a85234732c1ff96c0240b378595d24631fbe,"@@ -116,7 +116,7 @@ class CompositeGuard(Guard): + if rhs_exc is not None and lhs_exc is not None: + return CompositeGuardException(lhs_exc, rhs_exc) + elif self._op == OP_CODE.NOT: +- if lhs_exc is not None: ++ if lhs_exc is None: + return lhs_exc + else: + return ValueError(f'op not recognized, ""{self._op}""') +",pybiz/api/middleware/guard_middleware/guard.py,"ReplaceText(target=' is ' @(119,22)->(119,30))","class CompositeGuard(Guard): + if rhs_exc is not None and lhs_exc is not None: + return CompositeGuardException(lhs_exc, rhs_exc) + elif self._op == OP_CODE.NOT: + if lhs_exc is not None: + return lhs_exc + else: + return ValueError(f'op not recognized, ""{self._op}""')","class CompositeGuard(Guard): + if rhs_exc is not None and lhs_exc is not None: + return CompositeGuardException(lhs_exc, rhs_exc) + elif self._op == OP_CODE.NOT: + if lhs_exc is None: + return lhs_exc + else: + return ValueError(f'op not recognized, ""{self._op}""')" +661,https://:@github.com/gigaquads/pybiz.git,30e14e8c946edb447a76ea243a271c6a03895def,"@@ -43,7 +43,7 @@ class ActionDecorator(object): + else: + func = obj + action = self.setup_action(func, False) +- return action ++ return func + + def setup_action(self, func, overwrite): + action = self.app.action_type(func, self) +",ravel/app/base/action_decorator.py,"ReplaceText(target='func' @(46,19)->(46,25))","class ActionDecorator(object): + else: + func = obj + action = self.setup_action(func, False) + return action + + def setup_action(self, func, overwrite): + action = self.app.action_type(func, self)","class ActionDecorator(object): + else: + func = obj + action = self.setup_action(func, False) + return func + + def setup_action(self, func, overwrite): + action = self.app.action_type(func, self)" +662,https://:@github.com/a1phat0ny/noteboard.git,82eea493ff696d09af702a1cfd0c645f5f61b86e,"@@ -429,7 +429,7 @@ def display_board(date=False, sort=False, im=False): + (Fore.LIGHTBLACK_EX + ""(due: {})"".format(color + str(duedate) + Fore.LIGHTBLACK_EX)) if item[""due""] else """", + Fore.LIGHTBLACK_EX + str(item[""date""])) + else: +- p(star, Fore.LIGHTMAGENTA_EX + str(item[""id""]).rjust(2), mark, text_color + item[""text""], tag_text, due_text, day_text) ++ p(star, Fore.LIGHTMAGENTA_EX + str(item[""id""]).rjust(2), mark, text_color + item[""text""], tag_text, day_text, due_text) + print() + print_footer() + print_total() +",noteboard/cli.py,"ArgSwap(idxs=5<->6 @(432,16)->(432,17))","def display_board(date=False, sort=False, im=False): + (Fore.LIGHTBLACK_EX + ""(due: {})"".format(color + str(duedate) + Fore.LIGHTBLACK_EX)) if item[""due""] else """", + Fore.LIGHTBLACK_EX + str(item[""date""])) + else: + p(star, Fore.LIGHTMAGENTA_EX + str(item[""id""]).rjust(2), mark, text_color + item[""text""], tag_text, due_text, day_text) + print() + print_footer() + print_total()","def display_board(date=False, sort=False, im=False): + (Fore.LIGHTBLACK_EX + ""(due: {})"".format(color + str(duedate) + Fore.LIGHTBLACK_EX)) if item[""due""] else """", + Fore.LIGHTBLACK_EX + str(item[""date""])) + else: + p(star, Fore.LIGHTMAGENTA_EX + str(item[""id""]).rjust(2), mark, text_color + item[""text""], tag_text, day_text, due_text) + print() + print_footer() + print_total()" +663,https://:@github.com/tlevine/sheetmusic.git,5c919c8d4c6be39cd42847e44942305521c7fa52,"@@ -54,7 +54,7 @@ def _next_note(first_note, second_note_name): + If the second note name is less than the first (""G"" is greater than ""C""), + return a note of the second name in the octave above the first. + ''' +- if second_note_name > first_note.name: ++ if second_note_name >= first_note.name: + second_note_octave = first_note.octave + else: + second_note_octave = first_note.octave + 1 +",libsheetmusic/music.py,"ReplaceText(target='>=' @(57,24)->(57,25))","def _next_note(first_note, second_note_name): + If the second note name is less than the first (""G"" is greater than ""C""), + return a note of the second name in the octave above the first. + ''' + if second_note_name > first_note.name: + second_note_octave = first_note.octave + else: + second_note_octave = first_note.octave + 1","def _next_note(first_note, second_note_name): + If the second note name is less than the first (""G"" is greater than ""C""), + return a note of the second name in the octave above the first. + ''' + if second_note_name >= first_note.name: + second_note_octave = first_note.octave + else: + second_note_octave = first_note.octave + 1" +664,https://:@github.com/tlevine/sheetmusic.git,62a714388992483a00824d0ce16af7a7c8b9ee7e,"@@ -80,4 +80,4 @@ def util_functions(): + + def functions(): + callables = reduce(u.merge, [scale_functions(), chord_functions(), progression_functions(), interval_functions(), util_functions()]) +- return {k:u.to_function(v, k) for k,v in callables.items()} ++ return {k:u.to_function(k, v) for k,v in callables.items()} +",libsheetmusic/main.py,"ArgSwap(idxs=0<->1 @(83,14)->(83,27))","def util_functions(): + + def functions(): + callables = reduce(u.merge, [scale_functions(), chord_functions(), progression_functions(), interval_functions(), util_functions()]) + return {k:u.to_function(v, k) for k,v in callables.items()}","def util_functions(): + + def functions(): + callables = reduce(u.merge, [scale_functions(), chord_functions(), progression_functions(), interval_functions(), util_functions()]) + return {k:u.to_function(k, v) for k,v in callables.items()}" +665,https://:@gitlab.com/ebenhoeh/modelbase.git,dcc3cdf01cf74859ff59f4a641a9caf0faa21069,"@@ -207,7 +207,7 @@ class Model(core.ParameterModel): + raise TypeError(""Rate name must be str"") + if not callable(rate_function): + raise TypeError(""Rate function must be a function"") +- if variables is not None: ++ if variables is None: + variables = [] + if not isinstance(variables, list): + raise TypeError(""Variables must be a list"") +",modelbase/ode/model.py,"ReplaceText(target=' is ' @(210,20)->(210,28))","class Model(core.ParameterModel): + raise TypeError(""Rate name must be str"") + if not callable(rate_function): + raise TypeError(""Rate function must be a function"") + if variables is not None: + variables = [] + if not isinstance(variables, list): + raise TypeError(""Variables must be a list"")","class Model(core.ParameterModel): + raise TypeError(""Rate name must be str"") + if not callable(rate_function): + raise TypeError(""Rate function must be a function"") + if variables is None: + variables = [] + if not isinstance(variables, list): + raise TypeError(""Variables must be a list"")" +666,https://:@gitlab.com/ebenhoeh/modelbase.git,34fc0fc7c745eef34ae0edf0377347d83b733890,"@@ -281,7 +281,7 @@ class Model(core.ParameterModel): + def get_rate_indexes(self, rate_name=None): + v, k = zip(*enumerate(self.get_rate_names())) + rate_idx = dict(zip(k, v)) +- if rate_name is not None: ++ if rate_name is None: + return rate_idx + return rate_idx[rate_name] + +",modelbase/ode/model.py,"ReplaceText(target=' is ' @(284,20)->(284,28))","class Model(core.ParameterModel): + def get_rate_indexes(self, rate_name=None): + v, k = zip(*enumerate(self.get_rate_names())) + rate_idx = dict(zip(k, v)) + if rate_name is not None: + return rate_idx + return rate_idx[rate_name] + ","class Model(core.ParameterModel): + def get_rate_indexes(self, rate_name=None): + v, k = zip(*enumerate(self.get_rate_names())) + rate_idx = dict(zip(k, v)) + if rate_name is None: + return rate_idx + return rate_idx[rate_name] + " +667,https://:@github.com/kalombos/pynetsnmp.git,812b5789589ca0d99f6e6d2339fee7e4254e9c01,"@@ -637,7 +637,7 @@ class Session(object): + + + MAXFD = 1024 +-fdset = c_int32 * (MAXFD/32) ++fdset = c_int32 * (MAXFD//32) + + class timeval(Structure): + _fields_ = [ +",pynetsnmp/netsnmp.py,"ReplaceText(target='//' @(640,24)->(640,25))","class Session(object): + + + MAXFD = 1024 + fdset = c_int32 * (MAXFD/32) + + class timeval(Structure): + _fields_ = [","class Session(object): + + + MAXFD = 1024 + fdset = c_int32 * (MAXFD//32) + + class timeval(Structure): + _fields_ = [" +668,https://:@github.com/kalombos/pynetsnmp.git,f2883247d0b1df1804aa12653b06dce1d2137697,"@@ -312,7 +312,7 @@ def strToOid(oidStr): + return mkoid(tuple([int(x) for x in oidStr.strip('.').split('.')])) + + def decodeOid(pdu): +- return tuple([pdu.val.objid[i] for i in range(pdu.val_len / sizeof(u_long))]) ++ return tuple([pdu.val.objid[i] for i in range(pdu.val_len // sizeof(u_long))]) + + def decodeIp(pdu): + return '.'.join(map(str, pdu.val.bitstring[:4])) +",pynetsnmp/netsnmp.py,"ReplaceText(target='//' @(315,62)->(315,63))","def strToOid(oidStr): + return mkoid(tuple([int(x) for x in oidStr.strip('.').split('.')])) + + def decodeOid(pdu): + return tuple([pdu.val.objid[i] for i in range(pdu.val_len / sizeof(u_long))]) + + def decodeIp(pdu): + return '.'.join(map(str, pdu.val.bitstring[:4]))","def strToOid(oidStr): + return mkoid(tuple([int(x) for x in oidStr.strip('.').split('.')])) + + def decodeOid(pdu): + return tuple([pdu.val.objid[i] for i in range(pdu.val_len // sizeof(u_long))]) + + def decodeIp(pdu): + return '.'.join(map(str, pdu.val.bitstring[:4]))" +669,https://:@github.com/Swiftea/Crawler.git,fb03cfc257939d5b86fe00037ab6b00fd54c9afa,"@@ -14,7 +14,7 @@ def stats(dir_stats=DIR_STATS): + stat_links = ('Average links in webpage: ' + str(average(content))) + if len(content) > 10000: + compress_stats(dir_stats + 'stat_links') +- result += stat_links + '\n' ++ result = stat_links + '\n' + try: + with open(dir_stats + 'stat_webpages', 'r') as myfile: + content = myfile.read().split() +",crawler/stats.py,"ReplaceText(target='=' @(17,8)->(17,10))","def stats(dir_stats=DIR_STATS): + stat_links = ('Average links in webpage: ' + str(average(content))) + if len(content) > 10000: + compress_stats(dir_stats + 'stat_links') + result += stat_links + '\n' + try: + with open(dir_stats + 'stat_webpages', 'r') as myfile: + content = myfile.read().split()","def stats(dir_stats=DIR_STATS): + stat_links = ('Average links in webpage: ' + str(average(content))) + if len(content) > 10000: + compress_stats(dir_stats + 'stat_links') + result = stat_links + '\n' + try: + with open(dir_stats + 'stat_webpages', 'r') as myfile: + content = myfile.read().split()" +670,https://:@bitbucket.org/mikhail-makovenko/save-to-db.git,0b152880bfce8af5f211bfbb3d5677f283823bdc,"@@ -187,7 +187,7 @@ class AdapterBase(object): + :returns: Item list and corresponding ORM models as a list of lists + (in case one item updates multiple models). + """""" +- return db_persist(cls, item, adapter_settings) ++ return db_persist(item, cls, adapter_settings) + + + @classmethod +",save_to_db/adapters/utils/adapter_base.py,"ArgSwap(idxs=0<->1 @(190,15)->(190,25))","class AdapterBase(object): + :returns: Item list and corresponding ORM models as a list of lists + (in case one item updates multiple models). + """""" + return db_persist(cls, item, adapter_settings) + + + @classmethod","class AdapterBase(object): + :returns: Item list and corresponding ORM models as a list of lists + (in case one item updates multiple models). + """""" + return db_persist(item, cls, adapter_settings) + + + @classmethod" +671,https://:@github.com/itu-algorithms/itu.algs4.git,8a06e126f13f6d54802e342b1ad7c44ec792ffc3,"@@ -64,7 +64,7 @@ class Queue: + if __name__ == '__main__': + queue = Queue() + +- if len(sys.argv) > 0: ++ if len(sys.argv) > 1: + sys.stdin = open(sys.argv[1]) + while not stdio.isEmpty(): + input_item = stdio.readString() +",fundamentals/queue.py,"ReplaceText(target='1' @(67,23)->(67,24))","class Queue: + if __name__ == '__main__': + queue = Queue() + + if len(sys.argv) > 0: + sys.stdin = open(sys.argv[1]) + while not stdio.isEmpty(): + input_item = stdio.readString()","class Queue: + if __name__ == '__main__': + queue = Queue() + + if len(sys.argv) > 1: + sys.stdin = open(sys.argv[1]) + while not stdio.isEmpty(): + input_item = stdio.readString()" +672,https://:@github.com/itu-algorithms/itu.algs4.git,2282d1fa58d8c525d83890def4dc5b4d1902a0dd,"@@ -9,6 +9,6 @@ class ThreeSumFast: + count = 0 + for i in range(n): + for j in range(i+1, n): +- if binary_search.index_of(a, -a[i]-a[j]) > i: ++ if binary_search.index_of(a, -a[i]-a[j]) > j: + count += 1 + return count +",algs4/fundamentals/three_sum_fast.py,"ReplaceText(target='j' @(12,59)->(12,60))","class ThreeSumFast: + count = 0 + for i in range(n): + for j in range(i+1, n): + if binary_search.index_of(a, -a[i]-a[j]) > i: + count += 1 + return count","class ThreeSumFast: + count = 0 + for i in range(n): + for j in range(i+1, n): + if binary_search.index_of(a, -a[i]-a[j]) > j: + count += 1 + return count" +673,https://:@github.com/itu-algorithms/itu.algs4.git,62cc19d6f09e3f24abbe1551d69d67474518a7cb,"@@ -183,7 +183,7 @@ class BinarySearchST: + while j < self._n-1: + self._keys[j] = self._keys[j+1] + self._vals[j] = self._vals[j+1] +- j = 1 ++ j += 1 + + self._n -= 1 + n = self._n +",itu/algs4/searching/binary_search_st.py,"ReplaceText(target='+=' @(186,14)->(186,15))","class BinarySearchST: + while j < self._n-1: + self._keys[j] = self._keys[j+1] + self._vals[j] = self._vals[j+1] + j = 1 + + self._n -= 1 + n = self._n","class BinarySearchST: + while j < self._n-1: + self._keys[j] = self._keys[j+1] + self._vals[j] = self._vals[j+1] + j += 1 + + self._n -= 1 + n = self._n" +674,https://:@github.com/itu-algorithms/itu.algs4.git,616a6dd32cf80578bfae1ce36dbede8eb2e241cc,"@@ -481,7 +481,7 @@ class RedBlackBST(Generic[Key, Val]): + return + if lo < x.key: + self._keys(x.left, queue, lo, hi) +- if not x.key < lo and x.key < hi: ++ if not x.key < lo and x.key <= hi: + queue.enqueue(x.key) + if hi > x.key: + self._keys(x.right, queue, lo, hi) +",itu/algs4/searching/red_black_bst.py,"ReplaceText(target='<=' @(484,37)->(484,38))","class RedBlackBST(Generic[Key, Val]): + return + if lo < x.key: + self._keys(x.left, queue, lo, hi) + if not x.key < lo and x.key < hi: + queue.enqueue(x.key) + if hi > x.key: + self._keys(x.right, queue, lo, hi)","class RedBlackBST(Generic[Key, Val]): + return + if lo < x.key: + self._keys(x.left, queue, lo, hi) + if not x.key < lo and x.key <= hi: + queue.enqueue(x.key) + if hi > x.key: + self._keys(x.right, queue, lo, hi)" +675,https://:@github.com/kbytesys/django-recaptcha3.git,69219ca34dc834fede05f4e7f107ba17156f8f45,"@@ -15,7 +15,7 @@ logger = logging.getLogger(__name__) + + class ReCaptchaField(forms.CharField): + def __init__(self, attrs=None, *args, **kwargs): +- if os.environ.get('RECAPTCHA_DISABLE', None) is not None: ++ if os.environ.get('RECAPTCHA_DISABLE', None) is None: + self._private_key = kwargs.pop('private_key', settings.RECAPTCHA_PRIVATE_KEY) + self._score_threshold = kwargs.pop('score_threshold', settings.RECAPTCHA_SCORE_THRESHOLD) + +",snowpenguin/django/recaptcha3/fields.py,"ReplaceText(target=' is ' @(18,52)->(18,60))","logger = logging.getLogger(__name__) + + class ReCaptchaField(forms.CharField): + def __init__(self, attrs=None, *args, **kwargs): + if os.environ.get('RECAPTCHA_DISABLE', None) is not None: + self._private_key = kwargs.pop('private_key', settings.RECAPTCHA_PRIVATE_KEY) + self._score_threshold = kwargs.pop('score_threshold', settings.RECAPTCHA_SCORE_THRESHOLD) + ","logger = logging.getLogger(__name__) + + class ReCaptchaField(forms.CharField): + def __init__(self, attrs=None, *args, **kwargs): + if os.environ.get('RECAPTCHA_DISABLE', None) is None: + self._private_key = kwargs.pop('private_key', settings.RECAPTCHA_PRIVATE_KEY) + self._score_threshold = kwargs.pop('score_threshold', settings.RECAPTCHA_SCORE_THRESHOLD) + " +676,https://:@github.com/MonetDBSolutions/mal_analytics.git,0b7cd6d9394adc932e19a29eda69bb11e5a3fb19,"@@ -375,7 +375,7 @@ class ProfilerObjectParser: + except json.JSONDecodeError as json_error: + LOGGER.warning(""W001: Cannot parse object"") + LOGGER.warning(json_string) +- LOGGER.warning(""Decoder reports %s"", json_string) ++ LOGGER.warning(""Decoder reports %s"", json_error) + return + + dispatcher = { +",mal_profiler/profiler_parser.py,"ReplaceText(target='json_error' @(378,49)->(378,60))","class ProfilerObjectParser: + except json.JSONDecodeError as json_error: + LOGGER.warning(""W001: Cannot parse object"") + LOGGER.warning(json_string) + LOGGER.warning(""Decoder reports %s"", json_string) + return + + dispatcher = {","class ProfilerObjectParser: + except json.JSONDecodeError as json_error: + LOGGER.warning(""W001: Cannot parse object"") + LOGGER.warning(json_string) + LOGGER.warning(""Decoder reports %s"", json_error) + return + + dispatcher = {" +677,https://:@github.com/MonetDBSolutions/mal_analytics.git,a4e4a3d115ffc81721248d71176d8205c1866d98,"@@ -148,7 +148,7 @@ class DatabaseManager(object, metaclass=Singleton): + stmt = list() + for ln in sql_in: + cline = ln.strip() +- if ln.startswith('--') or len(cline) == 0: ++ if cline.startswith('--') or len(cline) == 0: + continue + + stmt.append(cline) +",mal_analytics/db_manager.py,"ReplaceText(target='cline' @(151,15)->(151,17))","class DatabaseManager(object, metaclass=Singleton): + stmt = list() + for ln in sql_in: + cline = ln.strip() + if ln.startswith('--') or len(cline) == 0: + continue + + stmt.append(cline)","class DatabaseManager(object, metaclass=Singleton): + stmt = list() + for ln in sql_in: + cline = ln.strip() + if cline.startswith('--') or len(cline) == 0: + continue + + stmt.append(cline)" +678,https://:@github.com/codepost-io/codePost-api-python.git,00320258dd53e987c66c9af2d021fb93b38ac20c,"@@ -812,7 +812,7 @@ def remove_comments(api_key, submission_id=None, file_id=None): + headers=auth_headers + ) + +- if r.status_code != 204: ++ if r.status_code == 204: + comments_to_delete += r.json().get(""comments"", list()) + deleted_comments += 1 + except: +",codePost_api/helpers.py,"ReplaceText(target='==' @(815,29)->(815,31))","def remove_comments(api_key, submission_id=None, file_id=None): + headers=auth_headers + ) + + if r.status_code != 204: + comments_to_delete += r.json().get(""comments"", list()) + deleted_comments += 1 + except:","def remove_comments(api_key, submission_id=None, file_id=None): + headers=auth_headers + ) + + if r.status_code == 204: + comments_to_delete += r.json().get(""comments"", list()) + deleted_comments += 1 + except:" +679,https://:@github.com/optimatorlab/veroviz.git,0c34d475219e023bbc77e96bbcf8c7bd2ec09fde,"@@ -527,7 +527,7 @@ def geoAreaOfPolygon(poly): + polyArea = 0 + + # Use polygon triangulation to cut the bounding region into a list of triangles, calculate the area of each triangle +- lstTriangle = tripy.earclip(poly) ++ lstTriangle = tripy.earclip(cleanPoly) + lstArea = [] + for i in range(len(lstTriangle)): + lstArea.append(geoAreaOfTriangle(lstTriangle[i][0], lstTriangle[i][1], lstTriangle[i][2])) +",veroviz/_geometry.py,"ReplaceText(target='cleanPoly' @(530,29)->(530,33))","def geoAreaOfPolygon(poly): + polyArea = 0 + + # Use polygon triangulation to cut the bounding region into a list of triangles, calculate the area of each triangle + lstTriangle = tripy.earclip(poly) + lstArea = [] + for i in range(len(lstTriangle)): + lstArea.append(geoAreaOfTriangle(lstTriangle[i][0], lstTriangle[i][1], lstTriangle[i][2]))","def geoAreaOfPolygon(poly): + polyArea = 0 + + # Use polygon triangulation to cut the bounding region into a list of triangles, calculate the area of each triangle + lstTriangle = tripy.earclip(cleanPoly) + lstArea = [] + for i in range(len(lstTriangle)): + lstArea.append(geoAreaOfTriangle(lstTriangle[i][0], lstTriangle[i][1], lstTriangle[i][2]))" +680,https://:@github.com/slipguru/adenine.git,0ea659ee40e7d0eff55de0da241e5e2566de4a48,"@@ -380,7 +380,7 @@ def analysis_worker(elem, root, y, feat_names, class_names, lock): + model=voronoi_mdl_obj) + elif hasattr(mdl_obj, 'n_leaves_'): + plotting.tree(root=rootname, data_in=step_in, +- labels=step_out, model=mdl_obj) ++ labels=y, model=mdl_obj) + plotting.dendrogram(root=rootname, data_in=step_in, + labels=y, model=mdl_obj) + +",adenine/core/analyze_results.py,"ReplaceText(target='y' @(383,37)->(383,45))","def analysis_worker(elem, root, y, feat_names, class_names, lock): + model=voronoi_mdl_obj) + elif hasattr(mdl_obj, 'n_leaves_'): + plotting.tree(root=rootname, data_in=step_in, + labels=step_out, model=mdl_obj) + plotting.dendrogram(root=rootname, data_in=step_in, + labels=y, model=mdl_obj) + ","def analysis_worker(elem, root, y, feat_names, class_names, lock): + model=voronoi_mdl_obj) + elif hasattr(mdl_obj, 'n_leaves_'): + plotting.tree(root=rootname, data_in=step_in, + labels=y, model=mdl_obj) + plotting.dendrogram(root=rootname, data_in=step_in, + labels=y, model=mdl_obj) + " +681,https://:@github.com/Tenchi2xh/Almonds.git,79cd9da8e404df197cbe23586aeacec156080722,"@@ -135,7 +135,7 @@ class Cursebox(object): + return EVENT_RIGHT + elif ch == 3: + return EVENT_CTRL_C +- elif 0 >= ch < 256: ++ elif 0 <= ch < 256: + return chr(ch) + else: + return EVENT_UNHANDLED +",almonds/cursebox/cursebox.py,"ReplaceText(target='<=' @(138,15)->(138,17))","class Cursebox(object): + return EVENT_RIGHT + elif ch == 3: + return EVENT_CTRL_C + elif 0 >= ch < 256: + return chr(ch) + else: + return EVENT_UNHANDLED","class Cursebox(object): + return EVENT_RIGHT + elif ch == 3: + return EVENT_CTRL_C + elif 0 <= ch < 256: + return chr(ch) + else: + return EVENT_UNHANDLED" +682,https://:@github.com/abrahamrhoffman/anaxdb.git,0ff2588e2af89bb06d04834ad6bef887ed5ebb14,"@@ -263,7 +263,7 @@ class Database(object): + try: + tableFile = (self._path + ""/"" + aTableName + "".pq"") + tableFileEnc = (self._path + ""/"" + aTableName + "".enc"") +- self._decrypt(tableFileEnc) ++ self._decrypt(tableFile) + dataframe = pq.read_table(tableFile).to_pandas() + os.remove(tableFile) + return dataframe +",anaxdb/anaxdb.py,"ReplaceText(target='tableFile' @(266,30)->(266,42))","class Database(object): + try: + tableFile = (self._path + ""/"" + aTableName + "".pq"") + tableFileEnc = (self._path + ""/"" + aTableName + "".enc"") + self._decrypt(tableFileEnc) + dataframe = pq.read_table(tableFile).to_pandas() + os.remove(tableFile) + return dataframe","class Database(object): + try: + tableFile = (self._path + ""/"" + aTableName + "".pq"") + tableFileEnc = (self._path + ""/"" + aTableName + "".enc"") + self._decrypt(tableFile) + dataframe = pq.read_table(tableFile).to_pandas() + os.remove(tableFile) + return dataframe" +683,https://:@github.com/badmetacoder/calculator.git,531135ec2a5b354165ad6e6e6b8d2e4d84b8ee38,"@@ -96,7 +96,7 @@ class SimpleCalculator(): + elif self.op == '+': + self.r1 = self.r1 + self.r2 + elif self.op == '-': +- self.r1 = self.r1 + self.r2 ++ self.r1 = self.r1 - self.r2 + elif self.op == '*': + self.r1 = self.r1 * self.r2 + elif self.op == '/': +",calculator/simple.py,"ReplaceText(target='-' @(99,34)->(99,35))","class SimpleCalculator(): + elif self.op == '+': + self.r1 = self.r1 + self.r2 + elif self.op == '-': + self.r1 = self.r1 + self.r2 + elif self.op == '*': + self.r1 = self.r1 * self.r2 + elif self.op == '/':","class SimpleCalculator(): + elif self.op == '+': + self.r1 = self.r1 + self.r2 + elif self.op == '-': + self.r1 = self.r1 - self.r2 + elif self.op == '*': + self.r1 = self.r1 * self.r2 + elif self.op == '/':" +684,https://:@github.com/mhantke/h5writer.git,b70deaa06e1b8043aa658410e6ffe2310f796c35,"@@ -150,7 +150,7 @@ class H5WriterMPI(AbstractH5Writer): + + def _write_solocache_group_to_file(self, data_dict, group_prefix=""/""): + if self._is_master() and group_prefix != ""/"": +- if group_prefix in self._f: ++ if group_prefix not in self._f: + self._f.create_group(group_prefix) + keys = data_dict.keys() + keys.sort() +",src/h5writer_mpi.py,"ReplaceText(target=' not in ' @(153,27)->(153,31))","class H5WriterMPI(AbstractH5Writer): + + def _write_solocache_group_to_file(self, data_dict, group_prefix=""/""): + if self._is_master() and group_prefix != ""/"": + if group_prefix in self._f: + self._f.create_group(group_prefix) + keys = data_dict.keys() + keys.sort()","class H5WriterMPI(AbstractH5Writer): + + def _write_solocache_group_to_file(self, data_dict, group_prefix=""/""): + if self._is_master() and group_prefix != ""/"": + if group_prefix not in self._f: + self._f.create_group(group_prefix) + keys = data_dict.keys() + keys.sort()" +685,https://:@github.com/MushroomRL/mushroom-rl.git,21a7d99f2c2f28a1de150b3464c7b649b096d757,"@@ -6,7 +6,7 @@ class EpsGreedy(object): + self._epsilon = epsilon + + def __call__(self): +- if np.random.uniform() > self._epsilon: ++ if np.random.uniform() < self._epsilon: + return False + return True + +",PyPi/policy/policy.py,"ReplaceText(target='<' @(9,31)->(9,32))","class EpsGreedy(object): + self._epsilon = epsilon + + def __call__(self): + if