kejian/codesearchnet-python-pep8-full · Datasets at Hugging Face

text stringlengths 75 104k	code_tokens sequence	avg_line_len float64 7.91 980	score float64 0 0.18
def save_group(self, group): """ Group was saved. """ # If group already exists, take over existing group rather then error. try: lgroup = self._get_group(group.name) changes = changeset(lgroup, {}) except ObjectDoesNotExist: lgroup = self._group_class() changes = changeset(lgroup, { 'cn': group.name, }) changes = changes.merge({ 'description': group.description }) save(changes, database=self._database)	[ "def", "save_group", "(", "self", ",", "group", ")", ":", "# If group already exists, take over existing group rather then error.", "try", ":", "lgroup", "=", "self", ".", "_get_group", "(", "group", ".", "name", ")", "changes", "=", "changeset", "(", "lgroup", ",", "{", "}", ")", "except", "ObjectDoesNotExist", ":", "lgroup", "=", "self", ".", "_group_class", "(", ")", "changes", "=", "changeset", "(", "lgroup", ",", "{", "'cn'", ":", "group", ".", "name", ",", "}", ")", "changes", "=", "changes", ".", "merge", "(", "{", "'description'", ":", "group", ".", "description", "}", ")", "save", "(", "changes", ",", "database", "=", "self", ".", "_database", ")" ]	33.5	0.00363
def get(self): """Gets the next item from the queue. Returns a Future that resolves to the next item once it is available. """ io_loop = IOLoop.current() new_get = Future() with self._lock: get, self._get = self._get, new_get answer = Future() def _on_node(future): if future.exception(): # pragma: no cover (never happens) return answer.set_exc_info(future.exc_info()) node = future.result() value = node.value new_hole, node.next = node.next, None new_get.set_result(new_hole) answer.set_result(value) def _on_get(future): if future.exception(): # pragma: no cover (never happens) return answer.set_exc_info(future.exc_info()) hole = future.result() io_loop.add_future(hole, _on_node) io_loop.add_future(get, _on_get) return answer	[ "def", "get", "(", "self", ")", ":", "io_loop", "=", "IOLoop", ".", "current", "(", ")", "new_get", "=", "Future", "(", ")", "with", "self", ".", "_lock", ":", "get", ",", "self", ".", "_get", "=", "self", ".", "_get", ",", "new_get", "answer", "=", "Future", "(", ")", "def", "_on_node", "(", "future", ")", ":", "if", "future", ".", "exception", "(", ")", ":", "# pragma: no cover (never happens)", "return", "answer", ".", "set_exc_info", "(", "future", ".", "exc_info", "(", ")", ")", "node", "=", "future", ".", "result", "(", ")", "value", "=", "node", ".", "value", "new_hole", ",", "node", ".", "next", "=", "node", ".", "next", ",", "None", "new_get", ".", "set_result", "(", "new_hole", ")", "answer", ".", "set_result", "(", "value", ")", "def", "_on_get", "(", "future", ")", ":", "if", "future", ".", "exception", "(", ")", ":", "# pragma: no cover (never happens)", "return", "answer", ".", "set_exc_info", "(", "future", ".", "exc_info", "(", ")", ")", "hole", "=", "future", ".", "result", "(", ")", "io_loop", ".", "add_future", "(", "hole", ",", "_on_node", ")", "io_loop", ".", "add_future", "(", "get", ",", "_on_get", ")", "return", "answer" ]	29.75	0.002035
def structure(self, obj, cl): # type: (Any, Type[T]) -> T """Convert unstructured Python data structures to structured data.""" return self._structure_func.dispatch(cl)(obj, cl)	[ "def", "structure", "(", "self", ",", "obj", ",", "cl", ")", ":", "# type: (Any, Type[T]) -> T", "return", "self", ".", "_structure_func", ".", "dispatch", "(", "cl", ")", "(", "obj", ",", "cl", ")" ]	39.6	0.014851
def file_to_str(fname): """ Read a file into a string PRE: fname is a small file (to avoid hogging memory and its discontents) """ data = None # rU = read with Universal line terminator with open(fname, 'rU') as fd: data = fd.read() return data	[ "def", "file_to_str", "(", "fname", ")", ":", "data", "=", "None", "# rU = read with Universal line terminator", "with", "open", "(", "fname", ",", "'rU'", ")", "as", "fd", ":", "data", "=", "fd", ".", "read", "(", ")", "return", "data" ]	27.5	0.003521
def round_to_x_digits(number, digits): """ Returns 'number' rounded to 'digits' digits. """ return round(number * math.pow(10, digits)) / math.pow(10, digits)	[ "def", "round_to_x_digits", "(", "number", ",", "digits", ")", ":", "return", "round", "(", "number", "*", "math", ".", "pow", "(", "10", ",", "digits", ")", ")", "/", "math", ".", "pow", "(", "10", ",", "digits", ")" ]	34	0.005747
