gurudesh/pytracebugs huggingface dataset:
# Buggy code
def createSaxChildren(self, sax_node, parent_v):
    """Create vnodes for all children in sax_node.children."""
    children = []
    for sax_child in sax_node.children:
        tnx = sax_child.tnx
        v = self.gnxDict.get(tnx)
        if v:  # A clone. Don't look at the children.
            ### v = self.createSaxVnode(sax_child, parent_v, v=v)
            self.updateSaxClone(sax_child, parent_v, v)
        else:
            v = self.createSaxVnode(sax_child, parent_v)
            self.createSaxChildren(sax_child, v)
        children.append(v)
    parent_v.children = children
    for child in children:
        child.parents.append(parent_v)
    return children


# Traceback (ValueError)
Traceback (most recent call last):

File "/pri/git/leo-editor/leo/core/leoCommands.py", line 2016, in executeAnyCommand
return command(event)

File "/pri/git/leo-editor/leo/core/leoGlobals.py", line 2445, in commander_command_wrapper
method(event=event)

File "/pri/git/leo-editor/leo/commands/commanderOutlineCommands.py", line 1390, in promote
p.promote()

File "/pri/git/leo-editor/leo/core/leoNodes.py", line 1596, in promote
child.parents.remove(p.v)

ValueError: list.remove(x): x not in list

# Fixed code
def createSaxChildren(self, sax_node, parent_v):
    """Create vnodes for all children in sax_node.children."""
    children = []
    for sax_child in sax_node.children:
        tnx = sax_child.tnx
        v = self.gnxDict.get(tnx)
        if v:  # A clone. Don't look at the children.
            self.updateSaxClone(sax_child, parent_v, v)
        else:
            v = self.createSaxVnode(sax_child, parent_v)
            self.createSaxChildren(sax_child, v)
        children.append(v)
    parent_v.children = children
    for child in children:
        child.parents.append(parent_v)
    return children
# Buggy code
def updateSaxClone(self, sax_node, parent_v, v):
    """
    Update the body text of v. It overrides any previous body text.
    """
    c = self.c
    at = c.atFileCommands
    b = sax_node.bodyString
    if v.b != b:
        v.setBodyString(b)
        at.bodySetInited(v)


# Traceback (ValueError)
Traceback (most recent call last):

File "/pri/git/leo-editor/leo/core/leoCommands.py", line 2016, in executeAnyCommand
return command(event)

File "/pri/git/leo-editor/leo/core/leoGlobals.py", line 2445, in commander_command_wrapper
method(event=event)

File "/pri/git/leo-editor/leo/commands/commanderOutlineCommands.py", line 1390, in promote
p.promote()

File "/pri/git/leo-editor/leo/core/leoNodes.py", line 1596, in promote
child.parents.remove(p.v)

ValueError: list.remove(x): x not in list

# Fixed code
def updateSaxClone(self, sax_node, parent_v, v):
    """
    Update the body text of v. It overrides any previous body text.
    """
    at = self.c.atFileCommands
    b = sax_node.bodyString
    if v.b != b:
        v.setBodyString(b)
        at.bodySetInited(v)
# Buggy code
def get_semver(tag):
    """Return 'Semantic Version' from tag string"""
    try:
        version = semantic_version.Version.coerce(tag, partial=True)
        # tuple of major, minor, build, pre-release, patch
        # 5.6b2 --> 5.6-b2
    except ValueError:
        print(
            """*** Failed to parse Semantic Version from git tag '{0}'.
        Expecting tag name like '5.7b2', 'leo-4.9.12', 'v4.3' for releases.
        This version can't be uploaded to PyPi.org.""".format(tag)
        )
        version = tag
    return version