np.random.uniform() > self._epsilon: + return False + return True + ","class EpsGreedy(object): + self._epsilon = epsilon + + def __call__(self): + if np.random.uniform() < self._epsilon: + return False + return True + " +686,https://:@github.com/MushroomRL/mushroom-rl.git,86fae8d69f4906e0e395163d1b2fa43371d28deb,"@@ -103,7 +103,7 @@ class Algorithm(object): + if render: + self.mdp._render() + +- last = 0 if n_steps < self.mdp.horizon or not absorbing else 1 ++ last = 0 if n_steps < self.mdp.horizon and not absorbing else 1 + sample = self.state.ravel().tolist() + action.ravel().tolist() + \ + [reward] + next_state.ravel().tolist() + \ + [absorbing, last] +",PyPi/algorithms/algorithm.py,"ReplaceText(target='and' @(106,51)->(106,53))","class Algorithm(object): + if render: + self.mdp._render() + + last = 0 if n_steps < self.mdp.horizon or not absorbing else 1 + sample = self.state.ravel().tolist() + action.ravel().tolist() + \ + [reward] + next_state.ravel().tolist() + \ + [absorbing, last]","class Algorithm(object): + if render: + self.mdp._render() + + last = 0 if n_steps < self.mdp.horizon and not absorbing else 1 + sample = self.state.ravel().tolist() + action.ravel().tolist() + \ + [reward] + next_state.ravel().tolist() + \ + [absorbing, last]" +687,https://:@github.com/MushroomRL/mushroom-rl.git,2f134a73ac9cdab98206afeab6cd39bb02b6a6fc,"@@ -113,7 +113,7 @@ class Core(object): + action_idx = self.agent.draw_action(self.state, + self.agent.approximator) + action_value = self.mdp.action_space.get_value(action_idx) +- next_state, reward, absorbing, _ = self.mdp.step(action_idx) ++ next_state, reward, absorbing, _ = self.mdp.step(action_value) + J += self.mdp.gamma ** n_steps * reward + n_steps += 1 + +",PyPi/core/core.py,"ReplaceText(target='action_value' @(116,61)->(116,71))","class Core(object): + action_idx = self.agent.draw_action(self.state, + self.agent.approximator) + action_value = self.mdp.action_space.get_value(action_idx) + next_state, reward, absorbing, _ = self.mdp.step(action_idx) + J += self.mdp.gamma ** n_steps * reward + n_steps += 1 + ","class Core(object): + action_idx = self.agent.draw_action(self.state, + self.agent.approximator) + action_value = self.mdp.action_space.get_value(action_idx) + next_state, reward, absorbing, _ = self.mdp.step(action_value) + J += self.mdp.gamma ** n_steps * reward + n_steps += 1 + " +688,https://:@github.com/MushroomRL/mushroom-rl.git,a38031ed8b004f73983b53919acfd4c36e1f2bf1,"@@ -75,4 +75,4 @@ class Binarizer(Preprocessor): + The binarized input data array. + + """""" +- return (x > self._threshold).astype(np.float) ++ return (x >= self._threshold).astype(np.float) +",mushroom/utils/preprocessor.py,"ReplaceText(target='>=' @(78,18)->(78,19))","class Binarizer(Preprocessor): + The binarized input data array. + + """""" + return (x > self._threshold).astype(np.float)","class Binarizer(Preprocessor): + The binarized input data array. + + """""" + return (x >= self._threshold).astype(np.float)" +689,https://:@github.com/MushroomRL/mushroom-rl.git,bcf82aaeed185c53d3f512491f80ec793e264bab,"@@ -237,7 +237,7 @@ class RDQN(DQN): + state, action, _, _, absorbing, _ =\ + self._replay_memory.get_idxs(idxs) + +- no_abs_idxs = idxs[np.argwhere(absorbing != 0).ravel()] ++ no_abs_idxs = idxs[np.argwhere(absorbing == 0).ravel()] + state, action, _, _, absorbing, _ =\ + self._replay_memory.get_idxs(no_abs_idxs) + next_state, next_action, next_reward, _, next_absorbing, _ =\ +",mushroom/algorithms/dqn.py,"ReplaceText(target='==' @(240,53)->(240,55))","class RDQN(DQN): + state, action, _, _, absorbing, _ =\ + self._replay_memory.get_idxs(idxs) + + no_abs_idxs = idxs[np.argwhere(absorbing != 0).ravel()] + state, action, _, _, absorbing, _ =\ + self._replay_memory.get_idxs(no_abs_idxs) + next_state, next_action, next_reward, _, next_absorbing, _ =\","class RDQN(DQN): + state, action, _, _, absorbing, _ =\ + self._replay_memory.get_idxs(idxs) + + no_abs_idxs = idxs[np.argwhere(absorbing == 0).ravel()] + state, action, _, _, absorbing, _ =\ + self._replay_memory.get_idxs(no_abs_idxs) + next_state, next_action, next_reward, _, next_absorbing, _ =\" +690,https://:@github.com/MushroomRL/mushroom-rl.git,d4ec7569d1f7409b05754abe8a11a69f016efd01,"@@ -258,7 +258,7 @@ class SARSALambdaDiscrete(TD): + for s in self.mdp_info.observation_space.values: + for a in self.mdp_info.action_space.values: + self.Q[s, a] += self.alpha(s, a) * delta * self.e[s, a] +- self.e[s, a] = self.mdp_info.gamma * self._lambda ++ self.e[s, a] *= self.mdp_info.gamma * self._lambda + + + class SARSALambdaContinuous(TD): +",mushroom/algorithms/value/td.py,"ReplaceText(target='*=' @(261,29)->(261,30))","class SARSALambdaDiscrete(TD): + for s in self.mdp_info.observation_space.values: + for a in self.mdp_info.action_space.values: + self.Q[s, a] += self.alpha(s, a) * delta * self.e[s, a] + self.e[s, a] = self.mdp_info.gamma * self._lambda + + + class SARSALambdaContinuous(TD):","class SARSALambdaDiscrete(TD): + for s in self.mdp_info.observation_space.values: + for a in self.mdp_info.action_space.values: + self.Q[s, a] += self.alpha(s, a) * delta * self.e[s, a] + self.e[s, a] *= self.mdp_info.gamma * self._lambda + + + class SARSALambdaContinuous(TD):" +691,https://:@github.com/MushroomRL/mushroom-rl.git,809c24e9b50202c6c06fbe6fc7e4b067894230c4,"@@ -161,7 +161,7 @@ class DoubleFQI(FQI): + next_state = list() + absorbing = list() + +- half = len(x) / 2 ++ half = len(x) // 2 + for i in range(2): + s, a, r, ss, ab, _ = parse_dataset(x[i * half:(i + 1) * half]) + state.append(s) +",mushroom/algorithms/value/batch_td.py,"ReplaceText(target='//' @(164,22)->(164,23))","class DoubleFQI(FQI): + next_state = list() + absorbing = list() + + half = len(x) / 2 + for i in range(2): + s, a, r, ss, ab, _ = parse_dataset(x[i * half:(i + 1) * half]) + state.append(s)","class DoubleFQI(FQI): + next_state = list() + absorbing = list() + + half = len(x) // 2 + for i in range(2): + s, a, r, ss, ab, _ = parse_dataset(x[i * half:(i + 1) * half]) + state.append(s)" +692,https://:@github.com/MushroomRL/mushroom-rl.git,809c24e9b50202c6c06fbe6fc7e4b067894230c4,"@@ -186,7 +186,7 @@ class AveragedDQN(DQN): + assert isinstance(self.target_approximator.model, Ensemble) + + def _update_target(self): +- idx = self._n_updates / self._target_update_frequency\ ++ idx = self._n_updates // self._target_update_frequency\ + % self._n_approximators + self.target_approximator.model[idx].set_weights( + self.approximator.model.get_weights()) +",mushroom/algorithms/value/dqn.py,"ReplaceText(target='//' @(189,30)->(189,31))","class AveragedDQN(DQN): + assert isinstance(self.target_approximator.model, Ensemble) + + def _update_target(self): + idx = self._n_updates / self._target_update_frequency\ + % self._n_approximators + self.target_approximator.model[idx].set_weights( + self.approximator.model.get_weights())","class AveragedDQN(DQN): + assert isinstance(self.target_approximator.model, Ensemble) + + def _update_target(self): + idx = self._n_updates // self._target_update_frequency\ + % self._n_approximators + self.target_approximator.model[idx].set_weights( + self.approximator.model.get_weights())" +693,https://:@github.com/MushroomRL/mushroom-rl.git,809c24e9b50202c6c06fbe6fc7e4b067894230c4,"@@ -108,7 +108,7 @@ def compute_probabilities(grid_map, cell_list, passenger_list, prob): + passenger_states = cartesian([[0, 1]] * len(passenger_list)) + + for i in range(n_states): +- idx = i / len(cell_list) ++ idx = i // len(cell_list) + collected_passengers = np.array( + passenger_list)[np.argwhere(passenger_states[idx] == 1).ravel()] + state = c[i % len(cell_list)] +",mushroom/environments/generators/taxi.py,"ReplaceText(target='//' @(111,16)->(111,17))","def compute_probabilities(grid_map, cell_list, passenger_list, prob): + passenger_states = cartesian([[0, 1]] * len(passenger_list)) + + for i in range(n_states): + idx = i / len(cell_list) + collected_passengers = np.array( + passenger_list)[np.argwhere(passenger_states[idx] == 1).ravel()] + state = c[i % len(cell_list)]","def compute_probabilities(grid_map, cell_list, passenger_list, prob): + passenger_states = cartesian([[0, 1]] * len(passenger_list)) + + for i in range(n_states): + idx = i // len(cell_list) + collected_passengers = np.array( + passenger_list)[np.argwhere(passenger_states[idx] == 1).ravel()] + state = c[i % len(cell_list)]" +694,https://:@github.com/MushroomRL/mushroom-rl.git,809c24e9b50202c6c06fbe6fc7e4b067894230c4,"@@ -54,7 +54,7 @@ class AbstractGridWorld(Environment): + + @staticmethod + def convert_to_grid(state, width): +- return np.array([state[0] / width, state[0] % width]) ++ return np.array([state[0] // width, state[0] % width]) + + @staticmethod + def convert_to_int(state, width): +",mushroom/environments/grid_world.py,"ReplaceText(target='//' @(57,34)->(57,35))","class AbstractGridWorld(Environment): + + @staticmethod + def convert_to_grid(state, width): + return np.array([state[0] / width, state[0] % width]) + + @staticmethod + def convert_to_int(state, width):","class AbstractGridWorld(Environment): + + @staticmethod + def convert_to_grid(state, width): + return np.array([state[0] // width, state[0] % width]) + + @staticmethod + def convert_to_int(state, width):" +695,https://:@github.com/MushroomRL/mushroom-rl.git,809c24e9b50202c6c06fbe6fc7e4b067894230c4,"@@ -90,7 +90,7 @@ def experiment(alg): + # evaluate initial policy + pi.set_epsilon(epsilon_test) + mdp.set_episode_end(ends_at_life=False) +- for n_epoch in range(1, max_steps / evaluation_frequency + 1): ++ for n_epoch in range(1, max_steps // evaluation_frequency + 1): + # learning step + pi.set_epsilon(epsilon) + mdp.set_episode_end(ends_at_life=True) +",tests/atari_dqn/atari_dqn.py,"ReplaceText(target='//' @(93,38)->(93,39))","def experiment(alg): + # evaluate initial policy + pi.set_epsilon(epsilon_test) + mdp.set_episode_end(ends_at_life=False) + for n_epoch in range(1, max_steps / evaluation_frequency + 1): + # learning step + pi.set_epsilon(epsilon) + mdp.set_episode_end(ends_at_life=True)","def experiment(alg): + # evaluate initial policy + pi.set_epsilon(epsilon_test) + mdp.set_episode_end(ends_at_life=False) + for n_epoch in range(1, max_steps // evaluation_frequency + 1): + # learning step + pi.set_epsilon(epsilon) + mdp.set_episode_end(ends_at_life=True)" +696,https://:@github.com/MushroomRL/mushroom-rl.git,a3695d7feb30d5fbb277fb1e8a7e3711d84545a2,"@@ -294,7 +294,7 @@ def experiment(): + agent.policy.set_q(agent.approximator) + + np.save(folder_name + '/scores.npy', scores) +- for n_epoch in range(1, max_steps / evaluation_frequency + 1): ++ for n_epoch in range(1, max_steps // evaluation_frequency + 1): + print_epoch(n_epoch) + print('- Learning:') + # learning step +",examples/atari_dqn/atari_dqn.py,"ReplaceText(target='//' @(297,42)->(297,43))","def experiment(): + agent.policy.set_q(agent.approximator) + + np.save(folder_name + '/scores.npy', scores) + for n_epoch in range(1, max_steps / evaluation_frequency + 1): + print_epoch(n_epoch) + print('- Learning:') + # learning step","def experiment(): + agent.policy.set_q(agent.approximator) + + np.save(folder_name + '/scores.npy', scores) + for n_epoch in range(1, max_steps // evaluation_frequency + 1): + print_epoch(n_epoch) + print('- Learning:') + # learning step" +697,https://:@github.com/MushroomRL/mushroom-rl.git,238a6a652a8ce6c7fb23eba48dd52a2bce343b92,"@@ -51,7 +51,7 @@ class DQN(Agent): + self._batch_size = batch_size + self._n_approximators = n_approximators + self._clip_reward = clip_reward +- self._target_update_frequency = target_update_frequency / train_frequency ++ self._target_update_frequency = target_update_frequency // train_frequency + self._max_no_op_actions = max_no_op_actions + self._no_op_action_value = no_op_action_value + +",mushroom/algorithms/value/dqn.py,"ReplaceText(target='//' @(54,64)->(54,65))","class DQN(Agent): + self._batch_size = batch_size + self._n_approximators = n_approximators + self._clip_reward = clip_reward + self._target_update_frequency = target_update_frequency / train_frequency + self._max_no_op_actions = max_no_op_actions + self._no_op_action_value = no_op_action_value + ","class DQN(Agent): + self._batch_size = batch_size + self._n_approximators = n_approximators + self._clip_reward = clip_reward + self._target_update_frequency = target_update_frequency // train_frequency + self._max_no_op_actions = max_no_op_actions + self._no_op_action_value = no_op_action_value + " +698,https://:@github.com/MushroomRL/mushroom-rl.git,bdd275227ed4e37833414e33176bbe0585f02a8b,"@@ -180,7 +180,7 @@ class InvertedPendulumDiscrete(Environment): + u = 0. + else: + u = self._max_u +- action += np.random.uniform(-self._noise_u, self._noise_u) ++ u += np.random.uniform(-self._noise_u, self._noise_u) + new_state = odeint(self._dynamics, self._state, [0, self._dt], + (u,)) + +",mushroom/environments/inverted_pendulum.py,"ReplaceText(target='u' @(183,8)->(183,14))","class InvertedPendulumDiscrete(Environment): + u = 0. + else: + u = self._max_u + action += np.random.uniform(-self._noise_u, self._noise_u) + new_state = odeint(self._dynamics, self._state, [0, self._dt], + (u,)) + ","class InvertedPendulumDiscrete(Environment): + u = 0. + else: + u = self._max_u + u += np.random.uniform(-self._noise_u, self._noise_u) + new_state = odeint(self._dynamics, self._state, [0, self._dt], + (u,)) + " +699,https://:@github.com/MushroomRL/mushroom-rl.git,590aabe042c74f6d6be4b1b821ad35d9ae1a47f7,"@@ -232,7 +232,7 @@ class ReplayMemory(object): + allows it to be used. + + """""" +- return self.size > self._initial_size ++ return self.size >= self._initial_size + + @property + def size(self): +",mushroom/utils/replay_memory.py,"ReplaceText(target='>=' @(235,25)->(235,26))","class ReplayMemory(object): + allows it to be used. + + """""" + return self.size > self._initial_size + + @property + def size(self):","class ReplayMemory(object): + allows it to be used. + + """""" + return self.size >= self._initial_size + + @property + def size(self):" +700,https://:@github.com/MushroomRL/mushroom-rl.git,00f820f10d492257264eb0587aac92193ba65650,"@@ -78,7 +78,7 @@ def experiment(n_epochs, n_steps, n_steps_test): + n_actions=mdp.info.action_space.n) + + # Agent +- agent = DQN(TorchApproximator, pi, mdp.info, ++ agent = DQN(mdp.info, pi, TorchApproximator, + approximator_params=approximator_params, batch_size=batch_size, + n_approximators=1, initial_replay_size=initial_replay_size, + max_replay_size=max_replay_size, +",examples/acrobot_dqn.py,"ArgSwap(idxs=0<->2 @(81,12)->(81,15))","def experiment(n_epochs, n_steps, n_steps_test): + n_actions=mdp.info.action_space.n) + + # Agent + agent = DQN(TorchApproximator, pi, mdp.info, + approximator_params=approximator_params, batch_size=batch_size, + n_approximators=1, initial_replay_size=initial_replay_size, + max_replay_size=max_replay_size,","def experiment(n_epochs, n_steps, n_steps_test): + n_actions=mdp.info.action_space.n) + + # Agent + agent = DQN(mdp.info, pi, TorchApproximator, + approximator_params=approximator_params, batch_size=batch_size, + n_approximators=1, initial_replay_size=initial_replay_size, + max_replay_size=max_replay_size," +701,https://:@github.com/MushroomRL/mushroom-rl.git,00f820f10d492257264eb0587aac92193ba65650,"@@ -37,7 +37,7 @@ def experiment(): + + # Agent + algorithm_params = dict(n_iterations=20) +- agent = FQI(approximator, pi, mdp.info, ++ agent = FQI(mdp.info, pi, approximator, + approximator_params=approximator_params, **algorithm_params) + + # Algorithm +",examples/car_on_hill_fqi.py,"ArgSwap(idxs=0<->2 @(40,12)->(40,15))","def experiment(): + + # Agent + algorithm_params = dict(n_iterations=20) + agent = FQI(approximator, pi, mdp.info, + approximator_params=approximator_params, **algorithm_params) + + # Algorithm","def experiment(): + + # Agent + algorithm_params = dict(n_iterations=20) + agent = FQI(mdp.info, pi, approximator, + approximator_params=approximator_params, **algorithm_params) + + # Algorithm" +702,https://:@github.com/MushroomRL/mushroom-rl.git,00f820f10d492257264eb0587aac92193ba65650,"@@ -33,7 +33,7 @@ def experiment(algorithm_class, exp): + # Agent + learning_rate = ExponentialParameter(value=1., exp=exp, size=mdp.info.size) + algorithm_params = dict(learning_rate=learning_rate) +- agent = algorithm_class(pi, mdp.info, **algorithm_params) ++ agent = algorithm_class(mdp.info, pi, **algorithm_params) + + # Algorithm + collect_Q = CollectQ(agent.approximator) +",examples/double_chain_q_learning/double_chain.py,"ArgSwap(idxs=0<->1 @(36,12)->(36,27))","def experiment(algorithm_class, exp): + # Agent + learning_rate = ExponentialParameter(value=1., exp=exp, size=mdp.info.size) + algorithm_params = dict(learning_rate=learning_rate) + agent = algorithm_class(pi, mdp.info, **algorithm_params) + + # Algorithm + collect_Q = CollectQ(agent.approximator)","def experiment(algorithm_class, exp): + # Agent + learning_rate = ExponentialParameter(value=1., exp=exp, size=mdp.info.size) + algorithm_params = dict(learning_rate=learning_rate) + agent = algorithm_class(mdp.info, pi, **algorithm_params) + + # Algorithm + collect_Q = CollectQ(agent.approximator)" +703,https://:@github.com/MushroomRL/mushroom-rl.git,00f820f10d492257264eb0587aac92193ba65650,"@@ -38,7 +38,7 @@ def experiment(algorithm_class, exp): + # Agent + learning_rate = ExponentialParameter(value=1, exp=exp, size=mdp.info.size) + algorithm_params = dict(learning_rate=learning_rate) +- agent = algorithm_class(pi, mdp.info, **algorithm_params) ++ agent = algorithm_class(mdp.info, pi, **algorithm_params) + + # Algorithm + start = mdp.convert_to_int(mdp._start, mdp._width) +",examples/grid_world_td.py,"ArgSwap(idxs=0<->1 @(41,12)->(41,27))","def experiment(algorithm_class, exp): + # Agent + learning_rate = ExponentialParameter(value=1, exp=exp, size=mdp.info.size) + algorithm_params = dict(learning_rate=learning_rate) + agent = algorithm_class(pi, mdp.info, **algorithm_params) + + # Algorithm + start = mdp.convert_to_int(mdp._start, mdp._width)","def experiment(algorithm_class, exp): + # Agent + learning_rate = ExponentialParameter(value=1, exp=exp, size=mdp.info.size) + algorithm_params = dict(learning_rate=learning_rate) + agent = algorithm_class(mdp.info, pi, **algorithm_params) + + # Algorithm + start = mdp.convert_to_int(mdp._start, mdp._width)" +704,https://:@github.com/MushroomRL/mushroom-rl.git,3644c74bf5069331dfd80f1b65e281460fefab21,"@@ -191,7 +191,7 @@ class TRPO(Agent): + new_loss = self._compute_loss(obs, act, adv, old_log_prob) + kl = self._compute_kl(obs, old_pol_dist) + improve = new_loss - prev_loss +- if kl <= self._max_kl * 1.5 or improve >= 0: ++ if kl <= self._max_kl * 1.5 and improve >= 0: + violation = False + break + stepsize *= .5 +",mushroom_rl/algorithms/actor_critic/deep_actor_critic/trpo.py,"ReplaceText(target='and' @(194,40)->(194,42))","class TRPO(Agent): + new_loss = self._compute_loss(obs, act, adv, old_log_prob) + kl = self._compute_kl(obs, old_pol_dist) + improve = new_loss - prev_loss + if kl <= self._max_kl * 1.5 or improve >= 0: + violation = False + break + stepsize *= .5","class TRPO(Agent): + new_loss = self._compute_loss(obs, act, adv, old_log_prob) + kl = self._compute_kl(obs, old_pol_dist) + improve = new_loss - prev_loss + if kl <= self._max_kl * 1.5 and improve >= 0: + violation = False + break + stepsize *= .5" +705,https://:@github.com/ska-sa/katsdpimager.git,9606d1eefd02b2fe7039fe09e6bf7647d0b6c30b,"@@ -20,7 +20,7 @@ def parse_quantity(str_value): + """"""Parse a string into an astropy Quantity. Rather than trying to guess + where the split occurs, we try every position from the back until we + succeed."""""" +- for i in range(len(str_value), -1, 0): ++ for i in range(len(str_value), 0, -1): + try: + value = float(str_value[:i]) + unit = units.Unit(str_value[i:]) +",scripts/imager.py,"ArgSwap(idxs=1<->2 @(23,13)->(23,18))","def parse_quantity(str_value): + """"""Parse a string into an astropy Quantity. Rather than trying to guess + where the split occurs, we try every position from the back until we + succeed."""""" + for i in range(len(str_value), -1, 0): + try: + value = float(str_value[:i]) + unit = units.Unit(str_value[i:])","def parse_quantity(str_value): + """"""Parse a string into an astropy Quantity. Rather than trying to guess + where the split occurs, we try every position from the back until we + succeed."""""" + for i in range(len(str_value), 0, -1): + try: + value = float(str_value[:i]) + unit = units.Unit(str_value[i:])" +706,https://:@github.com/ska-sa/katsdpimager.git,87edf0d372e8b40702cc72cc96c07ddb62fe19cc,"@@ -479,7 +479,7 @@ class Weights(accel.OperationSequence): + self.ensure_all_bound() + # If self._fill is set, it is not necessary to clear first because + # finalize will set all relevant values. +- if self._fill is not None: ++ if self._fill is None: + self.buffer('grid').zero(self.command_queue) + + def grid(self, uv, weights): +",katsdpimager/weight.py,"ReplaceText(target=' is ' @(482,21)->(482,29))","class Weights(accel.OperationSequence): + self.ensure_all_bound() + # If self._fill is set, it is not necessary to clear first because + # finalize will set all relevant values. + if self._fill is not None: + self.buffer('grid').zero(self.command_queue) + + def grid(self, uv, weights):","class Weights(accel.OperationSequence): + self.ensure_all_bound() + # If self._fill is set, it is not necessary to clear first because + # finalize will set all relevant values. + if self._fill is None: + self.buffer('grid').zero(self.command_queue) + + def grid(self, uv, weights):" +707,https://:@github.com/ska-sa/katsdpimager.git,c1790fa1bf597a5fb592ee05ff7205b17fbcc85e,"@@ -134,7 +134,7 @@ class Image(object): + # TODO: should use the WCS transformation + slices[i - 3] = 'IQUV'.find(stokes) + elif axis_type == 'VOPT': +- slices[i - 3] = channel ++ slices[i - 3] = rel_channel + self._render_thumb(output_dir, filename, slices, mode, stokes, channel) + self._render_full(output_dir, filename, slices, mode, stokes, channel) + +",tests/images_report.py,"ReplaceText(target='rel_channel' @(137,36)->(137,43))","class Image(object): + # TODO: should use the WCS transformation + slices[i - 3] = 'IQUV'.find(stokes) + elif axis_type == 'VOPT': + slices[i - 3] = channel + self._render_thumb(output_dir, filename, slices, mode, stokes, channel) + self._render_full(output_dir, filename, slices, mode, stokes, channel) + ","class Image(object): + # TODO: should use the WCS transformation + slices[i - 3] = 'IQUV'.find(stokes) + elif axis_type == 'VOPT': + slices[i - 3] = rel_channel + self._render_thumb(output_dir, filename, slices, mode, stokes, channel) + self._render_full(output_dir, filename, slices, mode, stokes, channel) + " +708,https://:@github.com/gdoumenc/coworks.git,4a24754388adcf2fb8b878fb6a97cce8bf443e55,"@@ -53,7 +53,7 @@ def invoke(initial, ctx): + handler = get_handler(project_dir, module, service) + cmd = project_config.get_command(handler, module, service, workspace) + if not cmd: +- raise CwsClientError(f""Undefined command {cmd}.\n"") ++ raise CwsClientError(f""Undefined command {cmd_name}.\n"") + + # Defines the proxy command with all user options + def call_execute(**command_options): +",coworks/cws/client.py,"ReplaceText(target='cmd_name' @(56,58)->(56,61))","def invoke(initial, ctx): + handler = get_handler(project_dir, module, service) + cmd = project_config.get_command(handler, module, service, workspace) + if not cmd: + raise CwsClientError(f""Undefined command {cmd}.\n"") + + # Defines the proxy command with all user options + def call_execute(**command_options):","def invoke(initial, ctx): + handler = get_handler(project_dir, module, service) + cmd = project_config.get_command(handler, module, service, workspace) + if not cmd: + raise CwsClientError(f""Undefined command {cmd_name}.