def get_sdc_by_name(self, name): """ Get ScaleIO SDC object by its name :param name: Name of SDC :return: ScaleIO SDC object :raise KeyError: No SDC with specified name found :rtype: SDC object """ for sdc in self.sdc: if sdc.name == name: return sdc raise KeyError("SDC of that name not found")	[ "def", "get_sdc_by_name", "(", "self", ",", "name", ")", ":", "for", "sdc", "in", "self", ".", "sdc", ":", "if", "sdc", ".", "name", "==", "name", ":", "return", "sdc", "raise", "KeyError", "(", "\"SDC of that name not found\"", ")" ]	32	0.005063
def _parse_impute2_line(self, line): """Parses the current IMPUTE2 line (a single variant). Args: line (str): An IMPUTE2 line. Returns: Genotypes: The genotype in dosage format. Warning ======= By default, the genotypes object has multiallelic set to False. """ # Splitting row = line.rstrip("\r\n").split(" ") # Constructing the probabilities prob = np.array(row[5:], dtype=float) prob.shape = (prob.shape[0] // 3, 3) # Constructing the dosage dosage = 2 * prob[:, 2] + prob[:, 1] if self.prob_t > 0: dosage[~np.any(prob >= self.prob_t, axis=1)] = np.nan return Genotypes( Variant(row[1], CHROM_STR_ENCODE.get(row[0], row[0]), int(row[2]), [row[3], row[4]]), dosage, reference=row[3], coded=row[4], multiallelic=False, )	[ "def", "_parse_impute2_line", "(", "self", ",", "line", ")", ":", "# Splitting", "row", "=", "line", ".", "rstrip", "(", "\"\\r\\n\"", ")", ".", "split", "(", "\" \"", ")", "# Constructing the probabilities", "prob", "=", "np", ".", "array", "(", "row", "[", "5", ":", "]", ",", "dtype", "=", "float", ")", "prob", ".", "shape", "=", "(", "prob", ".", "shape", "[", "0", "]", "//", "3", ",", "3", ")", "# Constructing the dosage", "dosage", "=", "2", "*", "prob", "[", ":", ",", "2", "]", "+", "prob", "[", ":", ",", "1", "]", "if", "self", ".", "prob_t", ">", "0", ":", "dosage", "[", "~", "np", ".", "any", "(", "prob", ">=", "self", ".", "prob_t", ",", "axis", "=", "1", ")", "]", "=", "np", ".", "nan", "return", "Genotypes", "(", "Variant", "(", "row", "[", "1", "]", ",", "CHROM_STR_ENCODE", ".", "get", "(", "row", "[", "0", "]", ",", "row", "[", "0", "]", ")", ",", "int", "(", "row", "[", "2", "]", ")", ",", "[", "row", "[", "3", "]", ",", "row", "[", "4", "]", "]", ")", ",", "dosage", ",", "reference", "=", "row", "[", "3", "]", ",", "coded", "=", "row", "[", "4", "]", ",", "multiallelic", "=", "False", ",", ")" ]	27.970588	0.002033
def _seed(self, seed=-1): """ Initialize the random seed """ if seed != -1: self.random = NupicRandom(seed) else: self.random = NupicRandom()	[ "def", "_seed", "(", "self", ",", "seed", "=", "-", "1", ")", ":", "if", "seed", "!=", "-", "1", ":", "self", ".", "random", "=", "NupicRandom", "(", "seed", ")", "else", ":", "self", ".", "random", "=", "NupicRandom", "(", ")" ]	20.75	0.017341
def fail(self, tup): """Indicate that processing of a Tuple has failed. :param tup: the Tuple to fail (its ``id`` if ``str``). :type tup: :class:`str` or :class:`pystorm.component.Tuple` """ tup_id = tup.id if isinstance(tup, Tuple) else tup self.send_message({"command": "fail", "id": tup_id})	[ "def", "fail", "(", "self", ",", "tup", ")", ":", "tup_id", "=", "tup", ".", "id", "if", "isinstance", "(", "tup", ",", "Tuple", ")", "else", "tup", "self", ".", "send_message", "(", "{", "\"command\"", ":", "\"fail\"", ",", "\"id\"", ":", "tup_id", "}", ")" ]	42	0.005831
def _oct_to_dec(ip, check=True): """Octal to decimal conversion.""" if check and not is_oct(ip): raise ValueError('_oct_to_dec: invalid IP: "%s"' % ip) if isinstance(ip, int): ip = oct(ip) return int(str(ip), 8)	[ "def", "_oct_to_dec", "(", "ip", ",", "check", "=", "True", ")", ":", "if", "check", "and", "not", "is_oct", "(", "ip", ")", ":", "raise", "ValueError", "(", "'_oct_to_dec: invalid IP: \"%s\"'", "%", "ip", ")", "if", "isinstance", "(", "ip", ",", "int", ")", ":", "ip", "=", "oct", "(", "ip", ")", "return", "int", "(", "str", "(", "ip", ")", ",", "8", ")" ]	33.857143	0.004115
def resizeEvent(self, event): """ Handles a resize event for this overlay, centering the central widget if one is found. :param event \| <QtCore.QEvent> """ super(XOverlayWidget, self).resizeEvent(event) self.adjustSize()	[ "def", "resizeEvent", "(", "self", ",", "event", ")", ":", "super", "(", "XOverlayWidget", ",", "self", ")", ".", "resizeEvent", "(", "event", ")", "self", ".", "adjustSize", "(", ")" ]	30.444444	0.010638