# Traceback (TypeError)
pip install --upgrade https://github.com/leo-editor/leo-editor/archive/5.7b2.zip
Collecting https://github.com/leo-editor/leo-editor/archive/5.7b2.zip
Downloading https://github.com/leo-editor/leo-editor/archive/5.7b2.zip
\ 11.4MB 4.9MB/s
Complete output from command python setup.py egg_info:
Removing build and dist directories
execGitCommand not found: C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\.git
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\setup.py", line 115, in <module>
version=git_version(__file__),
File "C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\setup.py", line 30, in git_version
tag, distance, commit = g.gitDescribe(root)
File "C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\leo\core\leoGlobals.py", line 4468, in gitDescribe
tag, distance, commit = describe[0].rsplit('-',2)
TypeError: 'NoneType' object is not subscriptable

# Fixed code
def get_semver(tag):
    """Return 'Semantic Version' from tag string"""
    try:
        version = str(semantic_version.Version.coerce(tag, partial=True))
        # tuple of major, minor, build, pre-release, patch
        # 5.6b2 --> 5.6-b2
    except ValueError:
        print(
            """*** Failed to parse Semantic Version from git tag '{0}'.
        Expecting tag name like '5.7b2', 'leo-4.9.12', 'v4.3' for releases.
        This version can't be uploaded to PyPi.org.""".format(tag)
        )
        version = tag
    return version
# Buggy code
def git_version(file):
    """Fetch from Git: {tag} {distance-from-tag} {current commit hash}
    Return as semantic version string compliant with PEP440"""
    root = os.path.dirname(os.path.realpath(file))
    tag, distance, commit = g.gitDescribe(root)
    # 5.6b2, 55, e1129da
    ctag = clean_git_tag(tag)
    try:
        version = semantic_version.Version.coerce(ctag, partial=True)
        # tuple of major, minor, build, pre-release, patch
        # 5.6b2 --> 5.6-b2
    except ValueError:
        print(
            """*** Failed to parse Semantic Version from git tag '{0}'.
        Expecting tag name like '5.7b2', 'leo-4.9.12', 'v4.3' for releases.
        This version can't be uploaded to PyPi.org.""".format(tag)
        )
        version = tag
    if int(distance) > 0:
        version = "{}-dev{}".format(version, distance)
    return version


# Traceback (TypeError)
pip install --upgrade https://github.com/leo-editor/leo-editor/archive/5.7b2.zip
Collecting https://github.com/leo-editor/leo-editor/archive/5.7b2.zip
Downloading https://github.com/leo-editor/leo-editor/archive/5.7b2.zip
\ 11.4MB 4.9MB/s
Complete output from command python setup.py egg_info:
Removing build and dist directories
execGitCommand not found: C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\.git
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\setup.py", line 115, in <module>
version=git_version(__file__),
File "C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\setup.py", line 30, in git_version
tag, distance, commit = g.gitDescribe(root)
File "C:\Users\mattw\AppData\Local\Temp\pip-usj2xnee-build\leo\core\leoGlobals.py", line 4468, in gitDescribe
tag, distance, commit = describe[0].rsplit('-',2)
TypeError: 'NoneType' object is not subscriptable

# Fixed code
def git_version(file):
    """Fetch from Git: {tag} {distance-from-tag} {current commit hash}
    Return as semantic version string compliant with PEP440"""
    root = os.path.dirname(os.path.realpath(file))
    tag, distance, commit = g.gitDescribe(root)
    # 5.6b2, 55, e1129da
    ctag = clean_git_tag(tag)
    version = get_semver(ctag)
    if int(distance) > 0:
        version = "{}-dev{}".format(version, distance)
    return version
# Buggy code
def put_help(self, c, s, short_title=""):
    """Put the help command."""
    s = g.adjustTripleString(s.rstrip(), c.tab_width)
    if s.startswith("<") and not s.startswith("<<"):
        pass  # how to do selective replace??
    pc = g.app.pluginsController
    table = (
        "viewrendered3.py",
        "viewrendered2.py",
        "viewrendered.py",
    )
    for name in table:
        if pc.isLoaded(name):
            vr = pc.loadOnePlugin(name)
            break
    else:
        vr = pc.loadOnePlugin("viewrendered.py")
    if vr:
        kw = {
            "c": c,
            "flags": "rst",
            "kind": "rst",
            "label": "",
            "msg": s,
            "name": "Apropos",
            "short_title": short_title,
            "title": "",
        }
        vr.show_scrolled_message(tag="Apropos", kw=kw)
        c.bodyWantsFocus()
        if g.unitTesting:
            vr.close_rendering_pane(event={"c": c})
    elif g.unitTesting:
        pass
    else:
        g.es(s)
    return vr  # For unit tests