\n"") + + # Defines the proxy command with all user options + def call_execute(**command_options):" +709,https://:@github.com/geokrety/geokrety-api.git,402a0659cc311fcb296865db0a8303130cb85f92,"@@ -9,5 +9,5 @@ def dasherize(text): + def require_relationship(resource_list, data): + for resource in resource_list: + if resource not in data: +- raise UnprocessableEntity({'pointer': '/data/relationships/{}'.format(resource)}, +- ""A valid relationship with {} resource is required"".format(resource)) ++ raise UnprocessableEntity(""A valid relationship with {} resource is required"".format(resource), ++ {'pointer': '/data/relationships/{}'.format(resource)}) +",app/api/helpers/utilities.py,"ArgSwap(idxs=0<->1 @(12,18)->(12,37))","def dasherize(text): + def require_relationship(resource_list, data): + for resource in resource_list: + if resource not in data: + raise UnprocessableEntity({'pointer': '/data/relationships/{}'.format(resource)}, + ""A valid relationship with {} resource is required"".format(resource))","def dasherize(text): + def require_relationship(resource_list, data): + for resource in resource_list: + if resource not in data: + raise UnprocessableEntity(""A valid relationship with {} resource is required"".format(resource), + {'pointer': '/data/relationships/{}'.format(resource)})" +710,https://:@github.com/troylar/mike-brady.git,51ac87ab42555fcea332280f21425fd0398ad22a,"@@ -43,7 +43,7 @@ def render_templates(target_path, replace_values, file_types): + template = env.get_template(f) + rendered = template.render(replace_values) + with open(full_path, ""w"") as fh: +- print('Writing {}'.format(f)) ++ print('Writing {}'.format(full_path)) + fh.write(rendered) + + +",src/main.py,"ReplaceText(target='full_path' @(46,42)->(46,43))","def render_templates(target_path, replace_values, file_types): + template = env.get_template(f) + rendered = template.render(replace_values) + with open(full_path, ""w"") as fh: + print('Writing {}'.format(f)) + fh.write(rendered) + + ","def render_templates(target_path, replace_values, file_types): + template = env.get_template(f) + rendered = template.render(replace_values) + with open(full_path, ""w"") as fh: + print('Writing {}'.format(full_path)) + fh.write(rendered) + + " +711,https://:@github.com/timwhite/greg.git,0a729af52a7ca3d66cefa89513f97fb5cd932b8e,"@@ -756,7 +756,7 @@ def sync(args): + feed.fix_linkdate(entry) + # Sort entries_to_download, but only if you want to download as + # many as there are +- if stop < len(entries_to_download): ++ if stop >= len(entries_to_download): + entries_to_download.sort(key=operator.attrgetter(""linkdate""), + reverse=False) + for entry in entries_to_download: +",greg/greg.py,"ReplaceText(target='>=' @(759,20)->(759,21))","def sync(args): + feed.fix_linkdate(entry) + # Sort entries_to_download, but only if you want to download as + # many as there are + if stop < len(entries_to_download): + entries_to_download.sort(key=operator.attrgetter(""linkdate""), + reverse=False) + for entry in entries_to_download:","def sync(args): + feed.fix_linkdate(entry) + # Sort entries_to_download, but only if you want to download as + # many as there are + if stop >= len(entries_to_download): + entries_to_download.sort(key=operator.attrgetter(""linkdate""), + reverse=False) + for entry in entries_to_download:" +712,https://:@github.com/yeago/question-stack.git,71958e8a2745787aacd5bf8b07867a4710b2bb4b,"@@ -61,7 +61,7 @@ def accepted_answer(request,slug,comment): + if not instance == comment.content_object: + raise Http404 + +- if not request.user.has_perm('stack.change_question') or not request.user == instance.comment.user: ++ if not request.user.has_perm('stack.change_question') and not request.user == instance.comment.user: + raise Http404 + + if instance.accepted_answer: +",views.py,"ReplaceText(target='and' @(64,55)->(64,57))","def accepted_answer(request,slug,comment): + if not instance == comment.content_object: + raise Http404 + + if not request.user.has_perm('stack.change_question') or not request.user == instance.comment.user: + raise Http404 + + if instance.accepted_answer:","def accepted_answer(request,slug,comment): + if not instance == comment.content_object: + raise Http404 + + if not request.user.has_perm('stack.change_question') and not request.user == instance.comment.user: + raise Http404 + + if instance.accepted_answer:" +713,https://:@github.com/jtbish/piecewise.git,5f227f50d16d04d756045804b21ca5bd18c83597,"@@ -14,7 +14,7 @@ class FuzzyXCSFLinearPredictionCreditAssignment: + ] + total_matching_degrees = sum(matching_degrees) + assert total_matching_degrees > 0.0 +- for (classifier, matching_degree) in zip(matching_degrees, action_set): ++ for (classifier, matching_degree) in zip(action_set, matching_degrees): + credit_weight = (matching_degree / total_matching_degrees) + self._update_experience(classifier, credit_weight) + payoff_diff = payoff - classifier.get_prediction(situation) +",piecewise/fuzzy/credit_assignment.py,"ArgSwap(idxs=0<->1 @(17,45)->(17,48))","class FuzzyXCSFLinearPredictionCreditAssignment: + ] + total_matching_degrees = sum(matching_degrees) + assert total_matching_degrees > 0.0 + for (classifier, matching_degree) in zip(matching_degrees, action_set): + credit_weight = (matching_degree / total_matching_degrees) + self._update_experience(classifier, credit_weight) + payoff_diff = payoff - classifier.get_prediction(situation)","class FuzzyXCSFLinearPredictionCreditAssignment: + ] + total_matching_degrees = sum(matching_degrees) + assert total_matching_degrees > 0.0 + for (classifier, matching_degree) in zip(action_set, matching_degrees): + credit_weight = (matching_degree / total_matching_degrees) + self._update_experience(classifier, credit_weight) + payoff_diff = payoff - classifier.get_prediction(situation)" +714,https://:@github.com/Clinical-Genomics/cg.git,f65fa404f3761f726a5bd32e3794e3c3d6771a26,"@@ -110,7 +110,7 @@ def update(context, answered_out, case_id): + if delivery_date is None: + log.warn(""sample not delivered: %s"", hk_sample.lims_id) + context.abort() +- delivery_dates.append(delivery_dates) ++ delivery_dates.append(delivery_date) + latest_date = sorted(delivery_dates)[-1] + log.debug(""fillin answered out date in HK"") + hk_run.answeredout_at = datetime.combine(latest_date, datetime.min.time()) +",cg/commands.py,"ReplaceText(target='delivery_date' @(113,34)->(113,48))","def update(context, answered_out, case_id): + if delivery_date is None: + log.warn(""sample not delivered: %s"", hk_sample.lims_id) + context.abort() + delivery_dates.append(delivery_dates) + latest_date = sorted(delivery_dates)[-1] + log.debug(""fillin answered out date in HK"") + hk_run.answeredout_at = datetime.combine(latest_date, datetime.min.time())","def update(context, answered_out, case_id): + if delivery_date is None: + log.warn(""sample not delivered: %s"", hk_sample.lims_id) + context.abort() + delivery_dates.append(delivery_date) + latest_date = sorted(delivery_dates)[-1] + log.debug(""fillin answered out date in HK"") + hk_run.answeredout_at = datetime.combine(latest_date, datetime.min.time())" +715,https://:@github.com/Clinical-Genomics/cg.git,a9c45156e08953c30b15eccd7431e76ce0809ac3,"@@ -174,7 +174,7 @@ def start(lims_api, customer_id, family_name): + log.debug(""%s has status %s"", sample.sample_id, sample_status) + statuses.add(sample_status) + +- if len(is_externals) == 0: ++ if len(is_externals) == 1: + data = dict(is_external=is_externals.pop()) + else: + # mix of internal and external samples +",cg/apps/lims.py,"ReplaceText(target='1' @(177,28)->(177,29))","def start(lims_api, customer_id, family_name): + log.debug(""%s has status %s"", sample.sample_id, sample_status) + statuses.add(sample_status) + + if len(is_externals) == 0: + data = dict(is_external=is_externals.pop()) + else: + # mix of internal and external samples","def start(lims_api, customer_id, family_name): + log.debug(""%s has status %s"", sample.sample_id, sample_status) + statuses.add(sample_status) + + if len(is_externals) == 1: + data = dict(is_external=is_externals.pop()) + else: + # mix of internal and external samples" +716,https://:@github.com/Clinical-Genomics/cg.git,ea94c447cec22ba9e9a5febcf78f1816f0b2de5d,"@@ -90,7 +90,7 @@ def family(context: click.Context, customer: str, name: bool, samples: bool, + families.append(family_obj) + + for family_obj in families: +- LOG.debug(f""{family_id.internal_id}: get info about family"") ++ LOG.debug(f""{family_obj.internal_id}: get info about family"") + row = [ + family_obj.internal_id, + family_obj.name, +",cg/cli/get.py,"ReplaceText(target='family_obj' @(93,21)->(93,30))","def family(context: click.Context, customer: str, name: bool, samples: bool, + families.append(family_obj) + + for family_obj in families: + LOG.debug(f""{family_id.internal_id}: get info about family"") + row = [ + family_obj.internal_id, + family_obj.name,","def family(context: click.Context, customer: str, name: bool, samples: bool, + families.append(family_obj) + + for family_obj in families: + LOG.debug(f""{family_obj.internal_id}: get info about family"") + row = [ + family_obj.internal_id, + family_obj.name," +717,https://:@github.com/Clinical-Genomics/cg.git,097837f7aeded32f7792fd77ede05c006732e06b,"@@ -18,7 +18,7 @@ class BackupApi(): + """"""Check if there's too many flowcells already ""ondisk""."""""" + ondisk_flowcells = self.status.flowcells(status='ondisk').count() + LOG.debug(f""ondisk flowcells: {ondisk_flowcells}"") +- return ondisk_flowcells < max_flowcells ++ return ondisk_flowcells > max_flowcells + + def check_processing(self, max_flowcells: int=3) -> bool: + """"""Check if the processing queue for flowcells is not full."""""" +",cg/meta/backup.py,"ReplaceText(target='>' @(21,32)->(21,33))","class BackupApi(): + """"""Check if there's too many flowcells already ""ondisk""."""""" + ondisk_flowcells = self.status.flowcells(status='ondisk').count() + LOG.debug(f""ondisk flowcells: {ondisk_flowcells}"") + return ondisk_flowcells < max_flowcells + + def check_processing(self, max_flowcells: int=3) -> bool: + """"""Check if the processing queue for flowcells is not full.""""""","class BackupApi(): + """"""Check if there's too many flowcells already ""ondisk""."""""" + ondisk_flowcells = self.status.flowcells(status='ondisk').count() + LOG.debug(f""ondisk flowcells: {ondisk_flowcells}"") + return ondisk_flowcells > max_flowcells + + def check_processing(self, max_flowcells: int=3) -> bool: + """"""Check if the processing queue for flowcells is not full.""""""" +718,https://:@github.com/codesyntax/Products.Bitakora.git,c9af30f2114b45151a57d527b6d87150d17ec226,"@@ -23,7 +23,7 @@ __version__ = ""$Revision$"" + def manage_addComment(self, author, body, url='', email='', date=None, bitakora_cpt='', random_cpt='', captcha_zz=0, REQUEST=None): + """""" Called from HTML form when commenting """""" + from utils import checkCaptchaValue, isCommentSpam +- if not captcha_zz: ++ if captcha_zz: + if not checkCaptchaValue(random_cpt, bitakora_cpt): + if REQUEST is not None: + return REQUEST.RESPONSE.redirect(self.absolute_url()+u'?msg=%s&body=%s&comment_author=%s&comment_email=%s&comment_url=%s#bitakora_cpt_control' % (self.gettext('Are you a bot? Please try again...'), url_quote(body.encode('utf-8')), url_quote(author.encode('utf-8')), url_quote(email.encode('utf-8')), url_quote(url.encode('utf-8')))) +",Comment.py,"ReplaceText(target='' @(26,7)->(26,11))","__version__ = ""$Revision$"" + def manage_addComment(self, author, body, url='', email='', date=None, bitakora_cpt='', random_cpt='', captcha_zz=0, REQUEST=None): + """""" Called from HTML form when commenting """""" + from utils import checkCaptchaValue, isCommentSpam + if not captcha_zz: + if not checkCaptchaValue(random_cpt, bitakora_cpt): + if REQUEST is not None: + return REQUEST.RESPONSE.redirect(self.absolute_url()+u'?msg=%s&body=%s&comment_author=%s&comment_email=%s&comment_url=%s#bitakora_cpt_control' % (self.gettext('Are you a bot? Please try again...'), url_quote(body.encode('utf-8')), url_quote(author.encode('utf-8')), url_quote(email.encode('utf-8')), url_quote(url.encode('utf-8'))))","__version__ = ""$Revision$"" + def manage_addComment(self, author, body, url='', email='', date=None, bitakora_cpt='', random_cpt='', captcha_zz=0, REQUEST=None): + """""" Called from HTML form when commenting """""" + from utils import checkCaptchaValue, isCommentSpam + if captcha_zz: + if not checkCaptchaValue(random_cpt, bitakora_cpt): + if REQUEST is not None: + return REQUEST.RESPONSE.redirect(self.absolute_url()+u'?msg=%s&body=%s&comment_author=%s&comment_email=%s&comment_url=%s#bitakora_cpt_control' % (self.gettext('Are you a bot? Please try again...'), url_quote(body.encode('utf-8')), url_quote(author.encode('utf-8')), url_quote(email.encode('utf-8')), url_quote(url.encode('utf-8'))))" +719,https://:@gitlab.com/saltspiro/spiro-deploy.git,660c01a080bb7c82a593146ca85c3d04f237881a,"@@ -112,7 +112,7 @@ def main(argv=sys.argv[1:]): + print(event, pprint.pformat(data), flush=True) + + if event == 'highstate-start': +- minions += set(data['minions']) ++ minions |= set(data['minions']) + elif event == 'highstate': + minions.discard(data['minion']) + +",spirodeploy/cli.py,"ReplaceText(target='|=' @(115,20)->(115,22))","def main(argv=sys.argv[1:]): + print(event, pprint.pformat(data), flush=True) + + if event == 'highstate-start': + minions += set(data['minions']) + elif event == 'highstate': + minions.discard(data['minion']) + ","def main(argv=sys.argv[1:]): + print(event, pprint.pformat(data), flush=True) + + if event == 'highstate-start': + minions |= set(data['minions']) + elif event == 'highstate': + minions.discard(data['minion']) + " +720,https://:@github.com/ymoch/preacher.git,5b49e834eb2c9ea03ba9619b9fb0cb2120ff68a7,"@@ -142,7 +142,7 @@ class Case: + + response_verification = self._response.verify( + response, +- ValueContext(origin_datetime=response.starts), ++ ValueContext(origin_datetime=execution.starts), + ) + return CaseResult( + label=self._label, +",preacher/core/scenario/case.py,"ReplaceText(target='execution' @(145,41)->(145,49))","class Case: + + response_verification = self._response.verify( + response, + ValueContext(origin_datetime=response.starts), + ) + return CaseResult( + label=self._label,","class Case: + + response_verification = self._response.verify( + response, + ValueContext(origin_datetime=execution.starts), + ) + return CaseResult( + label=self._label," +721,https://:@gitlab.com/socco/GliderTools.git,c0a6ae0924dabda3ddd6c03947a4038554e90eb1,"@@ -468,7 +468,7 @@ def savitzky_golay(arr, window_size, order, deriv=0, rate=1, interpolate=True): + + # allow to interpolate for half the window size + if interpolate: +- ser = Series(arr).interpolate(limit=half_window) ++ ser = Series(arr).interpolate(limit=window_size) + y = array(ser) + else: + y = array(arr) +",buoyancy_glider_utils/cleaning.py,"ReplaceText(target='window_size' @(471,44)->(471,55))","def savitzky_golay(arr, window_size, order, deriv=0, rate=1, interpolate=True): + + # allow to interpolate for half the window size + if interpolate: + ser = Series(arr).interpolate(limit=half_window) + y = array(ser) + else: + y = array(arr)","def savitzky_golay(arr, window_size, order, deriv=0, rate=1, interpolate=True): + + # allow to interpolate for half the window size + if interpolate: + ser = Series(arr).interpolate(limit=window_size) + y = array(ser) + else: + y = array(arr)" +722,https://:@github.com/hattya/scmver.git,9fc6568b7fc7814e4659e4140da9ffcfe69321ca,"@@ -95,7 +95,7 @@ def _is_wc_root(root, info): + p = os.path.dirname(root) + return (p == root + or not os.path.isdir(os.path.join(p, '.svn')) +- or _info(p).get('Repository UUID') == info['Repository UUID']) ++ or _info(p).get('Repository UUID') != info['Repository UUID']) + return False + + +",scmver/subversion.py,"ReplaceText(target='!=' @(98,51)->(98,53))","def _is_wc_root(root, info): + p = os.path.dirname(root) + return (p == root + or not os.path.isdir(os.path.join(p, '.svn')) + or _info(p).get('Repository UUID') == info['Repository UUID']) + return False + + ","def _is_wc_root(root, info): + p = os.path.dirname(root) + return (p == root + or not os.path.isdir(os.path.join(p, '.svn')) + or _info(p).get('Repository UUID') != info['Repository UUID']) + return False + + " +723,https://:@github.com/h0m3/python-mprint.git,782bec1d992d0ee19c8f0128d83ad4b9069bee3f,"@@ -82,7 +82,7 @@ def markup(string): + ) + newString += string.split("">"", 1)[1] + string = newString +- return newString ++ return string + + + # Print markup characters to screen +",mprint/mprint.py,"ReplaceText(target='string' @(85,11)->(85,20))","def markup(string): + ) + newString += string.split("">"", 1)[1] + string = newString + return newString + + + # Print markup characters to screen","def markup(string): + ) + newString += string.split("">"", 1)[1] + string = newString + return string + + + # Print markup characters to screen" +724,https://:@github.com/brettviren/worch.git,7941cffa22b2e9933e57139329e3c9d9cf555623,"@@ -31,7 +31,7 @@ def feature_command(tgen): + cmd_dir = tgen.make_node(tgen.worch.command_dir) + cmd_node = cmd_dir.make_node(tgen.worch.command_cmd) + cmd_target = \ +- map(cmd_dir.make_node, tgen.to_list(tgen.worch.command_target)) ++ map(tgen.make_node, tgen.to_list(tgen.worch.command_target)) + cmd_rule = '{command_cmd_prefix}{command_cmd} {command_cmd_options} {command_cmd_postfix}' + tgen.step('command', + rule = tgen.worch.format(cmd_rule), +",orch/features/feature_command.py,"ReplaceText(target='tgen' @(34,12)->(34,19))","def feature_command(tgen): + cmd_dir = tgen.make_node(tgen.worch.command_dir) + cmd_node = cmd_dir.make_node(tgen.worch.command_cmd) + cmd_target = \ + map(cmd_dir.make_node, tgen.to_list(tgen.worch.command_target)) + cmd_rule = '{command_cmd_prefix}{command_cmd} {command_cmd_options} {command_cmd_postfix}' + tgen.step('command', + rule = tgen.worch.format(cmd_rule),","def feature_command(tgen): + cmd_dir = tgen.make_node(tgen.worch.command_dir) + cmd_node = cmd_dir.make_node(tgen.worch.command_cmd) + cmd_target = \ + map(tgen.make_node, tgen.to_list(tgen.worch.command_target)) + cmd_rule = '{command_cmd_prefix}{command_cmd} {command_cmd_options} {command_cmd_postfix}' + tgen.step('command', + rule = tgen.worch.format(cmd_rule)," +725,https://:@github.com/slipguru/icing.git,a292074640464c3c407850db151595153d28cf0f,"@@ -109,7 +109,7 @@ def sim_function(ig1, ig2, method='jaccard', model='ham', + correction = correction_function(max(ig1.mut, ig2.mut)) + # ss = 1 - ((1 - ss) * max(correction, 0)) + # ss = 1 - ((1 - ss) * correction) +- ss *= correction ++ ss += correction + # return min(max(ss, 0), 1) + return max(ss, 0) + +",icing/core/cloning.py,"ReplaceText(target='+=' @(112,11)->(112,13))","def sim_function(ig1, ig2, method='jaccard', model='ham', + correction = correction_function(max(ig1.mut, ig2.mut)) + # ss = 1 - ((1 - ss) * max(correction, 0)) + # ss = 1 - ((1 - ss) * correction) + ss *= correction + # return min(max(ss, 0), 1) + return max(ss, 0) + ","def sim_function(ig1, ig2, method='jaccard', model='ham', + correction = correction_function(max(ig1.mut, ig2.mut)) + # ss = 1 - ((1 - ss) * max(correction, 0)) + # ss = 1 - ((1 - ss) * correction) + ss += correction + # return min(max(ss, 0), 1) + return max(ss, 0) + " +726,https://:@github.com/slipguru/icing.git,7179403bf32d1f649ef7ea63a060ecd4ffb5a9e6,"@@ -109,7 +109,7 @@ def sim_function(ig1, ig2, method='jaccard', model='ham', + correction = correction_function(max(ig1.mut, ig2.mut)) + # ss = 1 - ((1 - ss) * max(correction, 0)) + # ss = 1 - ((1 - ss) * correction) +- ss += (1. - correction) ++ ss *= (1. - correction) + # return min(max(ss, 0), 1) + return max(ss, 0) + +",icing/core/cloning.py,"ReplaceText(target='*=' @(112,11)->(112,13))","def sim_function(ig1, ig2, method='jaccard', model='ham', + correction = correction_function(max(ig1.mut, ig2.mut)) + # ss = 1 - ((1 - ss) * max(correction, 0)) + # ss = 1 - ((1 - ss) * correction) + ss += (1. - correction) + # return min(max(ss, 0), 1) + return max(ss, 0) + ","def sim_function(ig1, ig2, method='jaccard', model='ham', + correction = correction_function(max(ig1.mut, ig2.mut)) + # ss = 1 - ((1 - ss) * max(correction, 0)) + # ss = 1 - ((1 - ss) * correction) + ss *= (1. - correction) + # return min(max(ss, 0), 1) + return max(ss, 0) + " +727,https://:@github.com/jojoduquartier/dsdbmanager.git,d074b1099d1bb9b729760d42e36aaae1944c64c7,"@@ -246,7 +246,7 @@ class DbMiddleware(object): + def __init__(self, engine, connect_only, schema): + self.engine = engine + +- if connect_only: ++ if not connect_only: + inspection = reflection.Inspector.from_engine(self.engine) + views = inspection.get_view_names(schema=schema) + tables = inspection.get_table_names(schema=schema) +",dsdbmanager/dbobject.py,"ReplaceText(target='not ' @(249,11)->(249,11))","class DbMiddleware(object): + def __init__(self, engine, connect_only, schema): + self.engine = engine + + if connect_only: + inspection = reflection.Inspector.from_engine(self.engine) + views = inspection.get_view_names(schema=schema) + tables = inspection.get_table_names(schema=schema)","class DbMiddleware(object): + def __init__(self, engine, connect_only, schema): + self.engine = engine + + if not connect_only: + inspection = reflection.Inspector.from_engine(self.engine) + views = inspection.get_view_names(schema=schema) + tables = inspection.get_table_names(schema=schema)" +728,https://:@gitlab.com/HartkopfF/Purple.git,d8b25ebbe423fb005169913d63410713eb5a49ec,"@@ -414,7 +414,7 @@ def print_result(peps, print_peps,threshold): + # prints flagged peptides in console, if print_peps == True + # peptides are flagged, if they are greater than the average of all positive scores + scores = list(peps.values()) +- scores_in_tens = [int(round(i, -1)) if i >= threshold else -1 for i in scores] # only round positiv scores ++ scores_in_tens = [int(round(i, -1)) if i <= threshold else -1 for i in scores] # only round positiv scores + freq_scores = {x: scores_in_tens.count(x) for x in scores_in_tens} # Dictionary Comprehension + + if print_peps == 1: +",src/Purple_methods.py,"ReplaceText(target='<=' @(417,45)->(417,47))","def print_result(peps, print_peps,threshold): + # prints flagged peptides in console, if print_peps == True + # peptides are flagged, if they are greater than the average of all positive scores + scores = list(peps.values()) + scores_in_tens = [int(round(i, -1)) if i >= threshold else -1 for i in scores] # only round positiv scores + freq_scores = {x: scores_in_tens.count(x) for x in scores_in_tens} # Dictionary Comprehension + + if print_peps == 1:","def print_result(peps, print_peps,threshold): + # prints flagged peptides in console, if print_peps == True + # peptides are flagged, if they are greater than the average of all positive scores + scores = list(peps.values()) + scores_in_tens = [int(round(i, -1)) if i <= threshold else -1 for i in scores] # only round positiv scores + freq_scores = {x: scores_in_tens.count(x) for x in scores_in_tens} # Dictionary Comprehension + + if print_peps == 1:" +729,https://:@github.com/bjoernricks/python-quilt.git,2a4e97b554669b95bb1d22f220ac2d7ba6df9012,"@@ -46,7 +46,7 @@ class Import(Command): + """""" Import patch into the patch queue + The patch is inserted after the current top applied patch + """""" +- if not new_name: ++ if new_name: + dir_name = os.path.dirname(new_name) + name = os.path.basename(new_name) + dest_dir = self.quilt_patches + Directory(dir_name) +",quilt/patchimport.py,"ReplaceText(target='' @(49,11)->(49,15))","class Import(Command): + """""" Import patch into the patch queue + The patch is inserted after the current top applied patch + """""" + if not new_name: + dir_name = os.path.dirname(new_name) + name = os.path.basename(new_name) + dest_dir = self.quilt_patches + Directory(dir_name)","class Import(Command): + """""" Import patch into the patch queue + The patch is inserted after the current top applied patch + """""" + if new_name: + dir_name = os.path.dirname(new_name) + name = os.path.basename(new_name) + dest_dir = self.quilt_patches + Directory(dir_name)" +730,https://:@github.com/bjoernricks/python-quilt.git,1c2a80d50b73cf182574c0e1f0d7aa5b6ab91631,"@@ -93,7 +93,7 @@ class Push(Command): + applied = self.db.applied_patches() + for patch in applied: + if patch in patches: +- patches.remove(applied) ++ patches.remove(patch) + + if not patches: + raise AllPatchesApplied(self.series, self.db.top_patch()) +",quilt/push.py,"ReplaceText(target='patch' @(96,31)->(96,38))","class Push(Command): + applied = self.db.applied_patches() + for patch in applied: + if patch in patches: + patches.remove(applied) + + if not patches: + raise AllPatchesApplied(self.series, self.db.top_patch())","class Push(Command): + applied = self.db.applied_patches() + for patch in applied: + if patch in patches: + patches.remove(patch) + + if not patches: + raise AllPatchesApplied(self.series, self.db.top_patch())" +731,https://:@github.com/HypothesisWorks/hypothesis-python.git,7d201f06333b185a25a5d77df7a01d08790655cb,"@@ -69,7 +69,7 @@ def test_a_verifier_saves_any_failing_examples_in_its_database(): + def test_a_verifier_retrieves_previous_failing_examples_from_the_database(): + database = ExampleDatabase() + verifier = Verifier(settings=hs.Settings(database=database)) +- verifier.falsify(lambda x: x != 11, int) ++ verifier.falsify(lambda x: x < 11, int) + called = [] + + def save_calls(t): +",tests/test_database.py,"ReplaceText(target='<' @(72,33)->(72,35))","def test_a_verifier_saves_any_failing_examples_in_its_database(): + def test_a_verifier_retrieves_previous_failing_examples_from_the_database(): + database = ExampleDatabase() + verifier = Verifier(settings=hs.Settings(database=database)) + verifier.falsify(lambda x: x != 11, int) + called = [] + + def save_calls(t):","def test_a_verifier_saves_any_failing_examples_in_its_database(): + def test_a_verifier_retrieves_previous_failing_examples_from_the_database(): + database = ExampleDatabase() + verifier = Verifier(settings=hs.Settings(database=database)) + verifier.falsify(lambda x: x < 11, int) + called = [] + + def save_calls(t):" +732,https://:@github.com/HypothesisWorks/hypothesis-python.git,b5a59b2e474f1f2bcff898aeeba9cc3ca2e5d186,"@@ -89,7 +89,7 @@ class TestRunner(object): + raise RunIsComplete() + self.examples_considered += 1 + if ( +- buffer[:self.last_data.index] == ++ buffer[:self.last_data.index] >= + self.last_data.buffer[:self.last_data.index] + ): + return False +",src/hypothesis/internal/conjecture/engine.py,"ReplaceText(target='>=' @(92,42)->(92,44))","class TestRunner(object): + raise RunIsComplete() + self.examples_considered += 1 + if ( + buffer[:self.last_data.index] == + self.last_data.buffer[:self.last_data.index] + ): + return False","class TestRunner(object): + raise RunIsComplete() + self.examples_considered += 1 + if ( + buffer[:self.last_data.index] >= + self.last_data.buffer[:self.last_data.index] + ): + return False" +733,https://:@github.com/HypothesisWorks/hypothesis-python.git,5f990a2d351ad02ac698375428c54c86b907f505,"@@ -686,7 +686,7 @@ def characters(whitelist_categories=None, blacklist_categories=None, + if ( + whitelist_characters is not None and + blacklist_characters is not None and +- set(whitelist_characters).intersection(set(whitelist_characters)) ++ set(blacklist_characters).intersection(set(whitelist_characters)) + ): + raise InvalidArgument( + 'Cannot have characters in both whitelist_characters=%r, ' +",src/hypothesis/strategies.py,"ReplaceText(target='blacklist_characters' @(689,12)->(689,32))","def characters(whitelist_categories=None, blacklist_categories=None, + if ( + whitelist_characters is not None and + blacklist_characters is not None and + set(whitelist_characters).intersection(set(whitelist_characters)) + ): + raise InvalidArgument( + 'Cannot have characters in both whitelist_characters=%r, '","def characters(whitelist_categories=None, blacklist_categories=None, + if ( + whitelist_characters is not None and + blacklist_characters is not None and + set(blacklist_characters).intersection(set(whitelist_characters)) + ): + raise InvalidArgument( + 'Cannot have characters in both whitelist_characters=%r, '" +734,https://:@github.com/HypothesisWorks/hypothesis-python.git,5bd4086b1be92933cef2bb61f98770df1114ed7a,"@@ -691,7 +691,7 @@ def characters(whitelist_categories=None, blacklist_categories=None, + raise InvalidArgument( + 'Cannot have characters in both whitelist_characters=%r, ' + 'and blacklist_characters=%r' % ( +- whitelist_characters, blacklist_categories, ++ whitelist_characters, blacklist_characters, + ) + ) + +",src/hypothesis/strategies.py,"ReplaceText(target='blacklist_characters' @(694,38)->(694,58))","def characters(whitelist_categories=None, blacklist_categories=None, + raise InvalidArgument( + 'Cannot have characters in both whitelist_characters=%r, ' + 'and blacklist_characters=%r' % ( + whitelist_characters, blacklist_categories, + ) + ) + ","def characters(whitelist_categories=None, blacklist_categories=None, + raise InvalidArgument( + 'Cannot have characters in both whitelist_characters=%r, ' + 'and blacklist_characters=%r' % ( + whitelist_characters, blacklist_characters, + ) + ) + " +735,https://:@github.com/HypothesisWorks/hypothesis-python.git,a10d8cf98473dbdaedf1d317c8ad2d51b38699fe,"@@ -30,7 +30,7 @@ if __name__ == '__main__': + + if ( + os.environ['CIRCLE_BRANCH'] != 'master' and +- os.environ['CI_PULL_REQUEST'] != '' ++ os.environ['CI_PULL_REQUEST'] == '' + ): + print('We only run CI builds on the master branch or in pull requests') + sys.exit(0) +",scripts/run_circle.py,"ReplaceText(target='==' @(33,38)->(33,40))","if __name__ == '__main__': + + if ( + os.environ['CIRCLE_BRANCH'] != 'master' and + os.environ['CI_PULL_REQUEST'] != '' + ): + print('We only run CI builds on the master branch or in pull requests') + sys.exit(0)","if __name__ == '__main__': + + if ( + os.environ['CIRCLE_BRANCH'] != 'master' and + os.environ['CI_PULL_REQUEST'] == '' + ): + print('We only run CI builds on the master branch or in pull requests') + sys.exit(0)" +736,https://:@github.com/HypothesisWorks/hypothesis-python.git,8f9b8211e5c7b3d6e791bc9203e12b494eba9d64,"@@ -1119,7 +1119,7 @@ def find(specifier, condition, settings=None, random=None, database_key=None): + if success: + successful_examples[0] += 1 + +- if settings.verbosity == Verbosity.verbose: ++ if settings.verbosity >= Verbosity.verbose: + if not successful_examples[0]: + report( + u'Tried non-satisfying example %s' % (nicerepr(result),)) +",hypothesis-python/src/hypothesis/core.py,"ReplaceText(target='>=' @(1122,30)->(1122,32))","def find(specifier, condition, settings=None, random=None, database_key=None): + if success: + successful_examples[0] += 1 + + if settings.verbosity == Verbosity.verbose: + if not successful_examples[0]: + report( + u'Tried non-satisfying example %s' % (nicerepr(result),))","def find(specifier, condition, settings=None, random=None, database_key=None): + if success: + successful_examples[0] += 1 + + if settings.verbosity >= Verbosity.verbose: + if not successful_examples[0]: + report( + u'Tried non-satisfying example %s' % (nicerepr(result),))" +737,https://:@github.com/HypothesisWorks/hypothesis-python.git,8a912d3d94dbd45ada80476bfbf11eea334ec48d,"@@ -119,7 +119,7 @@ def assert_can_release(): + + + def has_travis_secrets(): +- return os.environ.get('TRAVIS_SECURE_ENV_VARS', None) != 'true' ++ return os.environ.get('TRAVIS_SECURE_ENV_VARS', None) == 'true' + + + def build_jobs(): +",tooling/src/hypothesistooling/__init__.py,"ReplaceText(target='==' @(122,58)->(122,60))","def assert_can_release(): + + + def has_travis_secrets(): + return os.environ.get('TRAVIS_SECURE_ENV_VARS', None) != 'true' + + + def build_jobs():","def assert_can_release(): + + + def has_travis_secrets(): + return os.environ.get('TRAVIS_SECURE_ENV_VARS', None) == 'true' + + + def build_jobs():" +738,https://:@github.com/HypothesisWorks/hypothesis-python.git,3dba57307b412696b30f86eb7d0fdb189421b5c7,"@@ -2209,7 +2209,7 @@ class Shrinker(object): + u, v = self.blocks[i] + b = int_from_bytes(self.shrink_target.buffer[u:v]) + lowered = b - offset +- if lowered <= 0: ++ if lowered < 0: + continue + attempt = bytearray(self.shrink_target.buffer) + attempt[u:v] = int_to_bytes(lowered, v - u) +",hypothesis-python/src/hypothesis/internal/conjecture/engine.py,"ReplaceText(target='<' @(2212,27)->(2212,29))","class Shrinker(object): + u, v = self.blocks[i] + b = int_from_bytes(self.shrink_target.buffer[u:v]) + lowered = b - offset + if lowered <= 0: + continue + attempt = bytearray(self.shrink_target.buffer) + attempt[u:v] = int_to_bytes(lowered, v - u)","class Shrinker(object): + u, v = self.blocks[i] + b = int_from_bytes(self.shrink_target.buffer[u:v]) + lowered = b - offset + if lowered < 0: + continue + attempt = bytearray(self.shrink_target.buffer) + attempt[u:v] = int_to_bytes(lowered, v - u)" +739,https://:@github.com/HypothesisWorks/hypothesis-python.git,a55eeda06ec2650b446a3ef0885a4f765d0c5513,"@@ -317,7 +317,7 @@ class settings( + bits = [] + for name, setting in all_settings.items(): + value = getattr(self, name) +- if value != setting.default or not setting.hide_repr: ++ if value != setting.default and not setting.hide_repr: + bits.append('%s=%r' % (name, value)) + return 'settings(%s)' % ', '.join(sorted(bits)) + +",hypothesis-python/src/hypothesis/_settings.py,"ReplaceText(target='and' @(320,40)->(320,42))","class settings( + bits = [] + for name, setting in all_settings.items(): + value = getattr(self, name) + if value != setting.default or not setting.hide_repr: + bits.append('%s=%r' % (name, value)) + return 'settings(%s)' % ', '.join(sorted(bits)) + ","class settings( + bits = [] + for name, setting in all_settings.items(): + value = getattr(self, name) + if value != setting.default and not setting.hide_repr: + bits.append('%s=%r' % (name, value)) + return 'settings(%s)' % ', '.join(sorted(bits)) + " +740,https://:@github.com/HypothesisWorks/hypothesis-python.git,feaa70b9ee7e4659bb31bcbd0bd6077c179516bf,"@@ -439,7 +439,7 @@ class StepCounter(RuleBasedStateMachine): + self.step_count += 1 + + def teardown(self): +- assert self.step_count == settings_step_count ++ assert self.step_count <= settings_step_count + + + test_settings_decorator_applies_to_rule_based_state_machine_class = \ +",hypothesis-python/tests/cover/test_settings.py,"ReplaceText(target='<=' @(442,31)->(442,33))","class StepCounter(RuleBasedStateMachine): + self.step_count += 1 + + def teardown(self): + assert self.step_count == settings_step_count + + + test_settings_decorator_applies_to_rule_based_state_machine_class = \","class StepCounter(RuleBasedStateMachine): + self.step_count += 1 + + def teardown(self): + assert self.step_count <= settings_step_count + + + test_settings_decorator_applies_to_rule_based_state_machine_class = \" +741,https://:@github.com/HypothesisWorks/hypothesis-python.git,012cdca96f6f3887bc5a93f5a1efaf4f58cde27d,"@@ -656,7 +656,7 @@ def sampled_from(elements): + return sets(sampled_from(values), min_size=1).map( + lambda s: reduce(operator.or_, s) + ) +- return SampledFromStrategy(values) ++ return SampledFromStrategy(elements) + + + @cacheable +",hypothesis-python/src/hypothesis/strategies/_internal/core.py,"ReplaceText(target='elements' @(659,31)->(659,37))","def sampled_from(elements): + return sets(sampled_from(values), min_size=1).map( + lambda s: reduce(operator.or_, s) + ) + return SampledFromStrategy(values) + + + @cacheable","def sampled_from(elements): + return sets(sampled_from(values), min_size=1).map( + lambda s: reduce(operator.or_, s) + ) + return SampledFromStrategy(elements) + + + @cacheable" +742,https://:@github.com/HypothesisWorks/hypothesis-python.git,a9c5902f94250156d80baff42da96e9d08778d26,"@@ -1842,7 +1842,7 @@ def complex_numbers( + # Order of conditions carefully tuned so that for a given pair of + # magnitude arguments, we always either draw or do not draw the bool + # (crucial for good shrinking behaviour) but only invert when needed. +- if min_magnitude != 0 and draw(booleans()) and math.fabs(zi) <= min_magnitude: ++ if min_magnitude > 0 and draw(booleans()) and math.fabs(zi) <= min_magnitude: + zr = -zr + return complex(zr, zi) + +",hypothesis-python/src/hypothesis/strategies/_internal/core.py,"ReplaceText(target='>' @(1845,25)->(1845,27))","def complex_numbers( + # Order of conditions carefully tuned so that for a given pair of + # magnitude arguments, we always either draw or do not draw the bool + # (crucial for good shrinking behaviour) but only invert when needed. + if min_magnitude != 0 and draw(booleans()) and math.fabs(zi) <= min_magnitude: + zr = -zr + return complex(zr, zi) + ","def complex_numbers( + # Order of conditions carefully tuned so that for a given pair of + # magnitude arguments, we always either draw or do not draw the bool + # (crucial for good shrinking behaviour) but only invert when needed. + if min_magnitude > 0 and draw(booleans()) and math.fabs(zi) <= min_magnitude: + zr = -zr + return complex(zr, zi) + " +743,https://:@github.com/pyfa-org/eos.git,4a87a594d189c71e916538d04026dc470cc12313,"@@ -418,7 +418,7 @@ class InfoBuilder: + # Negate condition for else clause processing + # We do not need to recombine it with conditions passed to our method, + # as condition being reverted is part of combined tree +- self.__invertCondition(currentConditions) ++ self.__invertCondition(newConditions) + self.__generic(elseClause, deepcopy(currentConditions)) + + def __makeConditionRouter(self, element): +",data/effect/builder/builder.py,"ReplaceText(target='newConditions' @(421,31)->(421,48))","class InfoBuilder: + # Negate condition for else clause processing + # We do not need to recombine it with conditions passed to our method, + # as condition being reverted is part of combined tree + self.__invertCondition(currentConditions) + self.__generic(elseClause, deepcopy(currentConditions)) + + def __makeConditionRouter(self, element):","class InfoBuilder: + # Negate condition for else clause processing + # We do not need to recombine it with conditions passed to our method, + # as condition being reverted is part of combined tree + self.__invertCondition(newConditions) + self.__generic(elseClause, deepcopy(currentConditions)) + + def __makeConditionRouter(self, element):" +744,https://:@github.com/pyfa-org/eos.git,23c14ff52c9ab1a52ca35887ca043680046dcaf7,"@@ -38,7 +38,7 @@ class TestSkillUniqueness(RestrictionTestCase): + restrictionError1 = fit.getRestrictionError(skill1, Restriction.skillUniqueness) + self.assertIsNotNone(restrictionError1) + self.assertEqual(restrictionError1.skill, 56) +- restrictionError2 = fit.getRestrictionError(skill1, Restriction.skillUniqueness) ++ restrictionError2 = fit.getRestrictionError(skill2, Restriction.skillUniqueness) + self.assertIsNotNone(restrictionError2) + self.assertEqual(restrictionError2.skill, 56) + fit.items.remove(skill1) +",tests/restrictionTracker/restrictions/testSkillUniqueness.py,"ReplaceText(target='skill2' @(41,52)->(41,58))","class TestSkillUniqueness(RestrictionTestCase): + restrictionError1 = fit.getRestrictionError(skill1, Restriction.skillUniqueness) + self.assertIsNotNone(restrictionError1) + self.assertEqual(restrictionError1.skill, 56) + restrictionError2 = fit.getRestrictionError(skill1, Restriction.skillUniqueness) + self.assertIsNotNone(restrictionError2) + self.assertEqual(restrictionError2.skill, 56) + fit.items.remove(skill1)","class TestSkillUniqueness(RestrictionTestCase): + restrictionError1 = fit.getRestrictionError(skill1, Restriction.skillUniqueness) + self.assertIsNotNone(restrictionError1) + self.assertEqual(restrictionError1.skill, 56) + restrictionError2 = fit.getRestrictionError(skill2, Restriction.skillUniqueness) + self.assertIsNotNone(restrictionError2) + self.assertEqual(restrictionError2.skill, 56) + fit.items.remove(skill1)" +745,https://:@github.com/pyfa-org/eos.git,ec16898d0f6e700159a14af551196f3d7e31aa43,"@@ -52,7 +52,7 @@ class SlotIndexRegister(RestrictionRegister): + def registerHolder(self, holder): + # Skip items which don't have index specifier + slotIndex = holder.item.attributes.get(self.__slotIndexAttr) +- if slotIndex is not None: ++ if slotIndex is None: + return + self.__slottedHolders.addData(slotIndex, holder) + +",fit/restrictionTracker/restriction/slotIndex.py,"ReplaceText(target=' is ' @(55,20)->(55,28))","class SlotIndexRegister(RestrictionRegister): + def registerHolder(self, holder): + # Skip items which don't have index specifier + slotIndex = holder.item.attributes.get(self.__slotIndexAttr) + if slotIndex is not None: + return + self.__slottedHolders.addData(slotIndex, holder) + ","class SlotIndexRegister(RestrictionRegister): + def registerHolder(self, holder): + # Skip items which don't have index specifier + slotIndex = holder.item.attributes.get(self.__slotIndexAttr) + if slotIndex is None: + return + self.__slottedHolders.addData(slotIndex, holder) + " +746,https://:@github.com/pyfa-org/eos.git,e8ea4b04ff260c186d55ece03df22dbd6aa509e9,"@@ -61,7 +61,7 @@ class ResourceRegister(RestrictionRegister): + # Can be None, so fall back to 0 in this case + output = stats.output or 0 + # If we're not out of resource, do nothing +- if totalUse > output: ++ if totalUse <= output: + return + taintedHolders = {} + for holder in self.__resourceUsers: +",fit/restrictionTracker/restriction/resource.py,"ReplaceText(target='<=' @(64,20)->(64,21))","class ResourceRegister(RestrictionRegister): + # Can be None, so fall back to 0 in this case + output = stats.output or 0 + # If we're not out of resource, do nothing + if totalUse > output: + return + taintedHolders = {} + for holder in self.__resourceUsers:","class ResourceRegister(RestrictionRegister): + # Can be None, so fall back to 0 in this case + output = stats.output or 0 + # If we're not out of resource, do nothing + if totalUse <= output: + return + taintedHolders = {} + for holder in self.__resourceUsers:" +747,https://:@github.com/pyfa-org/eos.git,700a4414cab25efe4e306e64c9cee28250f7363a,"@@ -151,7 +151,7 @@ class MsgHelper: + # Unapply effects from targets + tgt_getter = getattr(item, '_get_effects_tgts', None) + if tgt_getter: +- effects_tgts = tgt_getter(start_ids) ++ effects_tgts = tgt_getter(stop_ids) + for effect_id, tgt_items in effects_tgts.items(): + msgs.append(EffectUnapplied(item, effect_id, tgt_items)) + # Stop effects +",eos/pubsub/message/helper.py,"ReplaceText(target='stop_ids' @(154,42)->(154,51))","class MsgHelper: + # Unapply effects from targets + tgt_getter = getattr(item, '_get_effects_tgts', None) + if tgt_getter: + effects_tgts = tgt_getter(start_ids) + for effect_id, tgt_items in effects_tgts.items(): + msgs.append(EffectUnapplied(item, effect_id, tgt_items)) + # Stop effects","class MsgHelper: + # Unapply effects from targets + tgt_getter = getattr(item, '_get_effects_tgts', None) + if tgt_getter: + effects_tgts = tgt_getter(stop_ids) + for effect_id, tgt_items in effects_tgts.items(): + msgs.append(EffectUnapplied(item, effect_id, tgt_items)) + # Stop effects" +748,https://:@github.com/Hasenpfote/fpq.git,8220505c7830967477a5502c061d9efd91d66ae8,"@@ -58,7 +58,7 @@ def encode_fp_to_snorm(x, *, dtype=np.uint8, nbits=None): + if nbits is None: + nbits = max_nbits + assert (0 < nbits <= max_nbits), '`nbits` value is out of range.' +- mask = np.invert(dtype(np.iinfo(nbits).max) << dtype(nbits)) ++ mask = np.invert(dtype(np.iinfo(dtype).max) << dtype(nbits)) + return dtype(np.around(x * x.dtype.type((1 << (nbits-1)) - 1))) & mask + + def decode_snorm_to_fp(x, *, dtype=np.float32, nbits=None): +",fpq/d3d.py,"ReplaceText(target='dtype' @(61,36)->(61,41))","def encode_fp_to_snorm(x, *, dtype=np.uint8, nbits=None): + if nbits is None: + nbits = max_nbits + assert (0 < nbits <= max_nbits), '`nbits` value is out of range.' + mask = np.invert(dtype(np.iinfo(nbits).max) << dtype(nbits)) + return dtype(np.around(x * x.dtype.type((1 << (nbits-1)) - 1))) & mask + + def decode_snorm_to_fp(x, *, dtype=np.float32, nbits=None):","def encode_fp_to_snorm(x, *, dtype=np.uint8, nbits=None): + if nbits is None: + nbits = max_nbits + assert (0 < nbits <= max_nbits), '`nbits` value is out of range.' + mask = np.invert(dtype(np.iinfo(dtype).max) << dtype(nbits)) + return dtype(np.around(x * x.dtype.type((1 << (nbits-1)) - 1))) & mask + + def decode_snorm_to_fp(x, *, dtype=np.float32, nbits=None):" +749,https://:@github.com/theodo/flask-restful.git,4dfe49f1de3dfd9598b4ae92b9e6b6644fa999f7,"@@ -338,7 +338,7 @@ class APITestCase(unittest.TestCase): + def record(sender, exception): + recorded.append(exception) + +- got_request_exception.connect(record, api) ++ got_request_exception.connect(record, app) + try: + with app.test_request_context(""/foo""): + api.handle_error(exception) +",tests/test_api.py,"ReplaceText(target='app' @(341,46)->(341,49))","class APITestCase(unittest.TestCase): + def record(sender, exception): + recorded.append(exception) + + got_request_exception.connect(record, api) + try: + with app.test_request_context(""/foo""): + api.handle_error(exception)","class APITestCase(unittest.TestCase): + def record(sender, exception): + recorded.append(exception) + + got_request_exception.connect(record, app) + try: + with app.test_request_context(""/foo""): + api.handle_error(exception)" +750,https://:@github.com/askholme/django_minifiedstorage.git,0f7821618021d7fb4497a0ddd4312fbbc4e41262,"@@ -45,7 +45,7 @@ class MinifiedManifestStaticFilesStorage(ManifestStaticFilesStorage): + # save gziped file as fell, we overwrite the content_file variable to save a tiny bit memory + try: + content = zlib_compress(content) +- super(MinifiedManifestStaticFilesStorage, self)._save(""%s.gz"" % hashed_name,ContentFile(content)) ++ super(MinifiedManifestStaticFilesStorage, self)._save(""%s.gz"" % saved_name,ContentFile(content)) + except Exception as e: + raise MinifiedStorageException(""Could not gzip file %s, error: %s"" % (hashed_name,e,)) + return saved_name +\ No newline at end of file +",minifiedstorage/storages.py,"ReplaceText(target='saved_name' @(48,80)->(48,91))","class MinifiedManifestStaticFilesStorage(ManifestStaticFilesStorage): + # save gziped file as fell, we overwrite the content_file variable to save a tiny bit memory + try: + content = zlib_compress(content) + super(MinifiedManifestStaticFilesStorage, self)._save(""%s.gz"" % hashed_name,ContentFile(content)) + except Exception as e: + raise MinifiedStorageException(""Could not gzip file %s, error: %s"" % (hashed_name,e,)) + return saved_name +\ No newline at end of file","class MinifiedManifestStaticFilesStorage(ManifestStaticFilesStorage): + # save gziped file as fell, we overwrite the content_file variable to save a tiny bit memory + try: + content = zlib_compress(content) + super(MinifiedManifestStaticFilesStorage, self)._save(""%s.gz"" % saved_name,ContentFile(content)) + except Exception as e: + raise MinifiedStorageException(""Could not gzip file %s, error: %s"" % (hashed_name,e,)) + return saved_name +\ No newline at end of file" +751,https://:@github.com/SiLab-Bonn/pymosa.git,07741f8afef86a85bf61c13aa8733f6f211195ae,"@@ -133,7 +133,7 @@ class TluTuning(m26): + + # Determine best delay setting (center of working delay settings) + good_indices = np.where(np.logical_and(data_array['error_rate'][:-1] == 0, np.diff(data_array['error_rate']) == 0))[0] +- best_index = good_indices[good_indices.shape[0] / 2] ++ best_index = good_indices[good_indices.shape[0] // 2] + best_delay_setting = data_array['TRIGGER_DATA_DELAY'][best_index] + logging.info('The best delay setting for this setup is %d', best_delay_setting) + +",pymosa/tune_tlu.py,"ReplaceText(target='//' @(136,68)->(136,69))","class TluTuning(m26): + + # Determine best delay setting (center of working delay settings) + good_indices = np.where(np.logical_and(data_array['error_rate'][:-1] == 0, np.diff(data_array['error_rate']) == 0))[0] + best_index = good_indices[good_indices.shape[0] / 2] + best_delay_setting = data_array['TRIGGER_DATA_DELAY'][best_index] + logging.info('The best delay setting for this setup is %d', best_delay_setting) + ","class TluTuning(m26): + + # Determine best delay setting (center of working delay settings) + good_indices = np.where(np.logical_and(data_array['error_rate'][:-1] == 0, np.diff(data_array['error_rate']) == 0))[0] + best_index = good_indices[good_indices.shape[0] // 2] + best_delay_setting = data_array['TRIGGER_DATA_DELAY'][best_index] + logging.info('The best delay setting for this setup is %d', best_delay_setting) + " +752,https://:@github.com/dripton/Slugathon.git,641fc1e43403827b046dc1fe69cb6da162d9a83c,"@@ -70,7 +70,7 @@ class Marker(object): + label = str(self.height) + text_width, text_height = draw.textsize(label, font=font) + x = 0.65 * leng - 0.5 * text_width +- y = 0.55 * leng - 0.5 * text_width ++ y = 0.55 * leng - 0.5 * text_height + draw.rectangle(((x + 0.1 * text_width, y + 0.1 * text_height), + (x + 0.9 * text_width, y + 0.9 * text_height)), fill=white) + draw.text((x, y), label, fill=black, font=font) +",slugathon/Marker.py,"ReplaceText(target='text_height' @(73,32)->(73,42))","class Marker(object): + label = str(self.height) + text_width, text_height = draw.textsize(label, font=font) + x = 0.65 * leng - 0.5 * text_width + y = 0.55 * leng - 0.5 * text_width + draw.rectangle(((x + 0.1 * text_width, y + 0.1 * text_height), + (x + 0.9 * text_width, y + 0.9 * text_height)), fill=white) + draw.text((x, y), label, fill=black, font=font)","class Marker(object): + label = str(self.height) + text_width, text_height = draw.textsize(label, font=font) + x = 0.65 * leng - 0.5 * text_width + y = 0.55 * leng - 0.5 * text_height + draw.rectangle(((x + 0.1 * text_width, y + 0.1 * text_height), + (x + 0.9 * text_width, y + 0.9 * text_height)), fill=white) + draw.text((x, y), label, fill=black, font=font)" +753,https://:@github.com/dripton/Slugathon.git,d6957007cf4968b383c258c9894eb638fedb290a,"@@ -265,7 +265,7 @@ class