def _get_layout_as_etree(layout_dict): """ Convert something that looks like this: { 'color' : ['red'], 'shapefile' : ['blah.shp'] } Into something that looks like this: <layout> <item> <name>color</name> <value>red</value> </item> <item> <name>shapefile</name> <value>blah.shp</value> </item> </layout> """ if layout_dict is None: return None layout = etree.Element("layout") layout_dict = eval(layout_dict) for k, v in layout_dict.items(): item = etree.SubElement(layout, "item") name = etree.SubElement(item, "name") name.text = k value = etree.SubElement(item, "value") value.text = str(v) return layout	[ "def", "_get_layout_as_etree", "(", "layout_dict", ")", ":", "if", "layout_dict", "is", "None", ":", "return", "None", "layout", "=", "etree", ".", "Element", "(", "\"layout\"", ")", "layout_dict", "=", "eval", "(", "layout_dict", ")", "for", "k", ",", "v", "in", "layout_dict", ".", "items", "(", ")", ":", "item", "=", "etree", ".", "SubElement", "(", "layout", ",", "\"item\"", ")", "name", "=", "etree", ".", "SubElement", "(", "item", ",", "\"name\"", ")", "name", ".", "text", "=", "k", "value", "=", "etree", ".", "SubElement", "(", "item", ",", "\"value\"", ")", "value", ".", "text", "=", "str", "(", "v", ")", "return", "layout" ]	23.454545	0.001241
def init(self): """ Adds custom calculations to orbit simulation. This routine is run once, and only once, upon instantiation. Adds quasi-dipole coordiantes, velocity calculation in ECEF coords, adds the attitude vectors of spacecraft assuming x is ram pointing and z is generally nadir, adds ionospheric parameters from the Interational Reference Ionosphere (IRI), as well as simulated winds from the Horiontal Wind Model (HWM). """ self.custom.add(add_quasi_dipole_coordinates, 'modify') self.custom.add(add_aacgm_coordinates, 'modify') self.custom.add(calculate_ecef_velocity, 'modify') self.custom.add(add_sc_attitude_vectors, 'modify') self.custom.add(add_iri_thermal_plasma, 'modify') self.custom.add(add_hwm_winds_and_ecef_vectors, 'modify') self.custom.add(add_igrf, 'modify') # project simulated vectors onto s/c basis # IGRF # create metadata to be added along with vector projection in_meta = {'desc':'IGRF geomagnetic field expressed in the s/c basis.', 'units':'nT'} # project IGRF self.custom.add(project_ecef_vector_onto_sc, 'modify', 'end', 'B_ecef_x', 'B_ecef_y', 'B_ecef_z', 'B_sc_x', 'B_sc_y', 'B_sc_z', meta=[in_meta.copy(), in_meta.copy(), in_meta.copy()]) # project total wind vector self.custom.add(project_hwm_onto_sc, 'modify') # neutral parameters self.custom.add(add_msis, 'modify')	[ "def", "init", "(", "self", ")", ":", "self", ".", "custom", ".", "add", "(", "add_quasi_dipole_coordinates", ",", "'modify'", ")", "self", ".", "custom", ".", "add", "(", "add_aacgm_coordinates", ",", "'modify'", ")", "self", ".", "custom", ".", "add", "(", "calculate_ecef_velocity", ",", "'modify'", ")", "self", ".", "custom", ".", "add", "(", "add_sc_attitude_vectors", ",", "'modify'", ")", "self", ".", "custom", ".", "add", "(", "add_iri_thermal_plasma", ",", "'modify'", ")", "self", ".", "custom", ".", "add", "(", "add_hwm_winds_and_ecef_vectors", ",", "'modify'", ")", "self", ".", "custom", ".", "add", "(", "add_igrf", ",", "'modify'", ")", "# project simulated vectors onto s/c basis", "# IGRF", "# create metadata to be added along with vector projection", "in_meta", "=", "{", "'desc'", ":", "'IGRF geomagnetic field expressed in the s/c basis.'", ",", "'units'", ":", "'nT'", "}", "# project IGRF", "self", ".", "custom", ".", "add", "(", "project_ecef_vector_onto_sc", ",", "'modify'", ",", "'end'", ",", "'B_ecef_x'", ",", "'B_ecef_y'", ",", "'B_ecef_z'", ",", "'B_sc_x'", ",", "'B_sc_y'", ",", "'B_sc_z'", ",", "meta", "=", "[", "in_meta", ".", "copy", "(", ")", ",", "in_meta", ".", "copy", "(", ")", ",", "in_meta", ".", "copy", "(", ")", "]", ")", "# project total wind vector", "self", ".", "custom", ".", "add", "(", "project_hwm_onto_sc", ",", "'modify'", ")", "# neutral parameters", "self", ".", "custom", ".", "add", "(", "add_msis", ",", "'modify'", ")" ]	46.333333	0.005766
def active_language(self): """ Returns active language. """ # Current instance language (if user uses activate_language() method) if self._language is not None: return self._language # Current site language (translation.get_language()) current = utils.get_language() if current in self.supported_languages: return current # Default language descriptor return self.default_language	[ "def", "active_language", "(", "self", ")", ":", "# Current instance language (if user uses activate_language() method)", "if", "self", ".", "_language", "is", "not", "None", ":", "return", "self", ".", "_language", "# Current site language (translation.get_language())", "current", "=", "utils", ".", "get_language", "(", ")", "if", "current", "in", "self", ".", "supported_languages", ":", "return", "current", "# Default language descriptor", "return", "self", ".", "default_language" ]	31.466667	0.004115