# Traceback (NameError)
Traceback (most recent call last):
File "c:\leo.repo\leo-editor\leo\core\leoGlobals.py", line 2385, in new_cmd_wrapper
func(self, event=event)
File "c:\leo.repo\leo-editor\leo\commands\helpCommands.py", line 62, in help
self.c.putHelpFor(rst_s)
File "c:\leo.repo\leo-editor\leo\core\leoCommands.py", line 2322, in putHelpFor
g.app.gui.put_help(c, s, short_title)
File "c:\leo.repo\leo-editor\leo\plugins\qt_gui.py", line 1055, in put_help
vr.show_scrolled_message(tag='Apropos', kw=kw)
File "c:\leo.repo\leo-editor\leo\plugins\viewrendered2.py", line 299, in show_scrolled_message
vr = viewrendered(event=kw)
NameError: name 'viewrendered' is not defined

# Fixed code
def put_help(self, c, s, short_title=""):
    """Put the help command."""
    trace = False and not g.unitTesting
    s = g.adjustTripleString(s.rstrip(), c.tab_width)
    if s.startswith("<") and not s.startswith("<<"):
        pass  # how to do selective replace??
    pc = g.app.pluginsController
    table = (
        "viewrendered3.py",
        "viewrendered2.py",
        "viewrendered.py",
    )
    for name in table:
        if pc.isLoaded(name):
            if trace:
                g.trace("already loaded", name)
            vr = pc.loadOnePlugin(name)
            break
    else:
        if trace:
            g.trace("auto-loading viewrendered.py")
        vr = pc.loadOnePlugin("viewrendered.py")
    if vr:
        kw = {
            "c": c,
            "flags": "rst",
            "kind": "rst",
            "label": "",
            "msg": s,
            "name": "Apropos",
            "short_title": short_title,
            "title": "",
        }
        vr.show_scrolled_message(tag="Apropos", kw=kw)
        c.bodyWantsFocus()
        if g.unitTesting:
            vr.close_rendering_pane(event={"c": c})
    elif g.unitTesting:
        pass
    else:
        g.es(s)
    return vr  # For unit tests
# Buggy code
def init():
    """Return True if the plugin has loaded successfully."""
    global got_docutils
    if not got_docutils:
        g.es_print("Warning: viewrendered2.py running without docutils.")
    g.plugin_signon(__name__)
    g.registerHandler("after-create-leo-frame", onCreate)
    g.registerHandler("scrolledMessage", show_scrolled_message)
    return True


# Traceback (NameError)
Traceback (most recent call last):
File "c:\leo.repo\leo-editor\leo\core\leoGlobals.py", line 2385, in new_cmd_wrapper
func(self, event=event)
File "c:\leo.repo\leo-editor\leo\commands\helpCommands.py", line 62, in help
self.c.putHelpFor(rst_s)
File "c:\leo.repo\leo-editor\leo\core\leoCommands.py", line 2322, in putHelpFor
g.app.gui.put_help(c, s, short_title)
File "c:\leo.repo\leo-editor\leo\plugins\qt_gui.py", line 1055, in put_help
vr.show_scrolled_message(tag='Apropos', kw=kw)
File "c:\leo.repo\leo-editor\leo\plugins\viewrendered2.py", line 299, in show_scrolled_message
vr = viewrendered(event=kw)
NameError: name 'viewrendered' is not defined