Creature(object): + skill1 -= 1 + elif border == ""Wall"": + skill1 += 1 +- elif border2 == ""Slope"" and not self.is_native(border): ++ elif border2 == ""Slope"" and not self.is_native(border2): + skill1 -= 1 + elif border2 == ""Wall"": + skill1 -= 1 +",slugathon/Creature.py,"ReplaceText(target='border2' @(268,59)->(268,65))","class Creature(object): + skill1 -= 1 + elif border == ""Wall"": + skill1 += 1 + elif border2 == ""Slope"" and not self.is_native(border): + skill1 -= 1 + elif border2 == ""Wall"": + skill1 -= 1","class Creature(object): + skill1 -= 1 + elif border == ""Wall"": + skill1 += 1 + elif border2 == ""Slope"" and not self.is_native(border2): + skill1 -= 1 + elif border2 == ""Wall"": + skill1 -= 1" +754,https://:@github.com/dripton/Slugathon.git,f2bfd2d2c6429dfaa37c5844a52e13124690df13,"@@ -238,7 +238,7 @@ class Creature(object): + elif border == ""Dune"" and self.is_native(border): + dice += 2 + border2 = hex1.opposite_border(hexside) +- if border2 == ""Dune"" and not self.is_native(border): ++ if border2 == ""Dune"" and not self.is_native(border2): + dice -= 1 + elif target in self.rangestrike_targets: + dice = int(self.power / 2) +",slugathon/Creature.py,"ReplaceText(target='border2' @(241,56)->(241,62))","class Creature(object): + elif border == ""Dune"" and self.is_native(border): + dice += 2 + border2 = hex1.opposite_border(hexside) + if border2 == ""Dune"" and not self.is_native(border): + dice -= 1 + elif target in self.rangestrike_targets: + dice = int(self.power / 2)","class Creature(object): + elif border == ""Dune"" and self.is_native(border): + dice += 2 + border2 = hex1.opposite_border(hexside) + if border2 == ""Dune"" and not self.is_native(border2): + dice -= 1 + elif target in self.rangestrike_targets: + dice = int(self.power / 2)" +755,https://:@github.com/dripton/Slugathon.git,b971ac13adfde83f63ff75be45cc6851d769b86e,"@@ -267,7 +267,7 @@ class CleverBot(DimBot.DimBot): + max_mean_hits = max(mean_hits, max_mean_hits) + + # Don't encourage titans to charge early. +- if creature.name != ""Titan"" or game.battle_turn > 4: ++ if creature.name != ""Titan"" or game.battle_turn >= 4: + score += HIT_BONUS * max_mean_hits + score += KILL_BONUS * probable_kill + score -= DAMAGE_PENALTY * total_mean_damage_taken +",slugathon/ai/CleverBot.py,"ReplaceText(target='>=' @(270,60)->(270,61))","class CleverBot(DimBot.DimBot): + max_mean_hits = max(mean_hits, max_mean_hits) + + # Don't encourage titans to charge early. + if creature.name != ""Titan"" or game.battle_turn > 4: + score += HIT_BONUS * max_mean_hits + score += KILL_BONUS * probable_kill + score -= DAMAGE_PENALTY * total_mean_damage_taken","class CleverBot(DimBot.DimBot): + max_mean_hits = max(mean_hits, max_mean_hits) + + # Don't encourage titans to charge early. + if creature.name != ""Titan"" or game.battle_turn >= 4: + score += HIT_BONUS * max_mean_hits + score += KILL_BONUS * probable_kill + score -= DAMAGE_PENALTY * total_mean_damage_taken" +756,https://:@github.com/dripton/Slugathon.git,13e968722e4cf18f662d5405ee3bc895929300ec,"@@ -173,7 +173,7 @@ class GUIBattleHex(object): + if not os.path.exists(border_path): + sliceborder.slice_border_image(image_path, border_path, + hexsides) +- input_surface = cairo.ImageSurface.create_from_png(image_path) ++ input_surface = cairo.ImageSurface.create_from_png(border_path) + input_width = input_surface.get_width() + input_height = input_surface.get_height() + output_width = myboxsize[0] +",slugathon/gui/GUIBattleHex.py,"ReplaceText(target='border_path' @(176,67)->(176,77))","class GUIBattleHex(object): + if not os.path.exists(border_path): + sliceborder.slice_border_image(image_path, border_path, + hexsides) + input_surface = cairo.ImageSurface.create_from_png(image_path) + input_width = input_surface.get_width() + input_height = input_surface.get_height() + output_width = myboxsize[0]","class GUIBattleHex(object): + if not os.path.exists(border_path): + sliceborder.slice_border_image(image_path, border_path, + hexsides) + input_surface = cairo.ImageSurface.create_from_png(border_path) + input_width = input_surface.get_width() + input_height = input_surface.get_height() + output_width = myboxsize[0]" +757,https://:@bitbucket.org/fchampalimaud/pythonvideoannotator-models.git,cde08126d01f0e218cf5450cc39caa1bdeb689b6,"@@ -47,4 +47,4 @@ class Object2dIO(Object2dBase): + func = getattr(self, dataset_conf['factory-function']) + dataset = func() + dataset.name = name +- dataset.load(data, dataset_path) +\ No newline at end of file ++ dataset.load(dataset_conf, dataset_path) +\ No newline at end of file +",pythonvideoannotator_models/models/video/objects/object2d/object2d_io.py,"ReplaceText(target='dataset_conf' @(50,17)->(50,21))","class Object2dIO(Object2dBase): + func = getattr(self, dataset_conf['factory-function']) + dataset = func() + dataset.name = name + dataset.load(data, dataset_path) +\ No newline at end of file +\ No newline at end of file","class Object2dIO(Object2dBase): + func = getattr(self, dataset_conf['factory-function']) + dataset = func() + dataset.name = name +\ No newline at end of file + dataset.load(dataset_conf, dataset_path) +\ No newline at end of file" +758,https://:@bitbucket.org/fchampalimaud/pythonvideoannotator-models.git,b567c052b952ce719e2974564f8b6cefb1a1a753,"@@ -64,7 +64,7 @@ class PathBase(Dataset): + + def interpolate_range(self, begin, end, interpolation_mode=None): + positions = [[i, self.get_position(i)] for i in range(begin, end+1) if self.get_position(i) is not None] +- if len(positions)>2: ++ if len(positions)>=2: + positions = interpolate_positions(positions, begin, end, interpolation_mode) + for frame, pos in positions: self.set_position(frame, pos[0], pos[1]) + self._tmp_points= [] +",pythonvideoannotator_models/models/video/objects/object2d/datasets/path/path_base.py,"ReplaceText(target='>=' @(67,19)->(67,20))","class PathBase(Dataset): + + def interpolate_range(self, begin, end, interpolation_mode=None): + positions = [[i, self.get_position(i)] for i in range(begin, end+1) if self.get_position(i) is not None] + if len(positions)>2: + positions = interpolate_positions(positions, begin, end, interpolation_mode) + for frame, pos in positions: self.set_position(frame, pos[0], pos[1]) + self._tmp_points= []","class PathBase(Dataset): + + def interpolate_range(self, begin, end, interpolation_mode=None): + positions = [[i, self.get_position(i)] for i in range(begin, end+1) if self.get_position(i) is not None] + if len(positions)>=2: + positions = interpolate_positions(positions, begin, end, interpolation_mode) + for frame, pos in positions: self.set_position(frame, pos[0], pos[1]) + self._tmp_points= []" +759,https://:@bitbucket.org/fchampalimaud/pythonvideoannotator-models.git,190b462c6df6128fd6ffffb055d84a093a07d381,"@@ -57,7 +57,7 @@ class VideoIO(VideoBase): + dataset_conf = json.load(infile) + func = getattr(self, dataset_conf['factory-function']) + dataset = func() +- dataset.load(data, obj_dir) ++ dataset.load(dataset_conf, obj_dir) + dataset.name = name + + super(VideoIO, self).load(data, video_path) +\ No newline at end of file +",pythonvideoannotator_models/models/video/video_io.py,"ReplaceText(target='dataset_conf' @(60,17)->(60,21))","class VideoIO(VideoBase): + dataset_conf = json.load(infile) + func = getattr(self, dataset_conf['factory-function']) + dataset = func() + dataset.load(data, obj_dir) + dataset.name = name + + super(VideoIO, self).load(data, video_path) +\ No newline at end of file","class VideoIO(VideoBase): + dataset_conf = json.load(infile) + func = getattr(self, dataset_conf['factory-function']) + dataset = func() + dataset.load(dataset_conf, obj_dir) + dataset.name = name + + super(VideoIO, self).load(data, video_path) +\ No newline at end of file" +760,https://:@github.com/ch3pjw/junction.git,97f897e1fe41e165333f7a5248c951f686a13a89,"@@ -4,7 +4,7 @@ import blessings + class Terminal(blessings.Terminal): + def draw_block(self, block, x, y): + for y, line in enumerate(block, start=y): +- self.stream.write(self.move(x, y)) ++ self.stream.write(self.move(y, x)) + self.stream.write(line) + + _terminal = Terminal() +",junction/terminal.py,"ArgSwap(idxs=0<->1 @(7,30)->(7,39))","import blessings + class Terminal(blessings.Terminal): + def draw_block(self, block, x, y): + for y, line in enumerate(block, start=y): + self.stream.write(self.move(x, y)) + self.stream.write(line) + + _terminal = Terminal()","import blessings + class Terminal(blessings.Terminal): + def draw_block(self, block, x, y): + for y, line in enumerate(block, start=y): + self.stream.write(self.move(y, x)) + self.stream.write(line) + + _terminal = Terminal()" +761,https://:@gitlab.com/kamichal/renew.git,88823f6ffb58d69e34338f50893049c23739c42c,"@@ -90,7 +90,7 @@ class ArgsInspect(object): + msg = ""Variadic arg has to be stored as a tuple, list or OrderedDict, got {}"" + raise TypeError(msg.format(type(object_instance).__name__)) + +- if isinstance(object_instance, OrderedDict): ++ if isinstance(variadic_arg, OrderedDict): + variadic_arg = variadic_arg.items() + + for attribute_object in variadic_arg: +",renew/_inspection.py,"ReplaceText(target='variadic_arg' @(93,26)->(93,41))","class ArgsInspect(object): + msg = ""Variadic arg has to be stored as a tuple, list or OrderedDict, got {}"" + raise TypeError(msg.format(type(object_instance).__name__)) + + if isinstance(object_instance, OrderedDict): + variadic_arg = variadic_arg.items() + + for attribute_object in variadic_arg:","class ArgsInspect(object): + msg = ""Variadic arg has to be stored as a tuple, list or OrderedDict, got {}"" + raise TypeError(msg.format(type(object_instance).__name__)) + + if isinstance(variadic_arg, OrderedDict): + variadic_arg = variadic_arg.items() + + for attribute_object in variadic_arg:" +762,https://:@github.com/DataIntegrationAlliance/DIRestInvoker.git,968df11afd78a42bb3294d90a0b73a2ae8777ab7,"@@ -32,7 +32,7 @@ class WindRestInvoker: + ret_dic = None + + if ret_data.status_code != 200: +- if ret_dic is None and 'error_code' in ret_dic and ret_dic['error_code'] == -4001: ++ if ret_dic is not None and 'error_code' in ret_dic and ret_dic['error_code'] == -4001: + logger.error('%s post %s got error\n%s', self._url(path), req_data, ret_dic) + return None + else: +",direstinvoker/iwind.py,"ReplaceText(target=' is not ' @(35,22)->(35,26))","class WindRestInvoker: + ret_dic = None + + if ret_data.status_code != 200: + if ret_dic is None and 'error_code' in ret_dic and ret_dic['error_code'] == -4001: + logger.error('%s post %s got error\n%s', self._url(path), req_data, ret_dic) + return None + else:","class WindRestInvoker: + ret_dic = None + + if ret_data.status_code != 200: + if ret_dic is not None and 'error_code' in ret_dic and ret_dic['error_code'] == -4001: + logger.error('%s post %s got error\n%s', self._url(path), req_data, ret_dic) + return None + else:" +763,https://:@github.com/tlevine/blargparse.git,05ce9594f89b154fee2f25a0ece74867756a51ea,"@@ -109,7 +109,7 @@ def test_multiple_subparsers(): + + b = sps.add_parser('b') + b.add_argument('--bbb', '-b') +- a.add_aggregate('BBB', lambda args:args.bbb.upper()) ++ b.add_aggregate('BBB', lambda args:args.bbb.upper()) + + assert bp.parse_args([]) == argparse.Namespace(command = None) + assert bp.parse_args(['a', '--aaa', 'tom']) == argparse.Namespace(command = None, aaa = 'tom', AAA = 'TOM') +",test_blargparse.py,"ReplaceText(target='b' @(112,4)->(112,5))","def test_multiple_subparsers(): + + b = sps.add_parser('b') + b.add_argument('--bbb', '-b') + a.add_aggregate('BBB', lambda args:args.bbb.upper()) + + assert bp.parse_args([]) == argparse.Namespace(command = None) + assert bp.parse_args(['a', '--aaa', 'tom']) == argparse.Namespace(command = None, aaa = 'tom', AAA = 'TOM')","def test_multiple_subparsers(): + + b = sps.add_parser('b') + b.add_argument('--bbb', '-b') + b.add_aggregate('BBB', lambda args:args.bbb.upper()) + + assert bp.parse_args([]) == argparse.Namespace(command = None) + assert bp.parse_args(['a', '--aaa', 'tom']) == argparse.Namespace(command = None, aaa = 'tom', AAA = 'TOM')" +764,https://:@gitlab.com/larsyunker/unithandler.git,db31d7adb35e6ff60a6a719dbe9f7966eee8ab07,"@@ -151,7 +151,7 @@ def interpret_unit_block(unitblock: str) -> dict: + if char.isdigit(): # if a digit, increase counter + num += char + elif char == '-' or char == MINUS: # if a negative sign, change sign +- sign = -1 ++ sign *= -1 + elif char in [' ', DOT, '*']: # if a separator, ignore + pass + else: # otherwise add to unit +",unithandler/base.py,"ReplaceText(target='*=' @(154,17)->(154,18))","def interpret_unit_block(unitblock: str) -> dict: + if char.isdigit(): # if a digit, increase counter + num += char + elif char == '-' or char == MINUS: # if a negative sign, change sign + sign = -1 + elif char in [' ', DOT, '*']: # if a separator, ignore + pass + else: # otherwise add to unit","def interpret_unit_block(unitblock: str) -> dict: + if char.isdigit(): # if a digit, increase counter + num += char + elif char == '-' or char == MINUS: # if a negative sign, change sign + sign *= -1 + elif char in [' ', DOT, '*']: # if a separator, ignore + pass + else: # otherwise add to unit" +765,https://:@github.com/egtaonline/quiesce.git,9cfe8094d875d54dae3bddd8560e5010cd8bf6e8,"@@ -70,7 +70,7 @@ async def deviation_payoffs(sched, mix, num, *, boots=0, chunk_size=None): + n = num + while 0 < n: + new_profs = sched.random_deviation_profiles( +- min(num, chunk_size), mix).reshape((-1, mix.size)) ++ min(n, chunk_size), mix).reshape((-1, mix.size)) + n -= chunk_size + new_futures = [asyncio.ensure_future(sched.sample_payoffs(prof)) + for prof in new_profs] +",egta/bootstrap.py,"ReplaceText(target='n' @(73,16)->(73,19))","async def deviation_payoffs(sched, mix, num, *, boots=0, chunk_size=None): + n = num + while 0 < n: + new_profs = sched.random_deviation_profiles( + min(num, chunk_size), mix).reshape((-1, mix.size)) + n -= chunk_size + new_futures = [asyncio.ensure_future(sched.sample_payoffs(prof)) + for prof in new_profs]","async def deviation_payoffs(sched, mix, num, *, boots=0, chunk_size=None): + n = num + while 0 < n: + new_profs = sched.random_deviation_profiles( + min(n, chunk_size), mix).reshape((-1, mix.size)) + n -= chunk_size + new_futures = [asyncio.ensure_future(sched.sample_payoffs(prof)) + for prof in new_profs]" +766,https://:@github.com/benlindsay/job_tree.git,fd96b394a96e1eb0aac3e2d4df91505e41a4c604,"@@ -22,7 +22,7 @@ job_file_list = ['params.input', 'sub.sh'] + + # Generate a flat job tree submit the jobs. + # Add 'submit = False' to prevent submission. +-job_tree(tier_list, job_file_list) ++job_tree(job_file_list, tier_list) + + # Running this script should generate a directory tree that looks like this: + +",samples/flat_sample/test.py,"ArgSwap(idxs=0<->1 @(25,0)->(25,8))","job_file_list = ['params.input', 'sub.sh'] + + # Generate a flat job tree submit the jobs. + # Add 'submit = False' to prevent submission. + job_tree(tier_list, job_file_list) + + # Running this script should generate a directory tree that looks like this: + ","job_file_list = ['params.input', 'sub.sh'] + + # Generate a flat job tree submit the jobs. + # Add 'submit = False' to prevent submission. + job_tree(job_file_list, tier_list) + + # Running this script should generate a directory tree that looks like this: + " +767,https://:@github.com/lampwins/orangengine.git,27a79be91e8fe3dd41b02ca7e943a21e2bd2b12d,"@@ -189,7 +189,7 @@ class BaseDriver(object): + + if len(set_list) == 0 or len(target_element) > 1: + # no valid matches or more than one target element identified (meaning this will have to be a new policy) +- return CandidatePolicy(target_dict=target_element) ++ return CandidatePolicy(target_dict=param_dict) + else: + # found valid matches + # the intersection of all match sets is the set of all policies that the target element can to appended to +",orangengine/drivers/base.py,"ReplaceText(target='param_dict' @(192,47)->(192,61))","class BaseDriver(object): + + if len(set_list) == 0 or len(target_element) > 1: + # no valid matches or more than one target element identified (meaning this will have to be a new policy) + return CandidatePolicy(target_dict=target_element) + else: + # found valid matches + # the intersection of all match sets is the set of all policies that the target element can to appended to","class BaseDriver(object): + + if len(set_list) == 0 or len(target_element) > 1: + # no valid matches or more than one target element identified (meaning this will have to be a new policy) + return CandidatePolicy(target_dict=param_dict) + else: + # found valid matches + # the intersection of all match sets is the set of all policies that the target element can to appended to" +768,https://:@github.com/korijn/git-lfs-azure-transfer.git,f3d7d7992adb676929d29d12c213d5169d12ccdc,"@@ -48,7 +48,7 @@ def report_error(code, message, event=None, oid=None): + } + if event: + payload['event'] = event +- if event: ++ if oid: + payload['oid'] = oid + write(payload) + +",git_lfs_azure_transfer.py,"ReplaceText(target='oid' @(51,7)->(51,12))","def report_error(code, message, event=None, oid=None): + } + if event: + payload['event'] = event + if event: + payload['oid'] = oid + write(payload) + ","def report_error(code, message, event=None, oid=None): + } + if event: + payload['event'] = event + if oid: + payload['oid'] = oid + write(payload) + " +769,https://:@github.com/danielfrg/datasciencebox.git,74ca80ebb2ecf33b71e1926b4c2c6094179aa893,"@@ -31,7 +31,7 @@ class Project(object): + if not os.path.exists(os.path.join(dir_, 'dsbfile')): + raise DSBException('""{}"" not found on """"{}"" or its parents'.format(settingsfile, path)) + +- return cls.from_file(filepath=os.path.join(settingsfile, dir_)) ++ return cls.from_file(filepath=os.path.join(dir_, settingsfile)) + + @classmethod + def from_file(cls, filepath): +",datasciencebox/core/project.py,"ArgSwap(idxs=0<->1 @(34,38)->(34,50))","class Project(object): + if not os.path.exists(os.path.join(dir_, 'dsbfile')): + raise DSBException('""{}"" not found on """"{}"" or its parents'.format(settingsfile, path)) + + return cls.from_file(filepath=os.path.join(settingsfile, dir_)) + + @classmethod + def from_file(cls, filepath):","class Project(object): + if not os.path.exists(os.path.join(dir_, 'dsbfile')): + raise DSBException('""{}"" not found on """"{}"" or its parents'.format(settingsfile, path)) + + return cls.from_file(filepath=os.path.join(dir_, settingsfile)) + + @classmethod + def from_file(cls, filepath):" +770,https://:@github.com/nick-youngblut/SIPSim.git,f11ace61e1ba5fdb7afc8a9ec4409cb37e643558,"@@ -146,7 +146,7 @@ class SimFrags(object): + + # draw from fragment size distribution + fragSize = int(self.fld(size=1)) +- if fragSize < readTempSize: ++ if fragSize <= readTempSize: + tryCnt += 1 + continue + +",lib/SimFrags.py,"ReplaceText(target='<=' @(149,24)->(149,25))","class SimFrags(object): + + # draw from fragment size distribution + fragSize = int(self.fld(size=1)) + if fragSize < readTempSize: + tryCnt += 1 + continue + ","class SimFrags(object): + + # draw from fragment size distribution + fragSize = int(self.fld(size=1)) + if fragSize <= readTempSize: + tryCnt += 1 + continue + " +771,https://:@github.com/Akuli/pythotk.git,c16149611fdeb7017bf65828c54d4c5bdf9edcc4,"@@ -132,7 +132,7 @@ class Widget: + + # use some_widget.to_tcl() to access the _widget_path + self._widget_path = '%s.%s%d' % ( +- parentpath, safe_class_name, next(counts[widgetname])) ++ parentpath, safe_class_name, next(counts[safe_class_name])) + + # TODO: some config options can only be given when the widget is + # created, add support for them +",pythotk/_widgets.py,"ReplaceText(target='safe_class_name' @(135,53)->(135,63))","class Widget: + + # use some_widget.to_tcl() to access the _widget_path + self._widget_path = '%s.%s%d' % ( + parentpath, safe_class_name, next(counts[widgetname])) + + # TODO: some config options can only be given when the widget is + # created, add support for them","class Widget: + + # use some_widget.to_tcl() to access the _widget_path + self._widget_path = '%s.%s%d' % ( + parentpath, safe_class_name, next(counts[safe_class_name])) + + # TODO: some config options can only be given when the widget is + # created, add support for them" +772,https://:@github.com/claird/PyPDF4.git,d5738dccbca3cf4d2eaf7e307a853dc31baf4a53,"@@ -117,7 +117,7 @@ class FlateDecode(object): + rowlength = columns + 1 + assert len(data) % rowlength == 0 + prev_rowdata = (0,) * rowlength +- for row in range(len(data) / rowlength): ++ for row in range(len(data) // rowlength): + rowdata = [ord(x) for x in data[(row*rowlength):((row+1)*rowlength)]] + filterByte = rowdata[0] + if filterByte == 0: +",PyPDF2/filters.py,"ReplaceText(target='//' @(120,43)->(120,44))","class FlateDecode(object): + rowlength = columns + 1 + assert len(data) % rowlength == 0 + prev_rowdata = (0,) * rowlength + for row in range(len(data) / rowlength): + rowdata = [ord(x) for x in data[(row*rowlength):((row+1)*rowlength)]] + filterByte = rowdata[0] + if filterByte == 0:","class FlateDecode(object): + rowlength = columns + 1 + assert len(data) % rowlength == 0 + prev_rowdata = (0,) * rowlength + for row in range(len(data) // rowlength): + rowdata = [ord(x) for x in data[(row*rowlength):((row+1)*rowlength)]] + filterByte = rowdata[0] + if filterByte == 0:" +773,https://:@github.com/HUJI-Deep/FlowKet.git,cfb8f9d326ceeeb03c9daa2a4be25e9a1e74064d,"@@ -42,7 +42,7 @@ class ExactVariational(object): + if self.num_of_states % batch_size != 0: + raise Exception('In exact the batch size must divide the total number of states in the system') + self.batch_size = batch_size +- self.num_of_batch_until_full_cycle = self.num_of_states / self.batch_size ++ self.num_of_batch_until_full_cycle = self.num_of_states // self.batch_size + self.batch_complex_local_energies = np.zeros((self.batch_size, ), dtype=np.complex128) + self.batch_naive_complex_local_energies = np.zeros((self.batch_size, ), dtype=np.complex128) + +",src/pyket/optimization/exact_variational.py,"ReplaceText(target='//' @(45,64)->(45,65))","class ExactVariational(object): + if self.num_of_states % batch_size != 0: + raise Exception('In exact the batch size must divide the total number of states in the system') + self.batch_size = batch_size + self.num_of_batch_until_full_cycle = self.num_of_states / self.batch_size + self.batch_complex_local_energies = np.zeros((self.batch_size, ), dtype=np.complex128) + self.batch_naive_complex_local_energies = np.zeros((self.batch_size, ), dtype=np.complex128) + ","class ExactVariational(object): + if self.num_of_states % batch_size != 0: + raise Exception('In exact the batch size must divide the total number of states in the system') + self.batch_size = batch_size + self.num_of_batch_until_full_cycle = self.num_of_states // self.batch_size + self.batch_complex_local_energies = np.zeros((self.batch_size, ), dtype=np.complex128) + self.batch_naive_complex_local_energies = np.zeros((self.batch_size, ), dtype=np.complex128) + " +774,https://:@github.com/eriknyquist/text_game_maker.git,a890d63064b801645a425df5d2d69ad4a9056d8f,"@@ -61,7 +61,7 @@ def craft(name, word, inventory): + item = None + + if name in craftables: +- items, item = craftables[item] ++ items, item = craftables[name] + else: + for k in craftables: + if k.startswith(name) or k.endswith(name) or (k in name): +",text_game_maker/crafting/crafting.py,"ReplaceText(target='name' @(64,33)->(64,37))","def craft(name, word, inventory): + item = None + + if name in craftables: + items, item = craftables[item] + else: + for k in craftables: + if k.startswith(name) or k.endswith(name) or (k in name):","def craft(name, word, inventory): + item = None + + if name in craftables: + items, item = craftables[name] + else: + for k in craftables: + if k.startswith(name) or k.endswith(name) or (k in name):" +775,https://:@github.com/eriknyquist/text_game_maker.git,2868976cf5790d39282843924148eae25102c6be,"@@ -55,7 +55,7 @@ def help_text(): + def _find_item(item, items): + for i in items: + if (i.name == item.name) and isinstance(i, item.__class__): +- return item ++ return i + + return None + +",text_game_maker/crafting/crafting.py,"ReplaceText(target='i' @(58,19)->(58,23))","def help_text(): + def _find_item(item, items): + for i in items: + if (i.name == item.name) and isinstance(i, item.__class__): + return item + + return None + ","def help_text(): + def _find_item(item, items): + for i in items: + if (i.name == item.name) and isinstance(i, item.