def save_group(self, group): """ Group was saved. """ # If group already exists, take over existing group rather then error. try: lgroup = self._get_group(group.name) changes = changeset(lgroup, {}) except ObjectDoesNotExist: lgroup = self._group_class() changes = changeset(lgroup, { 'cn': group.name, }) changes = changes.merge({ 'description': group.description }) save(changes, database=self._database)

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def get(self): """Gets the next item from the queue. Returns a Future that resolves to the next item once it is available. """ io_loop = IOLoop.current() new_get = Future() with self._lock: get, self._get = self._get, new_get answer = Future() def _on_node(future): if future.exception(): # pragma: no cover (never happens) return answer.set_exc_info(future.exc_info()) node = future.result() value = node.value new_hole, node.next = node.next, None new_get.set_result(new_hole) answer.set_result(value) def _on_get(future): if future.exception(): # pragma: no cover (never happens) return answer.set_exc_info(future.exc_info()) hole = future.result() io_loop.add_future(hole, _on_node) io_loop.add_future(get, _on_get) return answer

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def structure(self, obj, cl): # type: (Any, Type[T]) -> T """Convert unstructured Python data structures to structured data.""" return self._structure_func.dispatch(cl)(obj, cl)

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def file_to_str(fname): """ Read a file into a string PRE: fname is a small file (to avoid hogging memory and its discontents) """ data = None # rU = read with Universal line terminator with open(fname, 'rU') as fd: data = fd.read() return data

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def round_to_x_digits(number, digits): """ Returns 'number' rounded to 'digits' digits. """ return round(number * math.pow(10, digits)) / math.pow(10, digits)