# Fixed code
def init():
    """Return True if the plugin has loaded successfully."""
    if import_ok:  # Fix #734.
        global got_docutils
        if not got_docutils:
            g.es_print("Warning: viewrendered2.py running without docutils.")
        g.plugin_signon(__name__)
        g.registerHandler("after-create-leo-frame", onCreate)
        g.registerHandler("scrolledMessage", show_scrolled_message)
        return True
    return False
# Buggy code
def init():
    """Return True if the plugin has loaded successfully."""
    if import_ok:  # Fix #734.
        global got_docutils
        if not got_docutils:
            g.es_print("Warning: viewrendered2.py running without docutils.")
        g.plugin_signon(__name__)
        g.registerHandler("after-create-leo-frame", onCreate)
        g.registerHandler("scrolledMessage", show_scrolled_message)
        return True
    return False


# Traceback (NameError)
Traceback (most recent call last):
File "c:\leo.repo\leo-editor\leo\core\leoGlobals.py", line 2385, in new_cmd_wrapper
func(self, event=event)
File "c:\leo.repo\leo-editor\leo\commands\helpCommands.py", line 62, in help
self.c.putHelpFor(rst_s)
File "c:\leo.repo\leo-editor\leo\core\leoCommands.py", line 2322, in putHelpFor
g.app.gui.put_help(c, s, short_title)
File "c:\leo.repo\leo-editor\leo\plugins\qt_gui.py", line 1055, in put_help
vr.show_scrolled_message(tag='Apropos', kw=kw)
File "c:\leo.repo\leo-editor\leo\plugins\viewrendered2.py", line 299, in show_scrolled_message
vr = viewrendered(event=kw)
NameError: name 'viewrendered' is not defined

# Fixed code
def init():
    """Return True if the plugin has loaded successfully."""
    global got_docutils
    if import_ok:  # Fix #734.
        if not got_docutils:
            g.es_print("Warning: viewrendered2.py running without docutils.")
        g.plugin_signon(__name__)
        g.registerHandler("after-create-leo-frame", onCreate)
        g.registerHandler("scrolledMessage", show_scrolled_message)
        return True
    return False
# Buggy code
def getUIconfig(self):
    """Get the rendering configuration from the GUI controls."""
    # Pull internal configuration options from GUI
    self.verbose = self.verbose_mode_action.isChecked()
    # self.output = 'html'
    self.tree = self.tree_mode_action.isChecked()
    self.execcode = self.execute_code_action.isChecked()
    # If executing code, don't allow auto-mode otherwise navigation
    # can lead to getting stuck doing many recalculations
    if self.execcode:
        self.auto_mode_action.setChecked(False)
    self.auto = self.auto_mode_action.isChecked()
    self.lock_mode = self.lock_mode_action.isChecked()
    self.slideshow = self.slideshow_mode_action.isChecked()
    self.showcode = self.visible_code_action.isChecked()
    self.restoutput = self.reST_code_action.isChecked()


# Traceback (NameError)
Traceback (most recent call last):
File "c:\leo.repo\leo-editor\leo\core\leoGlobals.py", line 2385, in new_cmd_wrapper
func(self, event=event)
File "c:\leo.repo\leo-editor\leo\commands\helpCommands.py", line 62, in help
self.c.putHelpFor(rst_s)
File "c:\leo.repo\leo-editor\leo\core\leoCommands.py", line 2322, in putHelpFor
g.app.gui.put_help(c, s, short_title)
File "c:\leo.repo\leo-editor\leo\plugins\qt_gui.py", line 1055, in put_help
vr.show_scrolled_message(tag='Apropos', kw=kw)
File "c:\leo.repo\leo-editor\leo\plugins\viewrendered2.py", line 299, in show_scrolled_message
vr = viewrendered(event=kw)
NameError: name 'viewrendered' is not defined