__class__): + return i + + return None + " +776,https://:@github.com/SkyTruth/gpsd_format.git,07dd93add6bd9e448eb4ac87ed6fdc43cc94f5d2,"@@ -92,6 +92,6 @@ def etl(ctx, infile, outfile, filter_expr, sort_field, + do=output_driver_opts, + co=output_compression_opts) as dst: + +- iterator = gpsdio.filter(src, filter_expr) if filter_expr else src ++ iterator = gpsdio.filter(filter_expr, src) if filter_expr else src + for msg in gpsdio.sort(iterator, sort_field) if sort_field else iterator: + dst.write(msg) +",gpsdio/cli/etl.py,"ArgSwap(idxs=0<->1 @(95,23)->(95,36))","def etl(ctx, infile, outfile, filter_expr, sort_field, + do=output_driver_opts, + co=output_compression_opts) as dst: + + iterator = gpsdio.filter(src, filter_expr) if filter_expr else src + for msg in gpsdio.sort(iterator, sort_field) if sort_field else iterator: + dst.write(msg)","def etl(ctx, infile, outfile, filter_expr, sort_field, + do=output_driver_opts, + co=output_compression_opts) as dst: + + iterator = gpsdio.filter(filter_expr, src) if filter_expr else src + for msg in gpsdio.sort(iterator, sort_field) if sort_field else iterator: + dst.write(msg)" +777,https://:@github.com/barry-lab/openEPhys_DACQ.git,14df7f0f939a8dace7020265f1695e06451d7f87,"@@ -67,7 +67,7 @@ def print_progress(iteration, total, prefix='', suffix='', decimals=1, bar_lengt + + sys.stdout.write('%s |%s| %s%s %s\r' % (prefix, bar, percents, '%', suffix)), + +- if iteration == total: ++ if iteration >= total: + sys.stdout.write('\n') + sys.stdout.flush() + # # +",HelperFunctions.py,"ReplaceText(target='>=' @(70,17)->(70,19))","def print_progress(iteration, total, prefix='', suffix='', decimals=1, bar_lengt + + sys.stdout.write('%s |%s| %s%s %s\r' % (prefix, bar, percents, '%', suffix)), + + if iteration == total: + sys.stdout.write('\n') + sys.stdout.flush() + # # ","def print_progress(iteration, total, prefix='', suffix='', decimals=1, bar_lengt + + sys.stdout.write('%s |%s| %s%s %s\r' % (prefix, bar, percents, '%', suffix)), + + if iteration >= total: + sys.stdout.write('\n') + sys.stdout.flush() + # # " +778,https://:@github.com/fy0/mapi.git,3c322eb25527f719a55a7de8eec82bd6620546d2,"@@ -530,7 +530,7 @@ class AbstractSQLView(BaseView): + logger.debug('set data: %s' % values) + code, data = await self._sql.update(info, values) + if code == RETCODE.SUCCESS: +- await async_call(self.after_update, data) ++ await async_call(self.after_update, values) + self.finish(code, data) + + async def new(self): +",slim/base/view.py,"ReplaceText(target='values' @(533,48)->(533,52))","class AbstractSQLView(BaseView): + logger.debug('set data: %s' % values) + code, data = await self._sql.update(info, values) + if code == RETCODE.SUCCESS: + await async_call(self.after_update, data) + self.finish(code, data) + + async def new(self):","class AbstractSQLView(BaseView): + logger.debug('set data: %s' % values) + code, data = await self._sql.update(info, values) + if code == RETCODE.SUCCESS: + await async_call(self.after_update, values) + self.finish(code, data) + + async def new(self):" +779,https://:@github.com/fy0/mapi.git,d340368fbcf91c1c9377fabcb5722ffdef798501,"@@ -15,7 +15,7 @@ def require_role(role=None): + def request_role(role=None): + def _(func): + async def __(view: AbstractSQLView, *args, **kwargs): +- if role == view.current_request_role: ++ if role != view.current_request_role: + return view.finish(RETCODE.INVALID_ROLE) + return await func(view, *args, **kwargs) + return __ +",slim/ext/decorator.py,"ReplaceText(target='!=' @(18,20)->(18,22))","def require_role(role=None): + def request_role(role=None): + def _(func): + async def __(view: AbstractSQLView, *args, **kwargs): + if role == view.current_request_role: + return view.finish(RETCODE.INVALID_ROLE) + return await func(view, *args, **kwargs) + return __","def require_role(role=None): + def request_role(role=None): + def _(func): + async def __(view: AbstractSQLView, *args, **kwargs): + if role != view.current_request_role: + return view.finish(RETCODE.INVALID_ROLE) + return await func(view, *args, **kwargs) + return __" +780,https://:@github.com/Gurbert/micawber_bs4_classes.git,7a07d3b013c907c11a54cf2cedc7954c554770de,"@@ -164,7 +164,7 @@ def _is_standalone(soup_elem): + def _inside_skip(soup_elem): + parent = soup_elem.parent + while parent is not None: +- if parent.name not in skip_elements: ++ if parent.name in skip_elements: + return True + parent = parent.parent + return False +",micawber/parsers.py,"ReplaceText(target=' in ' @(167,22)->(167,30))","def _is_standalone(soup_elem): + def _inside_skip(soup_elem): + parent = soup_elem.parent + while parent is not None: + if parent.name not in skip_elements: + return True + parent = parent.parent + return False","def _is_standalone(soup_elem): + def _inside_skip(soup_elem): + parent = soup_elem.parent + while parent is not None: + if parent.name in skip_elements: + return True + parent = parent.parent + return False" +781,https://:@github.com/pgeurin/autoregression.git,dc4b2c89e719c6a94f3a4e0ab632aec2a5990c35,"@@ -488,7 +488,7 @@ def compare_predictions(df, y_var_name, percent_data=None, + timeit(plot_rocs, models, df_X, y) + plt.show() + print(f'MAKE SUBSAMPLE TIME: {time() - starttotal}') +- return names, results, models, pipeline, df_X ++ return names, results, fit_models, pipeline, df_X + + def bootstrap_train_premade(model, X, y, bootstraps=1000, **kwargs): + """"""Train a (linear) model on multiple bootstrap samples of some data and +",autoregression/autoregression.py,"ReplaceText(target='fit_models' @(491,27)->(491,33))","def compare_predictions(df, y_var_name, percent_data=None, + timeit(plot_rocs, models, df_X, y) + plt.show() + print(f'MAKE SUBSAMPLE TIME: {time() - starttotal}') + return names, results, models, pipeline, df_X + + def bootstrap_train_premade(model, X, y, bootstraps=1000, **kwargs): + """"""Train a (linear) model on multiple bootstrap samples of some data and","def compare_predictions(df, y_var_name, percent_data=None, + timeit(plot_rocs, models, df_X, y) + plt.show() + print(f'MAKE SUBSAMPLE TIME: {time() - starttotal}') + return names, results, fit_models, pipeline, df_X + + def bootstrap_train_premade(model, X, y, bootstraps=1000, **kwargs): + """"""Train a (linear) model on multiple bootstrap samples of some data and" +782,https://:@github.com/xRodney/suds-sw.git,8b72570029cb884a8b5bf46aa00deedadb150c3c,"@@ -130,7 +130,7 @@ class UMBase: + return content.data + lang = attributes.lang() + if not len(node.children) and content.text is None: +- if self.nillable(content.data) and content.node.isnil(): ++ if self.nillable(content.data) or content.node.isnil(): + return None + else: + return xlstr.string('', lang) +",suds/bindings/unmarshaller.py,"ReplaceText(target='or' @(133,43)->(133,46))","class UMBase: + return content.data + lang = attributes.lang() + if not len(node.children) and content.text is None: + if self.nillable(content.data) and content.node.isnil(): + return None + else: + return xlstr.string('', lang)","class UMBase: + return content.data + lang = attributes.lang() + if not len(node.children) and content.text is None: + if self.nillable(content.data) or content.node.isnil(): + return None + else: + return xlstr.string('', lang)" +783,https://:@github.com/xRodney/suds-sw.git,c2ef63c56cdb827e47426ce8debd547275122cc6,"@@ -113,6 +113,6 @@ class Options(Skin): + Definition('retxml', bool, False), + Definition('autoblend', bool, False), + Definition('cachingpolicy', int, 0), +- Definition('plugins', [], (list, tuple)), ++ Definition('plugins', (list, tuple), []), + ] + Skin.__init__(self, domain, definitions, kwargs) +",suds/options.py,"ArgSwap(idxs=1<->2 @(116,12)->(116,22))","class Options(Skin): + Definition('retxml', bool, False), + Definition('autoblend', bool, False), + Definition('cachingpolicy', int, 0), + Definition('plugins', [], (list, tuple)), + ] + Skin.__init__(self, domain, definitions, kwargs)","class Options(Skin): + Definition('retxml', bool, False), + Definition('autoblend', bool, False), + Definition('cachingpolicy', int, 0), + Definition('plugins', (list, tuple), []), + ] + Skin.__init__(self, domain, definitions, kwargs)" +784,https://:@gitlab.com/frkl/bring.git,ccb052917ef3d193526ee99eec8968df96a1c199,"@@ -306,7 +306,7 @@ class Bring(SimpleTing): + ctx: BringDynamicContextTing = self._tingistry_obj.create_ting( # type: ignore + ""bring_dynamic_context_ting"", f""{BRING_CONTEXT_NAMESPACE}.{context_name}"" + ) +- indexes = [folder] ++ indexes = [_path] + ctx.input.set_values( # type: ignore + ting_dict={""indexes"": indexes} + ) +",src/bring/bring.py,"ReplaceText(target='_path' @(309,19)->(309,25))","class Bring(SimpleTing): + ctx: BringDynamicContextTing = self._tingistry_obj.create_ting( # type: ignore + ""bring_dynamic_context_ting"", f""{BRING_CONTEXT_NAMESPACE}.{context_name}"" + ) + indexes = [folder] + ctx.input.set_values( # type: ignore + ting_dict={""indexes"": indexes} + )","class Bring(SimpleTing): + ctx: BringDynamicContextTing = self._tingistry_obj.create_ting( # type: ignore + ""bring_dynamic_context_ting"", f""{BRING_CONTEXT_NAMESPACE}.{context_name}"" + ) + indexes = [_path] + ctx.input.set_values( # type: ignore + ting_dict={""indexes"": indexes} + )" +785,https://:@gitlab.com/frkl/bring.git,8e4f6b2742ec941ab386856234415827f8f77429,"@@ -10,7 +10,7 @@ app_name = ""bring"" + _hi = load_modules(BRINGISTRY_PRELOAD_MODULES) # type: ignore + + pyinstaller = {""hiddenimports"": [x.__name__ for x in _hi]} +-if os.name != ""nt"": ++if os.name == ""nt"": + import pkgutil + import jinxed.terminfo + +",src/bring/_meta.py,"ReplaceText(target='==' @(13,11)->(13,13))","app_name = ""bring"" + _hi = load_modules(BRINGISTRY_PRELOAD_MODULES) # type: ignore + + pyinstaller = {""hiddenimports"": [x.__name__ for x in _hi]} + if os.name != ""nt"": + import pkgutil + import jinxed.terminfo + ","app_name = ""bring"" + _hi = load_modules(BRINGISTRY_PRELOAD_MODULES) # type: ignore + + pyinstaller = {""hiddenimports"": [x.__name__ for x in _hi]} + if os.name == ""nt"": + import pkgutil + import jinxed.terminfo + " +786,https://:@gitlab.com/frkl/bring.git,d67c17a6b4f41c01764315a5f6205a1264b6d3f0,"@@ -242,4 +242,4 @@ class BringContextTing(InheriTing, SimpleTing): + + _all_values[""_bring_metadata_timestamp""] = str(arrow.now()) + +- return all_values ++ return _all_values +",src/bring/context/__init__.py,"ReplaceText(target='_all_values' @(245,15)->(245,25))","class BringContextTing(InheriTing, SimpleTing): + + _all_values[""_bring_metadata_timestamp""] = str(arrow.now()) + + return all_values","class BringContextTing(InheriTing, SimpleTing): + + _all_values[""_bring_metadata_timestamp""] = str(arrow.now()) + + return _all_values" +787,https://:@gitlab.com/frkl/bring.git,112f00eaba6972dab7ead12bea4ca077f4ef5a6c,"@@ -110,7 +110,7 @@ def create_table_from_pkg_args( + + _allowed_strings = [] + for _arg, _aliases in _allowed.items(): +- if not aliases: ++ if not _aliases: + a = _arg + elif len(_aliases) == 1: + a = f""{_arg} (alias: {_aliases[0]})"" +",src/bring/display/args.py,"ReplaceText(target='_aliases' @(113,23)->(113,30))","def create_table_from_pkg_args( + + _allowed_strings = [] + for _arg, _aliases in _allowed.items(): + if not aliases: + a = _arg + elif len(_aliases) == 1: + a = f""{_arg} (alias: {_aliases[0]})""","def create_table_from_pkg_args( + + _allowed_strings = [] + for _arg, _aliases in _allowed.items(): + if not _aliases: + a = _arg + elif len(_aliases) == 1: + a = f""{_arg} (alias: {_aliases[0]})""" +788,https://:@gitlab.com/frkl/bring.git,6ebf8d8d3c86da43d5fe0505544d7329e4c6abf5,"@@ -135,7 +135,7 @@ class BringInstallGroup(FrklBaseCommand): + install_args = {} + if target: + install_args[""target""] = target +- if install_args: ++ if target_config: + install_args[""target_config""] = target_config + + # install_args[""merge_strategy""] = merge_strategy +",src/bring/interfaces/cli/install.py,"ReplaceText(target='target_config' @(138,11)->(138,23))","class BringInstallGroup(FrklBaseCommand): + install_args = {} + if target: + install_args[""target""] = target + if install_args: + install_args[""target_config""] = target_config + + # install_args[""merge_strategy""] = merge_strategy","class BringInstallGroup(FrklBaseCommand): + install_args = {} + if target: + install_args[""target""] = target + if target_config: + install_args[""target_config""] = target_config + + # install_args[""merge_strategy""] = merge_strategy" +789,https://:@github.com/glyph/twitter-text-py.git,197cbd58689e6f12f0b2e931c615eb816b6a8051,"@@ -60,7 +60,7 @@ class HitHighlighter(object): + if index % 2: + # we're inside a + continue +- chunk_start = len(u''.join(text_chunks[0:index / 2])) ++ chunk_start = len(u''.join(text_chunks[0:index // 2])) + chunk_end = chunk_start + len(chunk) + if hit_start >= chunk_start and hit_start < chunk_end: + chunk = chunk[:hit_start - chunk_start] + tags[0] + chunk[hit_start - chunk_start:] +",twitter_text/highlighter.py,"ReplaceText(target='//' @(63,63)->(63,64))","class HitHighlighter(object): + if index % 2: + # we're inside a + continue + chunk_start = len(u''.join(text_chunks[0:index / 2])) + chunk_end = chunk_start + len(chunk) + if hit_start >= chunk_start and hit_start < chunk_end: + chunk = chunk[:hit_start - chunk_start] + tags[0] + chunk[hit_start - chunk_start:]","class HitHighlighter(object): + if index % 2: + # we're inside a + continue + chunk_start = len(u''.join(text_chunks[0:index // 2])) + chunk_end = chunk_start + len(chunk) + if hit_start >= chunk_start and hit_start < chunk_end: + chunk = chunk[:hit_start - chunk_start] + tags[0] + chunk[hit_start - chunk_start:]" +790,https://:@github.com/lbovet/yglu.git,73ec7a7721281cf2ab16b00be2a64da5ba43697f,"@@ -42,7 +42,7 @@ def import_definition(context, root): + errors = root.doc.errors + else: + errors = None +- result = build(file, filename, errors) ++ result = build(file, filepath, errors) + return Holder(result) + + context['$import'] = import_function +",yglu/functions.py,"ReplaceText(target='filepath' @(45,33)->(45,41))","def import_definition(context, root): + errors = root.doc.errors + else: + errors = None + result = build(file, filename, errors) + return Holder(result) + + context['$import'] = import_function","def import_definition(context, root): + errors = root.doc.errors + else: + errors = None + result = build(file, filepath, errors) + return Holder(result) + + context['$import'] = import_function" +791,https://:@github.com/inforian/django-password-manager.git,5e7e6c14fa393d7e814556c9b02869d9f3adcd84,"@@ -77,7 +77,7 @@ def check_password_expired(user): + # get latest password info + latest = user.password_history.latest(""pk"") + except PasswordHistory.DoesNotExist: +- return False ++ return True + + now = datetime.now(tz=pytz.UTC) + expiration = latest.timestamp + timedelta(days=expiry) +",pass_manager/utils.py,"ReplaceText(target='True' @(80,15)->(80,20))","def check_password_expired(user): + # get latest password info + latest = user.password_history.latest(""pk"") + except PasswordHistory.DoesNotExist: + return False + + now = datetime.now(tz=pytz.UTC) + expiration = latest.timestamp + timedelta(days=expiry)","def check_password_expired(user): + # get latest password info + latest = user.password_history.latest(""pk"") + except PasswordHistory.DoesNotExist: + return True + + now = datetime.now(tz=pytz.UTC) + expiration = latest.timestamp + timedelta(days=expiry)" +792,https://:@github.com/koriavinash1/DeepBrainSeg.git,a09812c3f5b8348b1bbfc0e06669490c9a204ec7,"@@ -109,7 +109,7 @@ def GenerateCSV(model, dataset_path, logs_root, iteration = 0): + spath['seg'] = os.path.join(subject_path, subject + '_seg.nii.gz') + spath['t1'] = os.path.join(subject_path, subject + '_t1.nii.gz') + spath['t2'] = os.path.join(subject_path, subject + '_t2.nii.gz') +- spath['mask'] = os.path.join(dataset_path, 'mask.nii.gz') ++ spath['mask'] = os.path.join(subject_path, 'mask.nii.gz') + + vol, seg, affine = nii_loader(spath) + predictions = _GenerateSegmentation_(subject_path, vol, seg, size = 64, nclasses = 5) +",DeepBrainSeg/tumor/finetune/generateCSV.py,"ReplaceText(target='subject_path' @(112,42)->(112,54))","def GenerateCSV(model, dataset_path, logs_root, iteration = 0): + spath['seg'] = os.path.join(subject_path, subject + '_seg.nii.gz') + spath['t1'] = os.path.join(subject_path, subject + '_t1.nii.gz') + spath['t2'] = os.path.join(subject_path, subject + '_t2.nii.gz') + spath['mask'] = os.path.join(dataset_path, 'mask.nii.gz') + + vol, seg, affine = nii_loader(spath) + predictions = _GenerateSegmentation_(subject_path, vol, seg, size = 64, nclasses = 5)","def GenerateCSV(model, dataset_path, logs_root, iteration = 0): + spath['seg'] = os.path.join(subject_path, subject + '_seg.nii.gz') + spath['t1'] = os.path.join(subject_path, subject + '_t1.nii.gz') + spath['t2'] = os.path.join(subject_path, subject + '_t2.nii.gz') + spath['mask'] = os.path.join(subject_path, 'mask.nii.gz') + + vol, seg, affine = nii_loader(spath) + predictions = _GenerateSegmentation_(subject_path, vol, seg, size = 64, nclasses = 5)" +793,https://:@github.com/codepost-io/codePost-python.git,00320258dd53e987c66c9af2d021fb93b38ac20c,"@@ -812,7 +812,7 @@ def remove_comments(api_key, submission_id=None, file_id=None): + headers=auth_headers + ) + +- if r.status_code != 204: ++ if r.status_code == 204: + comments_to_delete += r.json().get(""comments"", list()) + deleted_comments += 1 + except: +",codePost_api/helpers.py,"ReplaceText(target='==' @(815,29)->(815,31))","def remove_comments(api_key, submission_id=None, file_id=None): + headers=auth_headers + ) + + if r.status_code != 204: + comments_to_delete += r.json().get(""comments"", list()) + deleted_comments += 1 + except:","def remove_comments(api_key, submission_id=None, file_id=None): + headers=auth_headers + ) + + if r.status_code == 204: + comments_to_delete += r.json().get(""comments"", list()) + deleted_comments += 1 + except:" +794,https://:@github.com/yuvipanda/python-mwapi.git,908d0cbc6945c46acc6f9536d95ad78dc3e157e9,"@@ -16,7 +16,7 @@ + import sys + import os + +-sys.path.insert("".."", 0) ++sys.path.insert(0, "".."") + + import mwapi + +",doc/conf.py,"ArgSwap(idxs=0<->1 @(19,0)->(19,15))","-16,7 +16,7 @@ + import sys + import os + + sys.path.insert("".."", 0) + + import mwapi + ","-16,7 +16,7 @@ + import sys + import os + + sys.path.insert(0, "".."") + + import mwapi + " +795,https://:@github.com/jplusplus/thenmap-python.git,70432b792f441d2bac26c2da2744fa5d67f47af3,"@@ -26,7 +26,7 @@ def point_from_coordinates(input_): + for sep in ["","", "";"", ""|""]: + if len(input_.split(sep)) in range(2, 3): + t = input_.split(sep) +- if isinstance(input_, string_types): ++ if isinstance(t, string_types): + raise Exception(""Invalid coordinates: %s"" % input_) + + elif isinstance(input_, Iterable): +",thenmap/thenmap.py,"ReplaceText(target='t' @(29,22)->(29,28))","def point_from_coordinates(input_): + for sep in ["","", "";"", ""|""]: + if len(input_.split(sep)) in range(2, 3): + t = input_.split(sep) + if isinstance(input_, string_types): + raise Exception(""Invalid coordinates: %s"" % input_) + + elif isinstance(input_, Iterable):","def point_from_coordinates(input_): + for sep in ["","", "";"", ""|""]: + if len(input_.split(sep)) in range(2, 3): + t = input_.split(sep) + if isinstance(t, string_types): + raise Exception(""Invalid coordinates: %s"" % input_) + + elif isinstance(input_, Iterable):" +796,https://:@github.com/cardsurf/xcrawler.git,79aaaca3e4cbf7f79efa5f3a9168fb9089b73d40,"@@ -13,4 +13,4 @@ class UrlInfo: + + def is_relative(self, url): + domain = self.url_splitter.get_domain(url) +- return len(domain) > 0 ++ return len(domain) == 0 +",xcrawler/http/urls/url_info.py,"ReplaceText(target='==' @(16,27)->(16,28))","class UrlInfo: + + def is_relative(self, url): + domain = self.url_splitter.get_domain(url) + return len(domain) > 0","class UrlInfo: + + def is_relative(self, url): + domain = self.url_splitter.get_domain(url) + return len(domain) == 0" +797,https://:@github.com/asafpr/pro_clash.git,f487619296c37a989d4dc647d1c204c1acc15e44,"@@ -898,7 +898,7 @@ def get_names(gname, uid_names, annotations): + p1_desc = '-' + p0_desc += ' : %s'%p1_desc + +- elif len(gname)>2: ++ elif len(gname)>=2: + p0_name += '_%s'%gname[1] + + return p0_name, p0_desc +",pro_clash/__init__.py,"ReplaceText(target='>=' @(901,19)->(901,20))","def get_names(gname, uid_names, annotations): + p1_desc = '-' + p0_desc += ' : %s'%p1_desc + + elif len(gname)>2: + p0_name += '_%s'%gname[1] + + return p0_name, p0_desc","def get_names(gname, uid_names, annotations): + p1_desc = '-' + p0_desc += ' : %s'%p1_desc + + elif len(gname)>=2: + p0_name += '_%s'%gname[1] + + return p0_name, p0_desc" +798,https://:@github.com/asafpr/pro_clash.git,fcb3edb3acefd3224f0e5473495435d197989c81,"@@ -525,7 +525,7 @@ def read_bam_file(bamfile, chrnames_bam, max_NM=0): + for al in alt_list: + apos = int(al[1][1:]) + # test this alternative only if its NM is as the original one +- if int(apos[3])>nm_num: ++ if int(al[3])>nm_num: + continue + if apos < min_pos: + min_pos = apos +",pro_clash/__init__.py,"ReplaceText(target='al' @(528,23)->(528,27))","def read_bam_file(bamfile, chrnames_bam, max_NM=0): + for al in alt_list: + apos = int(al[1][1:]) + # test this alternative only if its NM is as the original one + if int(apos[3])>nm_num: + continue + if apos < min_pos: + min_pos = apos","def read_bam_file(bamfile, chrnames_bam, max_NM=0): + for al in alt_list: + apos = int(al[1][1:]) + # test this alternative only if its NM is as the original one + if int(al[3])>nm_num: + continue + if apos < min_pos: + min_pos = apos" +799,https://:@github.com/Anastadev/anastasia.git,03a356f19a8c995ff2dec074b8b133244fab1c2c,"@@ -21,7 +21,7 @@ steam_handler.setLevel(logging.DEBUG) + steam_handler.setFormatter(formatter) + log.addHandler(steam_handler) + +-updater = Updater(token=sys.argv[0]) ++updater = Updater(token=sys.argv[1]) + + dispatcher = updater.dispatcher + +",Main.py,"ReplaceText(target='1' @(24,33)->(24,34))","steam_handler.setLevel(logging.DEBUG) + steam_handler.setFormatter(formatter) + log.addHandler(steam_handler) + + updater = Updater(token=sys.argv[0]) + + dispatcher = updater.dispatcher + ","steam_handler.setLevel(logging.DEBUG) + steam_handler.setFormatter(formatter) + log.addHandler(steam_handler) + + updater = Updater(token=sys.argv[1]) + + dispatcher = updater.dispatcher + " +800,https://:@github.com/ankush13r/BvSalud.git,10216a189e9f63ab1a1d8cf7c647a026b7b941bb,"@@ -195,7 +195,7 @@ def get_mesh_major_list(document_dict,decsCodes_list_dict,with_header): #Method + else: + if len(header_before_slash) != 0: + final_header = str(header_code) +'/'+ str(header_after_slash) +- elif len(header_after_slash) == 0: ++ elif len(header_before_slash) == 0: + final_header = '/' + str(decsCodes_list_dict) + else: + print(header,""--"",header_before_slash,""--"",header_after_slash) +",BvSalud/makeSet.py,"ReplaceText(target='header_before_slash' @(198,21)->(198,39))","def get_mesh_major_list(document_dict,decsCodes_list_dict,with_header): #Method + else: + if len(header_before_slash) != 0: + final_header = str(header_code) +'/'+ str(header_after_slash) + elif len(header_after_slash) == 0: + final_header = '/' + str(decsCodes_list_dict) + else: + print(header,""--"",header_before_slash,""--"",header_after_slash)","def get_mesh_major_list(document_dict,decsCodes_list_dict,with_header): #Method + else: + if len(header_before_slash) != 0: + final_header = str(header_code) +'/'+ str(header_after_slash) + elif len(header_before_slash) == 0: + final_header = '/' + str(decsCodes_list_dict) + else: + print(header,""--"",header_before_slash,""--"",header_after_slash)" +801,https://:@github.com/Hypers-HFA/paraer.git,8a5fd8156012b94e50b1e6a3413244b95f3e323b,"@@ -112,7 +112,7 @@ def para_ok_or_400(itemset): + ] + value = None # 与 '' 区别 + para = paramap.get(name) +- if required and para not in (None, ''): # 如果是post方法并且传参是json的话，para可能为0 ++ if required and para in (None, ''): # 如果是post方法并且传参是json的话，para可能为0 + result.error(name, 'required') + if para is not None: + if para: +",paraer/para.py,"ReplaceText(target=' in ' @(115,36)->(115,44))","def para_ok_or_400(itemset): + ] + value = None # 与 '' 区别 + para = paramap.get(name) + if required and para not in (None, ''): # 如果是post方法并且传参是json的话，para可能为0 + result.error(name, 'required') + if para is not None: + if para:","def para_ok_or_400(itemset): + ] + value = None # 与 '' 区别 + para = paramap.get(name) + if required and para in (None, ''): # 如果是post方法并且传参是json的话，para可能为0 + result.error(name, 'required') + if para is not None: + if para:" +802,https://:@github.com/davidenunes/tensorx.git,34fb24ae4eeca927a7d7b5f376aeeddbb0b7aacd,"@@ -2604,7 +2604,7 @@ class