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def get_sdc_by_name(self, name): """ Get ScaleIO SDC object by its name :param name: Name of SDC :return: ScaleIO SDC object :raise KeyError: No SDC with specified name found :rtype: SDC object """ for sdc in self.sdc: if sdc.name == name: return sdc raise KeyError("SDC of that name not found")

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def _parse_impute2_line(self, line): """Parses the current IMPUTE2 line (a single variant). Args: line (str): An IMPUTE2 line. Returns: Genotypes: The genotype in dosage format. Warning ======= By default, the genotypes object has multiallelic set to False. """ # Splitting row = line.rstrip("\r\n").split(" ") # Constructing the probabilities prob = np.array(row[5:], dtype=float) prob.shape = (prob.shape[0] // 3, 3) # Constructing the dosage dosage = 2 * prob[:, 2] + prob[:, 1] if self.prob_t > 0: dosage[~np.any(prob >= self.prob_t, axis=1)] = np.nan return Genotypes( Variant(row[1], CHROM_STR_ENCODE.get(row[0], row[0]), int(row[2]), [row[3], row[4]]), dosage, reference=row[3], coded=row[4], multiallelic=False, )

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def _seed(self, seed=-1): """ Initialize the random seed """ if seed != -1: self.random = NupicRandom(seed) else: self.random = NupicRandom()

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def fail(self, tup): """Indicate that processing of a Tuple has failed. :param tup: the Tuple to fail (its ``id`` if ``str``). :type tup: :class:`str` or :class:`pystorm.component.Tuple` """ tup_id = tup.id if isinstance(tup, Tuple) else tup self.send_message({"command": "fail", "id": tup_id})

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def _oct_to_dec(ip, check=True): """Octal to decimal conversion.""" if check and not is_oct(ip): raise ValueError('_oct_to_dec: invalid IP: "%s"' % ip) if isinstance(ip, int): ip = oct(ip) return int(str(ip), 8)

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def resizeEvent(self, event): """ Handles a resize event for this overlay, centering the central widget if one is found. :param event | <QtCore.QEvent> """ super(XOverlayWidget, self).resizeEvent(event) self.adjustSize()

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def _get_layout_as_etree(layout_dict): """ Convert something that looks like this: { 'color' : ['red'], 'shapefile' : ['blah.shp'] } Into something that looks like this: <layout> <item> <name>color</name> <value>red</value> </item> <item> <name>shapefile</name> <value>blah.shp</value> </item> </layout> """ if layout_dict is None: return None layout = etree.Element("layout") layout_dict = eval(layout_dict) for k, v in layout_dict.items(): item = etree.SubElement(layout, "item") name = etree.SubElement(item, "name") name.text = k value = etree.SubElement(item, "value") value.text = str(v) return layout

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23.454545

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def init(self): """ Adds custom calculations to orbit simulation. This routine is run once, and only once, upon instantiation. Adds quasi-dipole coordiantes, velocity calculation in ECEF coords, adds the attitude vectors of spacecraft assuming x is ram pointing and z is generally nadir, adds ionospheric parameters from the Interational Reference Ionosphere (IRI), as well as simulated winds from the Horiontal Wind Model (HWM). """ self.custom.add(add_quasi_dipole_coordinates, 'modify') self.custom.add(add_aacgm_coordinates, 'modify') self.custom.add(calculate_ecef_velocity, 'modify') self.custom.add(add_sc_attitude_vectors, 'modify') self.custom.add(add_iri_thermal_plasma, 'modify') self.custom.add(add_hwm_winds_and_ecef_vectors, 'modify') self.custom.add(add_igrf, 'modify') # project simulated vectors onto s/c basis # IGRF # create metadata to be added along with vector projection in_meta = {'desc':'IGRF geomagnetic field expressed in the s/c basis.', 'units':'nT'} # project IGRF self.custom.add(project_ecef_vector_onto_sc, 'modify', 'end', 'B_ecef_x', 'B_ecef_y', 'B_ecef_z', 'B_sc_x', 'B_sc_y', 'B_sc_z', meta=[in_meta.copy(), in_meta.copy(), in_meta.copy()]) # project total wind vector self.custom.add(project_hwm_onto_sc, 'modify') # neutral parameters self.custom.add(add_msis, 'modify')

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46.333333

0.005766

def active_language(self): """ Returns active language. """ # Current instance language (if user uses activate_language() method) if self._language is not None: return self._language # Current site language (translation.get_language()) current = utils.get_language() if current in self.supported_languages: return current # Default language descriptor return self.default_language

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31.466667

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