# Fixed code
def getUIconfig(self):
    """Get the rendering configuration from the GUI controls."""
    # Pull internal configuration options from GUI
    self.verbose = self.verbose_mode_action.isChecked()
    # self.output = 'html'
    self.tree = self.tree_mode_action.isChecked()
    self.execcode = self.execute_code_action.isChecked()
    # If executing code, don't allow auto-mode otherwise navigation
    # can lead to getting stuck doing many recalculations
    if self.execcode:
        self.auto_mode_action.setChecked(False)
    self.auto = self.auto_mode_action.isChecked()
    self.lock_mode = self.lock_mode_action.isChecked()
    self.slideshow = self.slideshow_mode_action.isChecked()
    self.showcode = self.visible_code_action.isChecked()
    self.restoutput = self.reST_code_action.isChecked()
    self.code_only = self.code_only_action.isChecked()
    if self.code_only and not self.showcode:
        self.visible_code_action.setChecked(True)
        self.showcode = True
# Buggy code
def process_one_node(self, p, result, environment):
    """Handle one node."""
    c = self.c
    result.append(self.underline2(p))
    d = c.scanAllDirectives(p)
    if self.verbose:
        g.trace(d.get("language") or "None", ":", p.h)
    s, code = self.process_directives(p.b, d)
    result.append(s)
    result.append("\n\n")
    # Add an empty line so bullet lists display properly.
    if code and self.execcode:
        s, err = self.exec_code(code, environment)
        # execute code found in a node, append to reST
        if not self.restoutput and s.strip():
            s = self.format_output(s)  # if some non-reST to print
        result.append(s)  # append, whether plain or reST output
        if err:
            err = self.format_output(err, prefix="**Error**::")
            result.append(err)


# Traceback (NameError)
Traceback (most recent call last):
File "c:\leo.repo\leo-editor\leo\core\leoGlobals.py", line 2385, in new_cmd_wrapper
func(self, event=event)
File "c:\leo.repo\leo-editor\leo\commands\helpCommands.py", line 62, in help
self.c.putHelpFor(rst_s)
File "c:\leo.repo\leo-editor\leo\core\leoCommands.py", line 2322, in putHelpFor
g.app.gui.put_help(c, s, short_title)
File "c:\leo.repo\leo-editor\leo\plugins\qt_gui.py", line 1055, in put_help
vr.show_scrolled_message(tag='Apropos', kw=kw)
File "c:\leo.repo\leo-editor\leo\plugins\viewrendered2.py", line 299, in show_scrolled_message
vr = viewrendered(event=kw)
NameError: name 'viewrendered' is not defined

# Fixed code
def process_one_node(self, p, result, environment):
    """Handle one node."""
    c = self.c
    if not self.code_only:
        result.append(self.underline2(p))
    d = c.scanAllDirectives(p)
    if self.verbose:
        g.trace(d.get("language") or "None", ":", p.h)
    s, code = self.process_directives(p.b, d)
    result.append(s)
    result.append("\n\n")
    # Add an empty line so bullet lists display properly.
    if code and self.execcode:
        s, err = self.exec_code(code, environment)
        # execute code found in a node, append to reST
        if not self.restoutput and s.strip():
            s = self.format_output(s)  # if some non-reST to print
        result.append(s)  # append, whether plain or reST output
        if err:
            err = self.format_output(err, prefix="**Error**::")
            result.append(err)
# Buggy code
def md_process_one_node(self, p, result, environment):
    """Handle one node."""
    c = self.c
    result.append(self.md_underline2(p))
    d = c.scanAllDirectives(p)
    if self.verbose:
        g.trace(d.get("language") or "None", ":", p.h)
    s, code = self.md_process_directives(p.b, d)
    result.append(s)
    result.append("\n\n")
    # Add an empty line so bullet lists display properly.
    if code and self.execcode:
        s, err = self.md_exec_code(code, environment)
        # execute code found in a node, append to md
        if not self.restoutput and s.strip():
            s = self.md_format_output(s)  # if some non-md to print
        result.append(s)  # append, whether plain or md output
        if err:
            err = self.md_format_output(err, prefix="**Error**:")
            result.append(err)


# Traceback (NameError)
Traceback (most recent call last):
File "c:\leo.repo\leo-editor\leo\core\leoGlobals.py", line 2385, in new_cmd_wrapper
func(self, event=event)
File "c:\leo.repo\leo-editor\leo\commands\helpCommands.py", line 62, in help
self.c.putHelpFor(rst_s)
File "c:\leo.repo\leo-editor\leo\core\leoCommands.py", line 2322, in putHelpFor
g.app.gui.put_help(c, s, short_title)
File "c:\leo.repo\leo-editor\leo\plugins\qt_gui.py", line 1055, in put_help
vr.show_scrolled_message(tag='Apropos', kw=kw)
File "c:\leo.repo\leo-editor\leo\plugins\viewrendered2.py", line 299, in show_scrolled_message
vr = viewrendered(event=kw)
NameError: name 'viewrendered' is not defined