SaltPepperNoise(Layer): + else: + batch_size = noise_shape[0] + +- noise = salt_pepper_noise(batch_size, noise_shape[1], density, salt_value, pepper_value, seed) ++ noise = salt_pepper_noise(noise_shape[1], batch_size, density, salt_value, pepper_value, seed) + + if layer.is_sparse(): + tensor = transform.sparse_put(layer.tensor, noise) +",tensorx/layers.py,"ArgSwap(idxs=0<->1 @(2607,24)->(2607,41))","class SaltPepperNoise(Layer): + else: + batch_size = noise_shape[0] + + noise = salt_pepper_noise(batch_size, noise_shape[1], density, salt_value, pepper_value, seed) + + if layer.is_sparse(): + tensor = transform.sparse_put(layer.tensor, noise)","class SaltPepperNoise(Layer): + else: + batch_size = noise_shape[0] + + noise = salt_pepper_noise(noise_shape[1], batch_size, density, salt_value, pepper_value, seed) + + if layer.is_sparse(): + tensor = transform.sparse_put(layer.tensor, noise)" +803,https://:@github.com/sauliusl/dgw.git,9120263028d2e64983b9b9babe31c46b8f2caedd,"@@ -98,7 +98,7 @@ def dtw_std(x, y, metric='sqeuclidean', dist_only=True, constraint=None, k=None, + path_rev = (_reverse_path(path[0]), path[1]) + + if scale_first: +- path_rev = _scaled_path(path, scaling_path, flip_paths) ++ path_rev = _scaled_path(path_rev, scaling_path, flip_paths) + + # TODO: Reverse cost matrix here + cost = None +",dgw/dtw/distance.py,"ReplaceText(target='path_rev' @(101,40)->(101,44))","def dtw_std(x, y, metric='sqeuclidean', dist_only=True, constraint=None, k=None, + path_rev = (_reverse_path(path[0]), path[1]) + + if scale_first: + path_rev = _scaled_path(path, scaling_path, flip_paths) + + # TODO: Reverse cost matrix here + cost = None","def dtw_std(x, y, metric='sqeuclidean', dist_only=True, constraint=None, k=None, + path_rev = (_reverse_path(path[0]), path[1]) + + if scale_first: + path_rev = _scaled_path(path_rev, scaling_path, flip_paths) + + # TODO: Reverse cost matrix here + cost = None" +804,https://:@bitbucket.org/slicedice/aboutyou-shop-sdk-python.git,c125675219cbb473f47c78c57e9205d1be44d4f2,"@@ -439,7 +439,7 @@ class Search(object): + else: + product = Product(self.easy, p) + +- self.easy.product_cach[p.id] = product ++ self.easy.product_cach[product.id] = product + self.products.buffer[i+offset] = product + + +",collins/easy.py,"ReplaceText(target='product' @(442,35)->(442,36))","class Search(object): + else: + product = Product(self.easy, p) + + self.easy.product_cach[p.id] = product + self.products.buffer[i+offset] = product + + ","class Search(object): + else: + product = Product(self.easy, p) + + self.easy.product_cach[product.id] = product + self.products.buffer[i+offset] = product + + " +805,https://:@github.com/neizod/extmath.git,b66496463e3d724a29d652e97867f41e4e1d2aea,"@@ -117,7 +117,7 @@ def factorized(n): + break + while not n % i: + factor.append(i) +- n /= i ++ n //= i + if n == 1: + break + return factor +",mathapi/__init__.py,"ReplaceText(target='//=' @(120,14)->(120,16))","def factorized(n): + break + while not n % i: + factor.append(i) + n /= i + if n == 1: + break + return factor","def factorized(n): + break + while not n % i: + factor.append(i) + n //= i + if n == 1: + break + return factor" +806,https://:@github.com/storborg/axibot.git,4ffd9fc0f715bbe4ae8c1708fbeae45186d35f6e,"@@ -64,7 +64,7 @@ async def handle_user_message(app, ws, msg): + except Exception as e: + notify_error(app, ws, str(e)) + else: +- app['document'] = msg.document ++ app['document'] = job.document + app['job'] = job + app['estimated_time'] = job.duration().total_seconds() + notify_new_document(app, exclude_client=ws) +",axibot/server/handlers.py,"ReplaceText(target='job' @(67,30)->(67,33))","async def handle_user_message(app, ws, msg): + except Exception as e: + notify_error(app, ws, str(e)) + else: + app['document'] = msg.document + app['job'] = job + app['estimated_time'] = job.duration().total_seconds() + notify_new_document(app, exclude_client=ws)","async def handle_user_message(app, ws, msg): + except Exception as e: + notify_error(app, ws, str(e)) + else: + app['document'] = job.document + app['job'] = job + app['estimated_time'] = job.duration().total_seconds() + notify_new_document(app, exclude_client=ws)" +807,https://:@github.com/storborg/axibot.git,4ad752828696a789ef25fa001f1489f87344c3e4,"@@ -116,7 +116,7 @@ async def client_handler(request): + elif raw_msg.tp == aiohttp.MsgType.closed: + break + elif raw_msg.tp == aiohttp.MsgType.error: +- log.info(""User websocket error: %s"", msg) ++ log.info(""User websocket error: %s"", raw_msg) + break + else: + log.error(""Unknown user message type: %s, ignoring."", +",axibot/server/handlers.py,"ReplaceText(target='raw_msg' @(119,53)->(119,56))","async def client_handler(request): + elif raw_msg.tp == aiohttp.MsgType.closed: + break + elif raw_msg.tp == aiohttp.MsgType.error: + log.info(""User websocket error: %s"", msg) + break + else: + log.error(""Unknown user message type: %s, ignoring."",","async def client_handler(request): + elif raw_msg.tp == aiohttp.MsgType.closed: + break + elif raw_msg.tp == aiohttp.MsgType.error: + log.info(""User websocket error: %s"", raw_msg) + break + else: + log.error(""Unknown user message type: %s, ignoring.""," +808,https://:@github.com/tsuyukimakoto/biisan.git,4465b109a4e71dcb64499c14b579c762e54b4db4,"@@ -116,7 +116,7 @@ def process_image(elm, registry, container): + img.alt = subitem[1] + elif subitem[0] == 'witdh': + img.witdh = subitem[1] +- elif subitem[1] == 'height': ++ elif subitem[0] == 'height': + img.height = subitem[1] + elif subitem[0] == 'uri': + img.uri = subitem[1] +",biisan/processors/__init__.py,"ReplaceText(target='0' @(119,21)->(119,22))","def process_image(elm, registry, container): + img.alt = subitem[1] + elif subitem[0] == 'witdh': + img.witdh = subitem[1] + elif subitem[1] == 'height': + img.height = subitem[1] + elif subitem[0] == 'uri': + img.uri = subitem[1]","def process_image(elm, registry, container): + img.alt = subitem[1] + elif subitem[0] == 'witdh': + img.witdh = subitem[1] + elif subitem[0] == 'height': + img.height = subitem[1] + elif subitem[0] == 'uri': + img.uri = subitem[1]" +809,https://:@github.com/csm10495/csmlog.git,010e00e53545842d2dc1342c375c068c90138ca2,"@@ -262,7 +262,7 @@ def test_gsheets_calculate_periodic_loop_sleep_time(gsheets_handler_no_thread): + def test_gsheets_add_rows_to_active_sheet_sets_add_rows_time(gsheets_handler_no_thread): + gsheets_handler_no_thread._add_rows_time = 99 + assert isinstance(gsheets_handler_no_thread._add_rows_to_active_sheet([]), unittest.mock.Mock) +- assert gsheets_handler_no_thread._add_rows_time < 99 and gsheets_handler_no_thread._add_rows_time > 0 ++ assert gsheets_handler_no_thread._add_rows_time < 99 and gsheets_handler_no_thread._add_rows_time >= 0 + + def test_gsheets_add_rows_to_active_sheet_set_coerce_to_correct_exceptions(gsheets_handler_no_thread): + with unittest.mock.patch.object(gsheets_handler_no_thread.sheet, 'append_rows', side_effect=Exception(""RESOURCE_EXHAUSTED uh-oh"")) as mock: +",csmlog/tests/test_google_sheets_handler.py,"ReplaceText(target='>=' @(265,102)->(265,103))","def test_gsheets_calculate_periodic_loop_sleep_time(gsheets_handler_no_thread): + def test_gsheets_add_rows_to_active_sheet_sets_add_rows_time(gsheets_handler_no_thread): + gsheets_handler_no_thread._add_rows_time = 99 + assert isinstance(gsheets_handler_no_thread._add_rows_to_active_sheet([]), unittest.mock.Mock) + assert gsheets_handler_no_thread._add_rows_time < 99 and gsheets_handler_no_thread._add_rows_time > 0 + + def test_gsheets_add_rows_to_active_sheet_set_coerce_to_correct_exceptions(gsheets_handler_no_thread): + with unittest.mock.patch.object(gsheets_handler_no_thread.sheet, 'append_rows', side_effect=Exception(""RESOURCE_EXHAUSTED uh-oh"")) as mock:","def test_gsheets_calculate_periodic_loop_sleep_time(gsheets_handler_no_thread): + def test_gsheets_add_rows_to_active_sheet_sets_add_rows_time(gsheets_handler_no_thread): + gsheets_handler_no_thread._add_rows_time = 99 + assert isinstance(gsheets_handler_no_thread._add_rows_to_active_sheet([]), unittest.mock.Mock) + assert gsheets_handler_no_thread._add_rows_time < 99 and gsheets_handler_no_thread._add_rows_time >= 0 + + def test_gsheets_add_rows_to_active_sheet_set_coerce_to_correct_exceptions(gsheets_handler_no_thread): + with unittest.mock.patch.object(gsheets_handler_no_thread.sheet, 'append_rows', side_effect=Exception(""RESOURCE_EXHAUSTED uh-oh"")) as mock:" +810,https://:@github.com/JorrandeWit/django-oscar-fees.git,7d18c7bdbeb881f4af5f81c1adf989422e134995,"@@ -26,7 +26,7 @@ class FeeApplications(object): + 'fee': fee, + 'result': result, + 'name': fee.name, +- 'description': result.description, ++ 'description': fee.description, + 'freq': 0, + 'amount': D('0.00')} + self.applications[fee.id]['amount'] += result.fee +",django_oscar_fees/results.py,"ReplaceText(target='fee' @(29,31)->(29,37))","class FeeApplications(object): + 'fee': fee, + 'result': result, + 'name': fee.name, + 'description': result.description, + 'freq': 0, + 'amount': D('0.00')} + self.applications[fee.id]['amount'] += result.fee","class FeeApplications(object): + 'fee': fee, + 'result': result, + 'name': fee.name, + 'description': fee.description, + 'freq': 0, + 'amount': D('0.00')} + self.applications[fee.id]['amount'] += result.fee" +811,https://:@gitlab.com/yhtang/graphdot.git,2ac46e719092b1e78bc2bd860bce1dd23e152638,"@@ -27,7 +27,7 @@ class OctileGraph(object): + nnz = len(edges) + + ''' add phantom label if none exists to facilitate C++ interop ''' +- assert(len(edges.columns) >= 1) ++ assert(len(nodes.columns) >= 1) + if len(nodes.columns) == 1: + nodes['labeled'] = np.zeros(len(nodes), np.bool_) + +",graphdot/kernel/marginalized/_octilegraph.py,"ReplaceText(target='nodes' @(30,19)->(30,24))","class OctileGraph(object): + nnz = len(edges) + + ''' add phantom label if none exists to facilitate C++ interop ''' + assert(len(edges.columns) >= 1) + if len(nodes.columns) == 1: + nodes['labeled'] = np.zeros(len(nodes), np.bool_) + ","class OctileGraph(object): + nnz = len(edges) + + ''' add phantom label if none exists to facilitate C++ interop ''' + assert(len(nodes.columns) >= 1) + if len(nodes.columns) == 1: + nodes['labeled'] = np.zeros(len(nodes), np.bool_) + " +812,https://:@gitlab.com/yhtang/graphdot.git,c1d46fe384aaac63a6e32b0a30cf6f3aa2b04183,"@@ -315,7 +315,7 @@ class MarginalizedGraphKernel: + if traits.eval_gradient is True: + output_shape = (output_length, 1 + self.n_dims) + else: +- output_shape = (output_shape, 1) ++ output_shape = (output_length, 1) + output = backend.empty(int(np.prod(output_shape)), np.float32) + timer.toc('creating output buffer') + +",graphdot/kernel/marginalized/_kernel.py,"ReplaceText(target='output_length' @(318,28)->(318,40))","class MarginalizedGraphKernel: + if traits.eval_gradient is True: + output_shape = (output_length, 1 + self.n_dims) + else: + output_shape = (output_shape, 1) + output = backend.empty(int(np.prod(output_shape)), np.float32) + timer.toc('creating output buffer') + ","class MarginalizedGraphKernel: + if traits.eval_gradient is True: + output_shape = (output_length, 1 + self.n_dims) + else: + output_shape = (output_length, 1) + output = backend.empty(int(np.prod(output_shape)), np.float32) + timer.toc('creating output buffer') + " +813,https://:@gitlab.com/yhtang/graphdot.git,f1499423ac76e790b77f729e92b2cc3223d64f58,"@@ -117,7 +117,7 @@ class SpectralApprox(FactorApprox): + def __init__(self, X, rcut=0, acut=0): + if isinstance(X, np.ndarray): + U, S, _ = np.linalg.svd(X, full_matrices=False) +- mask = (S >= S.max() * rcut) | (S >= acut) ++ mask = (S >= S.max() * rcut) & (S >= acut) + self.U = U[:, mask] + self.S = S[mask] + elif isinstance(X, tuple) and len(X) == 2: +",graphdot/linalg/low_rank.py,"ReplaceText(target='&' @(120,41)->(120,42))","class SpectralApprox(FactorApprox): + def __init__(self, X, rcut=0, acut=0): + if isinstance(X, np.ndarray): + U, S, _ = np.linalg.svd(X, full_matrices=False) + mask = (S >= S.max() * rcut) | (S >= acut) + self.U = U[:, mask] + self.S = S[mask] + elif isinstance(X, tuple) and len(X) == 2:","class SpectralApprox(FactorApprox): + def __init__(self, X, rcut=0, acut=0): + if isinstance(X, np.ndarray): + U, S, _ = np.linalg.svd(X, full_matrices=False) + mask = (S >= S.max() * rcut) & (S >= acut) + self.U = U[:, mask] + self.S = S[mask] + elif isinstance(X, tuple) and len(X) == 2:" +814,https://:@github.com/straga/micropython.git,1679696612007107dac55d936006b1923eda2475,"@@ -7,7 +7,7 @@ desc = { + + data = bytearray(b""01234567"") + +-S = uctypes.struct(desc, uctypes.addressof(data), uctypes.LITTLE_ENDIAN) ++S = uctypes.struct(uctypes.addressof(data), desc, uctypes.LITTLE_ENDIAN) + + # Arrays of UINT8 are accessed as bytearrays + print(S.arr) +",tests/extmod/uctypes_bytearray.py,"ArgSwap(idxs=0<->1 @(10,4)->(10,18))","desc = { + + data = bytearray(b""01234567"") + + S = uctypes.struct(desc, uctypes.addressof(data), uctypes.LITTLE_ENDIAN) + + # Arrays of UINT8 are accessed as bytearrays + print(S.arr)","desc = { + + data = bytearray(b""01234567"") + + S = uctypes.struct(uctypes.addressof(data), desc, uctypes.LITTLE_ENDIAN) + + # Arrays of UINT8 are accessed as bytearrays + print(S.arr)" +815,https://:@github.com/straga/micropython.git,1679696612007107dac55d936006b1923eda2475,"@@ -22,7 +22,7 @@ desc = { + + data = bytearray(b""01"") + +-S = uctypes.struct(desc, uctypes.addressof(data), uctypes.LITTLE_ENDIAN) ++S = uctypes.struct(uctypes.addressof(data), desc, uctypes.LITTLE_ENDIAN) + + #print(S) + print(hex(S.s0)) +",tests/extmod/uctypes_le.py,"ArgSwap(idxs=0<->1 @(25,4)->(25,18))","desc = { + + data = bytearray(b""01"") + + S = uctypes.struct(desc, uctypes.addressof(data), uctypes.LITTLE_ENDIAN) + + #print(S) + print(hex(S.s0))","desc = { + + data = bytearray(b""01"") + + S = uctypes.struct(uctypes.addressof(data), desc, uctypes.LITTLE_ENDIAN) + + #print(S) + print(hex(S.s0))" +816,https://:@github.com/straga/micropython.git,1679696612007107dac55d936006b1923eda2475,"@@ -31,7 +31,7 @@ desc = { + + data = bytearray(b""01"") + +-S = uctypes.struct(desc, uctypes.addressof(data), uctypes.NATIVE) ++S = uctypes.struct(uctypes.addressof(data), desc, uctypes.NATIVE) + + #print(S) + print(hex(S.s0)) +",tests/extmod/uctypes_native_le.py,"ArgSwap(idxs=0<->1 @(34,4)->(34,18))","desc = { + + data = bytearray(b""01"") + + S = uctypes.struct(desc, uctypes.addressof(data), uctypes.NATIVE) + + #print(S) + print(hex(S.s0))","desc = { + + data = bytearray(b""01"") + + S = uctypes.struct(uctypes.addressof(data), desc, uctypes.NATIVE) + + #print(S) + print(hex(S.s0))" +817,https://:@github.com/straga/micropython.git,1679696612007107dac55d936006b1923eda2475,"@@ -16,7 +16,7 @@ bytes = b""01"" + addr = uctypes.addressof(bytes) + buf = addr.to_bytes(uctypes.sizeof(desc)) + +-S = uctypes.struct(desc, uctypes.addressof(buf), uctypes.LITTLE_ENDIAN) ++S = uctypes.struct(uctypes.addressof(buf), desc, uctypes.LITTLE_ENDIAN) + + print(S.ptr[0]) + assert S.ptr[0] == ord(""0"") +",tests/extmod/uctypes_ptr_le.py,"ArgSwap(idxs=0<->1 @(19,4)->(19,18))","bytes = b""01"" + addr = uctypes.addressof(bytes) + buf = addr.to_bytes(uctypes.sizeof(desc)) + + S = uctypes.struct(desc, uctypes.addressof(buf), uctypes.LITTLE_ENDIAN) + + print(S.ptr[0]) + assert S.ptr[0] == ord(""0"")","bytes = b""01"" + addr = uctypes.addressof(bytes) + buf = addr.to_bytes(uctypes.sizeof(desc)) + + S = uctypes.struct(uctypes.addressof(buf), desc, uctypes.LITTLE_ENDIAN) + + print(S.ptr[0]) + assert S.ptr[0] == ord(""0"")" +818,https://:@github.com/IL2HorusTeam/il2fb-ds-airbridge.git,bc69d1a47a4994071d0b46c7dd29aebf6a7d4169,"@@ -60,7 +60,7 @@ class TextFileWatchDog: + + def stop(self) -> None: + with self._stop_lock: +- self._do_stop = False ++ self._do_stop = True + + def run(self) -> None: + try: +",il2fb/ds/airbridge/watch_dog.py,"ReplaceText(target='True' @(63,28)->(63,33))","class TextFileWatchDog: + + def stop(self) -> None: + with self._stop_lock: + self._do_stop = False + + def run(self) -> None: + try:","class TextFileWatchDog: + + def stop(self) -> None: + with self._stop_lock: + self._do_stop = True + + def run(self) -> None: + try:" +819,https://:@github.com/south-coast-science/scs_dfe_eng.git,060bd36c51a20f4586ed199b1e3996c70b0318a7,"@@ -49,7 +49,7 @@ class AFE(object): + self.__wrk_adc = ADS1115(ADS1115.ADDR_WRK, AFE.__RATE) + self.__aux_adc = ADS1115(ADS1115.ADDR_AUX, AFE.__RATE) + +- self.__pt1000_adc = pt1000_conf.adc(MCP342X.GAIN_4, MCP342X.RATE_15) if pt1000_conf else None ++ self.__pt1000_adc = pt1000_conf.adc(MCP342X.GAIN_4, MCP342X.RATE_15) if pt1000 else None + + self.__tconv = self.__wrk_adc.tconv + +",scs_dfe/gas/afe.py,"ReplaceText(target='pt1000' @(52,80)->(52,91))","class AFE(object): + self.__wrk_adc = ADS1115(ADS1115.ADDR_WRK, AFE.__RATE) + self.__aux_adc = ADS1115(ADS1115.ADDR_AUX, AFE.__RATE) + + self.__pt1000_adc = pt1000_conf.adc(MCP342X.GAIN_4, MCP342X.RATE_15) if pt1000_conf else None + + self.__tconv = self.__wrk_adc.tconv + ","class AFE(object): + self.__wrk_adc = ADS1115(ADS1115.ADDR_WRK, AFE.__RATE) + self.__aux_adc = ADS1115(ADS1115.ADDR_AUX, AFE.__RATE) + + self.__pt1000_adc = pt1000_conf.adc(MCP342X.GAIN_4, MCP342X.RATE_15) if pt1000 else None + + self.__tconv = self.__wrk_adc.tconv + " +820,https://:@github.com/ionox0/toil.git,3f065a27c433b1cb9c5266ed4c28b643419d4466,"@@ -456,7 +456,7 @@ def mainLoop(config, batchSystem): + reissueOverLongJobs(updatedJobFiles, jobBatcher, config, batchSystem, childJobFileToParentJob, childCounts) + logger.info(""Reissued any over long jobs"") + +- hasNoMissingJobs = reissueMissingJobs(updatedJobFiles, jobBatcher, batchSystem, childJobFileToParentJob, config, childCounts) ++ hasNoMissingJobs = reissueMissingJobs(updatedJobFiles, jobBatcher, batchSystem, childJobFileToParentJob, childCounts, config) + if hasNoMissingJobs: + timeSinceJobsLastRescued = time.time() + else: +",src/master.py,"ArgSwap(idxs=4<->5 @(459,35)->(459,53))","def mainLoop(config, batchSystem): + reissueOverLongJobs(updatedJobFiles, jobBatcher, config, batchSystem, childJobFileToParentJob, childCounts) + logger.info(""Reissued any over long jobs"") + + hasNoMissingJobs = reissueMissingJobs(updatedJobFiles, jobBatcher, batchSystem, childJobFileToParentJob, config, childCounts) + if hasNoMissingJobs: + timeSinceJobsLastRescued = time.time() + else:","def mainLoop(config, batchSystem): + reissueOverLongJobs(updatedJobFiles, jobBatcher, config, batchSystem, childJobFileToParentJob, childCounts) + logger.info(""Reissued any over long jobs"") + + hasNoMissingJobs = reissueMissingJobs(updatedJobFiles, jobBatcher, batchSystem, childJobFileToParentJob, childCounts, config) + if hasNoMissingJobs: + timeSinceJobsLastRescued = time.time() + else:" +821,https://:@github.com/ionox0/toil.git,a0e4eadb87f09791088b6c11dc6aec0bf8002991,"@@ -99,7 +99,7 @@ please ensure you re-import targets defined in main"" % self.__class__.__name__) + """"""Takes a file (as a path) and uploads it to to the global file store, returns + an ID that can be used to retrieve the file. + """""" +- return self.jobStore.writeFile(localFileName, self.job.jobStoreID) ++ return self.jobStore.writeFile(self.job.jobStoreID, localFileName) + + def updateGlobalFile(self, fileStoreID, localFileName): + """"""Replaces the existing version of a file in the global file store, keyed by the fileStoreID. +",src/target.py,"ArgSwap(idxs=0<->1 @(102,15)->(102,38))","please ensure you re-import targets defined in main"" % self.__class__.__name__) + """"""Takes a file (as a path) and uploads it to to the global file store, returns + an ID that can be used to retrieve the file. + """""" + return self.jobStore.writeFile(localFileName, self.job.jobStoreID) + + def updateGlobalFile(self, fileStoreID, localFileName): + """"""Replaces the existing version of a file in the global file store, keyed by the fileStoreID. ","please ensure you re-import targets defined in main"" % self.__class__.__name__) + """"""Takes a file (as a path) and uploads it to to the global file store, returns + an ID that can be used to retrieve the file. + """""" + return self.jobStore.writeFile(self.job.jobStoreID, localFileName) + + def updateGlobalFile(self, fileStoreID, localFileName): + """"""Replaces the existing version of a file in the global file store, keyed by the fileStoreID. " +822,https://:@github.com/ionox0/toil.git,06718f425d5981afabd30bcfa39d866edb5c09b4,"@@ -46,7 +46,7 @@ class Job( object ): + #The IDs of predecessors that have finished. + #When len(predecessorsFinished) == predecessorNumber then the + #job can be run. +- self.predecessorsFinished = predecessorNumber or set() ++ self.predecessorsFinished = predecessorsFinished or set() + + #The list of successor jobs to run. Successor jobs are stored + #as 4-tuples of the form (jobStoreId, memory, cpu, predecessorNumber). +",src/jobTree/job.py,"ReplaceText(target='predecessorsFinished' @(49,36)->(49,53))","class Job( object ): + #The IDs of predecessors that have finished. + #When len(predecessorsFinished) == predecessorNumber then the + #job can be run. + self.predecessorsFinished = predecessorNumber or set() + + #The list of successor jobs to run. Successor jobs are stored + #as 4-tuples of the form (jobStoreId, memory, cpu, predecessorNumber).","class Job( object ): + #The IDs of predecessors that have finished. + #When len(predecessorsFinished) == predecessorNumber then the + #job can be run. + self.predecessorsFinished = predecessorsFinished or set() + + #The list of successor jobs to run. Successor jobs are stored + #as 4-tuples of the form (jobStoreId, memory, cpu, predecessorNumber)." +823,https://:@github.com/ionox0/toil.git,47ec5287d747036c524100cc49fa4262a73293cf,"@@ -107,7 +107,7 @@ class JobWrapper( object ): + """""" + if self.logJobStoreFileID is not None: + self.clearLogFile(jobStore) +- self.logJobStoreFileID = jobStore.writeFile( self.jobStoreID, logFile ) ++ self.logJobStoreFileID = jobStore.writeFile( logFile, self.jobStoreID ) + assert self.logJobStoreFileID is not None + + def getLogFileHandle( self, jobStore ): +",src/toil/jobWrapper.py,"ArgSwap(idxs=0<->1 @(110,33)->(110,51))","class JobWrapper( object ): + """""" + if self.logJobStoreFileID is not None: + self.clearLogFile(jobStore) + self.logJobStoreFileID = jobStore.writeFile( self.jobStoreID, logFile ) + assert self.logJobStoreFileID is not None + + def getLogFileHandle( self, jobStore ):","class JobWrapper( object ): + """""" + if self.logJobStoreFileID is not None: + self.clearLogFile(jobStore) + self.logJobStoreFileID = jobStore.writeFile( logFile, self.jobStoreID ) + assert self.logJobStoreFileID is not None + + def getLogFileHandle( self, jobStore ):" +824,https://:@github.com/ionox0/toil.git,cad17f6cbe391264e00675c51a8bfe9221ba1091,"@@ -159,7 +159,7 @@ class AbstractJobStore( object ): + break + + #Reset the retry count of the jobWrapper +- if jobWrapper.remainingRetryCount < self._defaultTryCount(): ++ if jobWrapper.remainingRetryCount != self._defaultTryCount(): + jobWrapper.remainingRetryCount = self._defaultTryCount() + changed = True + +",src/toil/jobStores/abstractJobStore.py,"ReplaceText(target='!=' @(162,46)->(162,47))","class AbstractJobStore( object ): + break + + #Reset the retry count of the jobWrapper + if jobWrapper.remainingRetryCount < self._defaultTryCount(): + jobWrapper.remainingRetryCount = self._defaultTryCount() + changed = True + ","class AbstractJobStore( object ): + break + + #Reset the retry count of the jobWrapper + if jobWrapper.remainingRetryCount != self._defaultTryCount(): + jobWrapper.remainingRetryCount = self._defaultTryCount() + changed = True + " +825,https://:@github.com/ionox0/toil.git,dcd5e6f86c0f9d376140f4626e97666348683b73,"@@ -437,7 +437,7 @@ class ModuleDescriptor(namedtuple('ModuleDescriptor', ('dirPath', 'name'))): + + :rtype: toil.resource.Resource + """""" +- if self._runningOnWorker(): ++ if not self._runningOnWorker(): + log.warn('The localize() method should only be invoked on a worker.') + resource = Resource.lookup(self._resourcePath) + if resource is None: +",src/toil/resource.py,"ReplaceText(target='not ' @(440,11)->(440,11))","class ModuleDescriptor(namedtuple('ModuleDescriptor', ('dirPath', 'name'))): + + :rtype: toil.resource.Resource + """""" + if self._runningOnWorker(): + log.warn('The localize() method should only be invoked on a worker.') + resource = Resource.lookup(self._resourcePath) + if resource is None:","class ModuleDescriptor(namedtuple('ModuleDescriptor', ('dirPath', 'name'))): + + :rtype: toil.resource.Resource + """""" + if not self._runningOnWorker(): + log.warn('The localize() method should only be invoked on a worker.') + resource = Resource.lookup(self._resourcePath) + if resource is None:" +826,https://:@github.com/ionox0/toil.git,bee00f3fc4f68af0e7c00b884627f728ca20f792,"@@ -649,7 +649,7 @@ def main(args=None, stdout=sys.stdout): + if options.logLevel: + cwllogger.setLevel(options.logLevel) + +- useStrict = not args.not_strict ++ useStrict = not options.not_strict + try: + t = cwltool.load_tool.load_tool(options.cwltool, cwltool.workflow.defaultMakeTool, + resolver=cwltool.resolver.tool_resolver, strict=useStrict) +",src/toil/cwl/cwltoil.py,"ReplaceText(target='options' @(652,20)->(652,24))","def main(args=None, stdout=sys.stdout): + if options.logLevel: + cwllogger.setLevel(options.logLevel) + + useStrict = not args.not_strict + try: + t = cwltool.load_tool.load_tool(options.cwltool, cwltool.workflow.defaultMakeTool, + resolver=cwltool.resolver.tool_resolver, strict=useStrict)","def main(args=None, stdout=sys.stdout): + if options.logLevel: + cwllogger.setLevel(options.logLevel) + + useStrict = not options.not_strict + try: + t = cwltool.load_tool.load_tool(options.cwltool, cwltool.workflow.defaultMakeTool, + resolver=cwltool.resolver.tool_resolver, strict=useStrict)" +827,https://:@github.com/ionox0/toil.git,231b6665bde956aae5b3469a7147e2358097fca4,"@@ -143,7 +143,7 @@ class SingleMachineBatchSystem(BatchSystemSupport): + startTime = time.time() # Time job is started + popen = None + statusCode = None +- forkWorker = not (self.debugWorker and ""_toil_worker"" not in jobCommand) ++ forkWorker = not (self.debugWorker and ""_toil_worker"" in jobCommand) + if forkWorker: + with self.popenLock: + popen = subprocess.Popen(jobCommand, +",src/toil/batchSystems/singleMachine.py,"ReplaceText(target=' in ' @(146,61)->(146,69))","class SingleMachineBatchSystem(BatchSystemSupport): + startTime = time.time() # Time job is started + popen = None + statusCode = None + forkWorker = not (self.debugWorker and ""_toil_worker"" not in jobCommand) + if forkWorker: + with self.popenLock: + popen = subprocess.Popen(jobCommand,","class SingleMachineBatchSystem(BatchSystemSupport): + startTime = time.time() # Time job is started + popen = None + statusCode = None + forkWorker = not (self.debugWorker and ""_toil_worker"" in jobCommand) + if forkWorker: + with self.popenLock: + popen = subprocess.Popen(jobCommand," +828,https://:@github.com/ionox0/toil.git,f5054aca67788f976c72b1e3f42334afe3a1dfaa,"@@ -138,7 +138,7 @@ class AbstractProvisioner(with_metaclass(ABCMeta, object)): + self._spotBidsMap[nodeType] = bid + else: + self.nodeTypes.append(nodeTypeStr) +- self.nodeShapes.append(self.getNodeShape(nodeType, preemptable=False)) ++ self.nodeShapes.append(self.getNodeShape(nodeTypeStr, preemptable=False)) + + @staticmethod + def retryPredicate(e): +",src/toil/provisioners/abstractProvisioner.py,"ReplaceText(target='nodeTypeStr' @(141,57)->(141,65))","class AbstractProvisioner(with_metaclass(ABCMeta, object)): + self._spotBidsMap[nodeType] = bid + else: + self.nodeTypes.append(nodeTypeStr) + self.nodeShapes.append(self.getNodeShape(nodeType, preemptable=False)) + + @staticmethod + def retryPredicate(e):","class AbstractProvisioner(with_metaclass(ABCMeta, object)): + self._spotBidsMap[nodeType] = bid + else: + self.nodeTypes.append(nodeTypeStr) + self.nodeShapes.append(self.getNodeShape(nodeTypeStr, preemptable=False)) + + @staticmethod + def retryPredicate(e):" +829,https://:@github.com/ionox0/toil.git,59f716aed0363adba211e7c1f18ebe3802edb636,"@@ -108,7 +108,7 @@ class GridEngineBatchSystem(AbstractGridEngineBatchSystem): + if not self.boss.config.manualMemArgs: + # for UGE instead of SGE; see #2309 + reqline += ['vf=' + memStr, 'h_vmem=' + memStr] +- elif self.boss.config.manualMemArgs and sgeArgs: ++ elif self.boss.config.manualMemArgs and not sgeArgs: + raise ValueError(""--manualMemArgs set to True, but TOIL_GRIDGENGINE_ARGS is not set."" + ""Please set TOIL_GRIDGENGINE_ARGS to specify memory allocation for "" + ""your system. Default adds the arguments: vf= h_vmem= "" +",src/toil/batchSystems/gridengine.py,"ReplaceText(target='not ' @(111,56)->(111,56))","class GridEngineBatchSystem(AbstractGridEngineBatchSystem): + if not self.boss.config.manualMemArgs: + # for UGE instead of SGE; see #2309 + reqline += ['vf=' + memStr, 'h_vmem=' + memStr] + elif self.boss.config.manualMemArgs and sgeArgs: + raise ValueError(""--manualMemArgs set to True, but TOIL_GRIDGENGINE_ARGS is not set."" + ""Please set TOIL_GRIDGENGINE_ARGS to specify memory allocation for "" + ""your system. Default adds the arguments: vf= h_vmem= ""","class GridEngineBatchSystem(AbstractGridEngineBatchSystem): + if not self.boss.config.manualMemArgs: + # for UGE instead of SGE; see #2309 + reqline += ['vf=' + memStr, 'h_vmem=' + memStr] + elif self.boss.config.manualMemArgs and not sgeArgs: + raise ValueError(""--manualMemArgs set to True, but TOIL_GRIDGENGINE_ARGS is not set."" + ""Please set TOIL_GRIDGENGINE_ARGS to specify memory allocation for "" + ""your system. Default adds the arguments: vf= h_vmem= """ +830,https://:@github.com/tkf/railgun.git,f49414f39ca7c6bbbd5e000d45db46b77a4e514d,"@@ -64,7 +64,7 @@ DATA_TEST_CDEC_PARSE = [ + (""int a[i] =2"", dict_cdec_parse('int', 'a', tuple('i'), 1, 2)), + (""int a[i][j]=3"", dict_cdec_parse('int', 'a', tuple('ij'), 2, 3)), + ('num_i = 10', dict_cdec_parse('int', 'num_i', default=10)), +- (cmem('obj', DmyCDT), dict_cdec_parse(DmyCDT, 'obj', valtype='object')), ++ (cmem(DmyCDT, 'obj'), dict_cdec_parse(DmyCDT, 'obj', valtype='object')), + ] + + +",tests/test_cdata.py,"ArgSwap(idxs=0<->1 @(67,5)->(67,9))","DATA_TEST_CDEC_PARSE = [ + (""int a[i] =2"", dict_cdec_parse('int', 'a', tuple('i'), 1, 2)), + (""int a[i][j]=3"", dict_cdec_parse('int', 'a', tuple('ij'), 2, 3)), + ('num_i = 10', dict_cdec_parse('int', 'num_i', default=10)), + (cmem('obj', DmyCDT), dict_cdec_parse(DmyCDT, 'obj', valtype='object')), + ] + + ","DATA_TEST_CDEC_PARSE = [ + (""int a[i] =2"", dict_cdec_parse('int', 'a', tuple('i'), 1, 2)), + (""int a[i][j]=3"", dict_cdec_parse('int', 'a', tuple('ij'), 2, 3)), + ('num_i = 10', dict_cdec_parse('int', 'num_i', default=10)), + (cmem(DmyCDT, 'obj'), dict_cdec_parse(DmyCDT, 'obj', valtype='object')), + ] + + " +831,https://:@github.com/hubzero/hublib.git,8921395b8feda7af6d59ed2133dd1a4068ae9803,"@@ -486,7 +486,7 @@ def copy_files(errnum, etime, toolname, runName): + else: + # nonparametric run. Results are in current working directory. + # Use the timestamp to copy all newer files to the cacheName. +- if errnum > 0: ++ if errnum == 0: + files = os.listdir('.') + for f in files: + if os.path.getmtime(f) > self.start_time: +",hublib/ui/submit.py,"ReplaceText(target='==' @(489,18)->(489,19))","def copy_files(errnum, etime, toolname, runName): + else: + # nonparametric run. Results are in current working directory. + # Use the timestamp to copy all newer files to the cacheName. + if errnum > 0: + files = os.listdir('.') + for f in files: + if os.path.getmtime(f) > self.start_time:","def copy_files(errnum, etime, toolname, runName): + else: + # nonparametric run. Results are in current working directory. + # Use the timestamp to copy all newer files to the cacheName. + if errnum == 0: + files = os.listdir('.') + for f in files: + if os.path.getmtime(f) > self.start_time:" +832,https://:@github.com/tjstretchalot/ignite-simple.git,944f32fd5421cb01c0c75be5959277e1a1a2c741,"@@ -240,7 +240,7 @@ class ParamsTaskQueue(disp.TaskQueue, ps.SweepListener): + # remove from params_to_task + # add to in_progress + # return built disp.Task +- if cores > self.sweep_cores and self.sweeps: ++ if cores >= self.sweep_cores and self.sweeps: + swp: ParamsTask = self.sweeps.pop() + del self.params_to_sweeps_ind[swp.params] + self._len -= 1 +",ignite_simple/gen_sweep/sweeper.py,"ReplaceText(target='>=' @(243,17)->(243,18))","class ParamsTaskQueue(disp.TaskQueue, ps.SweepListener): + # remove from params_to_task + # add to in_progress + # return built disp.Task + if cores > self.sweep_cores and self.sweeps: + swp: ParamsTask = self.sweeps.pop() + del self.params_to_sweeps_ind[swp.params] + self._len -= 1","class ParamsTaskQueue(disp.TaskQueue, ps.SweepListener): + # remove from params_to_task + # add to in_progress + # return built disp.Task + if cores >= self.sweep_cores and self.sweeps: + swp: ParamsTask = self.sweeps.pop() + del self.params_to_sweeps_ind[swp.params] + self._len -= 1" +833,https://:@github.com/jessemyers/lxmlbind.git,35bb1bbc635ea9dca813dffe25165b14576c4a00,"@@ -75,7 +75,7 @@ class Base(object): + child = etree.SubElement(parent, head) + else: + return None +- return self.search(child, tail, create) if tail else child ++ return self.search(tail, child, create) if tail else child + + def __str__(self): + """""" +",lxmlbind/base.py,"ArgSwap(idxs=0<->1 @(78,15)->(78,26))","class Base(object): + child = etree.SubElement(parent, head) + else: + return None + return self.search(child, tail, create) if tail else child + + def __str__(self): + """"""","class Base(object): + child = etree.SubElement(parent, head) + else: + return None + return self.search(tail, child, create) if tail else child + + def __str__(self): + """"""" +834,https://:@github.com/dieterv/etk.docking.git,f7e423f2e5d2a68183238c2d1eb39dcb4cf7ec30,"@@ -521,7 +521,7 @@ class DockPaned(gtk.Container): + width = max(width, w) + height += h + # Store the minimum weight for usage in do_size_allocate +- item.min_size = w ++ item.min_size = h + + # Add handles + if self._orientation == gtk.ORIENTATION_HORIZONTAL: +",lib/etk/docking/dockpaned.py,"ReplaceText(target='h' @(524,32)->(524,33))","class DockPaned(gtk.Container): + width = max(width, w) + height += h + # Store the minimum weight for usage in do_size_allocate + item.min_size = w + + # Add handles + if self._orientation == gtk.ORIENTATION_HORIZONTAL:","class DockPaned(gtk.Container): + width = max(width, w) + height += h + # Store the minimum weight for usage in do_size_allocate + item.min_size = h + + # Add handles + if self._orientation == gtk.ORIENTATION_HORIZONTAL:" +835,https://:@github.com/isnok/asciidrumming.git,66e35371a4b96774d931516f7131e19ccf6e2c43,"@@ -42,7 +42,7 @@ def assemble_pieces(phrases, pieces): + def clean_phrases(phrases): + for phrase in phrases.values(): + phrase['pattern'] = ''.join(phrase['pattern']).replace(' ', '') +- phrase['length'] = (len(phrase['pattern']) // phrase['beat']) + bool(len(phrase['pattern']) % phrase['beat']) ++ phrase['length'] = (len(phrase['pattern']) / phrase['beat']) + bool(len(phrase['pattern']) % phrase['beat']) + + + def assemble_phrases(config): +",asciidrumming/assemble.py,"ReplaceText(target='/' @(45,51)->(45,53))","def assemble_pieces(phrases, pieces): + def clean_phrases(phrases): + for phrase in phrases.values(): + phrase['pattern'] = ''.join(phrase['pattern']).replace(' ', '') + phrase['length'] = (len(phrase['pattern']) // phrase['beat']) + bool(len(phrase['pattern']) % phrase['beat']) + + + def assemble_phrases(config):","def assemble_pieces(phrases, pieces): + def clean_phrases(phrases): + for phrase in phrases.values(): + phrase['pattern'] = ''.join(phrase['pattern']).replace(' ', '') + phrase['length'] = (len(phrase['pattern']) / phrase['beat']) + bool(len(phrase['pattern']) % phrase['beat']) + + + def assemble_phrases(config):" +836,https://:@github.com/FedericoCinus/WoMG.git,75addc91cd520c8e7ebf8975ceaf24b79b2cf49f,"@@ -390,7 +390,7 @@ class LDA(TLTTopicModel): + saved_model_fname = str(hash(saved_model))+'.model' + if os.path.exists(saved_model_fname): + #lda_model = pickle.load(os.path.abspath(saved_model)) +- lda_model = gensim.models.ldamodel.LdaModel.load(os.path.abspath(saved_model)) ++ lda_model = gensim.models.ldamodel.LdaModel.load(os.path.abspath(saved_model_fname)) + else: + lda_model = gensim.models.ldamodel.LdaModel(corpus=corpus, + id2word=self.dictionary, +",src/test_version/topic/lda.py,"ReplaceText(target='saved_model_fname' @(393,77)->(393,88))","class LDA(TLTTopicModel): + saved_model_fname = str(hash(saved_model))+'.model' + if os.path.exists(saved_model_fname): + #lda_model = pickle.load(os.path.abspath(saved_model)) + lda_model = gensim.models.ldamodel.LdaModel.load(os.path.abspath(saved_model)) + else: + lda_model = gensim.models.ldamodel.LdaModel(corpus=corpus, + id2word=self.dictionary,","class LDA(TLTTopicModel): + saved_model_fname = str(hash(saved_model))+'.model' + if os.path.exists(saved_model_fname): + #lda_model = pickle.load(os.path.abspath(saved_model)) + lda_model = gensim.models.ldamodel.LdaModel.load(os.path.abspath(saved_model_fname)) + else: + lda_model = gensim.models.ldamodel.LdaModel(corpus=corpus, + id2word=self.dictionary," +837,https://:@github.com/waikato-datamining/wai-annotations.git,1c1e29a44b802c45c83af7278b1637aa98855a68,"@@ -63,4 +63,4 @@ def get_all_sharded_filenames(filename: str) -> Tuple[str, ...]: + if shards == 0: + raise ValueError(f""{filename} is not a shard filename"") + +- return tuple(format_sharded_filename(base_name, shards, i) for i in range(index)) ++ return tuple(format_sharded_filename(base_name, shards, i) for i in range(shards)) +",src/wai/annotations/tf/utils/_sharded_filenames.py,"ReplaceText(target='shards' @(66,78)->(66,83))","def get_all_sharded_filenames(filename: str) -> Tuple[str, ...]: + if shards == 0: + raise ValueError(f""{filename} is not a shard filename"") + + return tuple(format_sharded_filename(base_name, shards, i) for i in range(index))","def get_all_sharded_filenames(filename: str) -> Tuple[str, ...]: + if shards == 0: + raise ValueError(f""{filename} is not a shard filename"") + + return tuple(format_sharded_filename(base_name, shards, i) for i in range(shards))" +838,https://:@github.com/broundal/Pytolemaic.git,c407b7b2410fe04641d0261ca209a2e57a728ded,"@@ -220,7 +220,7 @@ class SensitivityAnalysis(): + vulnerability_report = self._vulnerability_report( + shuffled_sensitivity=self.shuffled_sensitivity, + missing_sensitivity=self.missing_sensitivity, +- shuffled_sensitivity_stats=missing_stats_report) ++ shuffled_sensitivity_stats=shuffle_stats_report) + + return SensitivityFullReport( + shuffle_report=self.shuffled_sensitivity, +",pytolemaic/analysis_logic/model_analysis/sensitivity/sensitivity.py,"ReplaceText(target='shuffle_stats_report' @(223,39)->(223,59))","class SensitivityAnalysis(): + vulnerability_report = self._vulnerability_report( + shuffled_sensitivity=self.shuffled_sensitivity, + missing_sensitivity=self.missing_sensitivity, + shuffled_sensitivity_stats=missing_stats_report) + + return SensitivityFullReport( + shuffle_report=self.shuffled_sensitivity,","class SensitivityAnalysis(): + vulnerability_report = self._vulnerability_report( + shuffled_sensitivity=self.shuffled_sensitivity, + missing_sensitivity=self.missing_sensitivity, + shuffled_sensitivity_stats=shuffle_stats_report) + + return SensitivityFullReport( + shuffle_report=self.shuffled_sensitivity," +839,https://:@github.com/damoti/shipmaster.git,f81614acecb36da1343ec9e114679b06f0d8b0ba,"@@ -94,7 +94,7 @@ class LayerBase: + # Only tag image if container was built successfully. + repository, tag = self.image_name, None + if ':' in repository: +- repository, tag = tag.split(':') ++ repository, tag = repository.split(':') + conf = client.create_container_config(self.image_name, cmd, working_dir=APP_PATH) + client.commit(container, repository=repository, tag=tag, conf=conf) + client.remove_container(container) +",shipmaster/base/builder.py,"ReplaceText(target='repository' @(97,34)->(97,37))","class LayerBase: + # Only tag image if container was built successfully. + repository, tag = self.image_name, None + if ':' in repository: + repository, tag = tag.split(':') + conf = client.create_container_config(self.image_name, cmd, working_dir=APP_PATH) + client.commit(container, repository=repository, tag=tag, conf=conf) + client.remove_container(container)","class LayerBase: + # Only tag image if container was built successfully. + repository, tag = self.image_name, None + if ':' in repository: + repository, tag = repository.split(':') + conf = client.create_container_config(self.image_name, cmd, working_dir=APP_PATH) + client.commit(container, repository=repository, tag=tag, conf=conf) + client.remove_container(container)" +840,https://:@github.com/ldo/pybidi.git,ef93e8fdd0220fb446238060c7b4f30422251943,"@@ -1352,7 +1352,7 @@ def remove_bidi_marks(string, positions_to_this = None, position_from_this_list + if position_from_this_list != None : + c_position_from_this_list = seq_to_ct(position_from_this_list, FRIBIDI.StrIndex) + else : +- position_from_this_list = None ++ c_position_from_this_list = None + #end if + if embedding_levels != None : + c_embedding_levels = seq_to_ct(embedding_levels, FRIBIDI.StrIndex) +",fribidi.py,"ReplaceText(target='c_position_from_this_list' @(1355,8)->(1355,31))","def remove_bidi_marks(string, positions_to_this = None, position_from_this_list + if position_from_this_list != None : + c_position_from_this_list = seq_to_ct(position_from_this_list, FRIBIDI.StrIndex) + else : + position_from_this_list = None + #end if + if embedding_levels != None : + c_embedding_levels = seq_to_ct(embedding_levels, FRIBIDI.StrIndex)","def remove_bidi_marks(string, positions_to_this = None, position_from_this_list + if position_from_this_list != None : + c_position_from_this_list = seq_to_ct(position_from_this_list, FRIBIDI.StrIndex) + else : + c_position_from_this_list = None + #end if + if embedding_levels != None : + c_embedding_levels = seq_to_ct(embedding_levels, FRIBIDI.StrIndex)" +841,https://:@github.com/wbolster/cardinality.git,cfc729bc337f8d796d7bfe11a64ef3a3d516575b,"@@ -68,7 +68,7 @@ def between(min, max, iterable): + """""" + if min < 0: + raise ValueError(""'min' must be positive (or zero)"") +- if min < 0: ++ if max < 0: + raise ValueError(""'max' must be positive (or zero)"") + if min > max: + raise ValueError(""'max' must be greater or equal than 'min'"") +",cardinality.py,"ReplaceText(target='max' @(71,7)->(71,10))","def between(min, max, iterable): + """""" + if min < 0: + raise ValueError(""'min' must be positive (or zero)"") + if min < 0: + raise ValueError(""'max' must be positive (or zero)"") + if min > max: + raise ValueError(""'max' must be greater or equal than 'min'"")","def between(min, max, iterable): + """""" + if min < 0: + raise ValueError(""'min' must be positive (or zero)"") + if max < 0: + raise ValueError(""'max' must be positive (or zero)"") + if min > max: + raise ValueError(""'max' must be greater or equal than 'min'"")" +842,https://:@github.com/zongzhenh/pymysql-pool.git,66b07cdf844554245cf209a72de89bd17133269c,"@@ -169,7 +169,7 @@ class Pool(object): + if self.ping_check: + now = int(time()) + timeout = now +- if isinstance(int, self.ping_check): ++ if isinstance(self.ping_check, int): + timeout = timeout - self.ping_check + if not hasattr(c, '__ping_check_timestamp'): + c.__ping_check_timestamp = now +",pymysqlpool/pool.py,"ArgSwap(idxs=0<->1 @(172,15)->(172,25))","class Pool(object): + if self.ping_check: + now = int(time()) + timeout = now + if isinstance(int, self.ping_check): + timeout = timeout - self.ping_check + if not hasattr(c, '__ping_check_timestamp'): + c.__ping_check_timestamp = now","class Pool(object): + if self.ping_check: + now = int(time()) + timeout = now + if isinstance(self.ping_check, int): + timeout = timeout - self.ping_check + if not hasattr(c, '__ping_check_timestamp'): + c.__ping_check_timestamp = now" +843,https://:@github.com/kanzure/python-vba-wrapper.git,98edf03512c8f7960f10fa615867269cdf0821d6,"@@ -315,7 +315,7 @@ class VBA(object): + # 29 registers + buf = (ctypes.c_int32 * self.register_count)() + buf[:] = registers +- self._vba.set_registers(registers) ++ self._vba.set_registers(buf) + + def _get_max_save_size(self): + return self._vba.get_max_save_size() +",vba_wrapper/core.py,"ReplaceText(target='buf' @(318,32)->(318,41))","class VBA(object): + # 29 registers + buf = (ctypes.c_int32 * self.register_count)() + buf[:] = registers + self._vba.set_registers(registers) + + def _get_max_save_size(self): + return self._vba.get_max_save_size()","class VBA(object): + # 29 registers + buf = (ctypes.c_int32 * self.register_count)() + buf[:] = registers + self._vba.set_registers(buf) + + def _get_max_save_size(self): + return self._vba.get_max_save_size()" +844,https://:@github.com/severb/flowy.git,82cbab85d672880b7c3db69b5e1707e90da7686e,"@@ -191,7 +191,7 @@ class DecisionPoller(object): + elif e_type == 'StartChildWorkflowExecutionFailed': + SCWEFEA = 'startChildWorkflowExecutionFailedEventAttributes' + id = _subworkflow_id(e[SCWEFEA]['workflowId']) +- reason = e[SCWEIEA]['cause'] ++ reason = e[SCWEFEA]['cause'] + errors[id] = reason + elif e_type == 'TimerStarted': + id = e['timerStartedEventAttributes']['timerId'] +",flowy/swf/poller.py,"ReplaceText(target='SCWEFEA' @(194,27)->(194,34))","class DecisionPoller(object): + elif e_type == 'StartChildWorkflowExecutionFailed': + SCWEFEA = 'startChildWorkflowExecutionFailedEventAttributes' + id = _subworkflow_id(e[SCWEFEA]['workflowId']) + reason = e[SCWEIEA]['cause'] + errors[id] = reason + elif e_type == 'TimerStarted': + id = e['timerStartedEventAttributes']['timerId']","class DecisionPoller(object): + elif e_type == 'StartChildWorkflowExecutionFailed': + SCWEFEA = 'startChildWorkflowExecutionFailedEventAttributes' + id = _subworkflow_id(e[SCWEFEA]['workflowId']) + reason = e[SCWEFEA]['cause'] + errors[id] = reason + elif e_type == 'TimerStarted': + id = e['timerStartedEventAttributes']['timerId']" +845,https://:@github.com/brthor/codetransformer-py2.git,7c327683df810265d01a995d2704c9f8218b0ef7,"@@ -141,7 +141,7 @@ class Instruction(InstructionMeta._marker, metaclass=InstructionMeta): + 'little', + ) + +- yield cls(arg) ++ yield instr(arg) + + @classmethod + def from_opcode(cls, opcode): +",codetransformer/instructions.py,"ReplaceText(target='instr' @(144,18)->(144,21))","class Instruction(InstructionMeta._marker, metaclass=InstructionMeta): + 'little', + ) + + yield cls(arg) + + @classmethod + def from_opcode(cls, opcode):","class Instruction(InstructionMeta._marker, metaclass=InstructionMeta): + 'little', + ) + + yield instr(arg) + + @classmethod + def from_opcode(cls, opcode):" +846,https://:@github.com/bacadra/bacadra.git,74346189dfe3cac99821fd0a32ddeb3290886c4d,"@@ -1256,7 +1256,7 @@ class texme(TeXM, object, metaclass=texmemeta): + elif type(inherit)==str: + self.store(inherit, tex) + elif inherit is False: +- self.data = [tex + '\n%'] ++ self.data += [tex + '\n%'] + if self.echo: + print('[texme.' + name + ']\n' + tex) + +",bacadra/pinky/texme/texme.py,"ReplaceText(target='+=' @(1259,22)->(1259,23))","class texme(TeXM, object, metaclass=texmemeta): + elif type(inherit)==str: + self.store(inherit, tex) + elif inherit is False: + self.data = [tex + '\n%'] + if self.echo: + print('[texme.' + name + ']\n' + tex) + ","class texme(TeXM, object, metaclass=texmemeta): + elif type(inherit)==str: + self.store(inherit, tex) + elif inherit is False: + self.data += [tex + '\n%'] + if self.echo: + print('[texme.' + name + ']\n' + tex) + " +847,https://:@github.com/bacadra/bacadra.git,3e4cd62c6a0769ea886aaae2104aeb5dff18dbea,"@@ -1131,7 +1131,7 @@ class texme(metaclass=texmemeta): + + return self.add( + submodule = _name1, +- code = code, ++ code = tex, + inherit = inherit, + echo = echo, + ) +",bacadra/pinky/texme/texme.py,"ReplaceText(target='tex' @(1134,24)->(1134,28))","class texme(metaclass=texmemeta): + + return self.add( + submodule = _name1, + code = code, + inherit = inherit, + echo = echo, + )","class texme(metaclass=texmemeta): + + return self.add( + submodule = _name1, + code = tex, + inherit = inherit, + echo = echo, + )" +848,https://:@github.com/ulif/diceware-list.git,744223382d439315c8195d3ddff170e3542d80f0,"@@ -92,4 +92,4 @@ def local_android_download(request, monkeypatch, tmpdir): + monkeypatch.setattr( + ""diceware_list.libwordlist.AndroidWordList.base_url"", + fake_base_url) +- return dictfile ++ return tmpdir +",tests/conftest.py,"ReplaceText(target='tmpdir' @(95,11)->(95,19))","def local_android_download(request, monkeypatch, tmpdir): + monkeypatch.setattr( + ""diceware_list.libwordlist.AndroidWordList.base_url"", + fake_base_url) + return dictfile","def local_android_download(request, monkeypatch, tmpdir): + monkeypatch.setattr( + ""diceware_list.libwordlist.AndroidWordList.base_url"", + fake_base_url) + return tmpdir" +849,https://:@github.com/AeGean-Studio/pysolr_aio.git,056f4e2d4284fc740bcc7862fabab673ea1a439b,"@@ -747,7 +747,7 @@ class Solr(object): + m = force_unicode(m) + + end_time = time.time() +- se
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