# Fixed code
def md_process_one_node(self, p, result, environment):
    """Handle one node."""
    c = self.c
    if not self.code_only:
        result.append(self.md_underline2(p))
    d = c.scanAllDirectives(p)
    if self.verbose:
        g.trace(d.get("language") or "None", ":", p.h)
    s, code = self.md_process_directives(p.b, d)
    result.append(s)
    result.append("\n\n")
    # Add an empty line so bullet lists display properly.
    if code and self.execcode:
        s, err = self.md_exec_code(code, environment)
        # execute code found in a node, append to md
        if not self.restoutput and s.strip():
            s = self.md_format_output(s)  # if some non-md to print
        result.append(s)  # append, whether plain or md output
        if err:
            err = self.md_format_output(err, prefix="**Error**:")
            result.append(err)
# Buggy code
def calculate_starts(dims: Tuple[Tuple[int, ...]]) -> Tuple[int, ...]:
    """Calculate starting indexes given dims."""
    s = [np.prod(d) for d in dims]
    starts = np.cumsum([0] + s)[: len(dims)]
    return tuple(int(i) for i in starts)


# Traceback (RuntimeError)
Traceback (most recent call last):
File "scripts/pickle_error.py", line 45, in <module>
print(fit2["mu"])
File "<redacted>/lib/python3.7/site-packages/stan/fit.py", line 131, in __getitem__
raise RuntimeError("Still collecting draws for fit.")
RuntimeError: Still collecting draws for fit.

# Fixed code
def calculate_starts(dims: Tuple[Tuple[int, ...]]) -> Tuple[int, ...]:
    """Calculate starting indexes given dims."""
    s = [cast(int, np.prod(d)) for d in dims]
    starts = np.cumsum([0] + s)[: len(dims)]
    return tuple(int(i) for i in starts)
# Buggy code
def __contains__(self, key):
    if not self._finished:
        raise RuntimeError("Still collecting draws for fit.")
    return key in self.param_names


# Traceback (RuntimeError)
Traceback (most recent call last):
File "scripts/pickle_error.py", line 45, in <module>
print(fit2["mu"])
File "<redacted>/lib/python3.7/site-packages/stan/fit.py", line 131, in __getitem__
raise RuntimeError("Still collecting draws for fit.")
RuntimeError: Still collecting draws for fit.

# Fixed code
def __contains__(self, key):
    return key in self.param_names
# Buggy code
def __getitem__(self, param):
    """Returns array with shape (stan_dimensions, num_chains * num_samples)"""
    if not self._finished:
        raise RuntimeError("Still collecting draws for fit.")
    assert param.endswith("__") or param in self.param_names, param
    param_indexes = self._parameter_indexes(param)
    param_dim = (
        []
        if param in self.sample_and_sampler_param_names
        else self.dims[self.param_names.index(param)]
    )
    # fmt: off
    num_samples_saved = (self.num_samples + self.num_warmup * self.save_warmup) // self.num_thin
    assert self._draws.shape == (len(self.sample_and_sampler_param_names) + len(self.constrained_param_names), num_samples_saved, self.num_chains)
    # fmt: on
    # Stack chains together. Parameter is still stored flat.
    view = self._draws[param_indexes, :, :].reshape(len(param_indexes), -1).view()
    assert view.shape == (len(param_indexes), num_samples_saved * self.num_chains)
    # reshape must yield something with least two dimensions
    reshape_args = param_dim + [-1] if param_dim else (1, -1)
    # reshape, recover the shape of the stan parameter
    return view.reshape(*reshape_args, order="F")


# Traceback (RuntimeError)
Traceback (most recent call last):
File "scripts/pickle_error.py", line 45, in <module>
print(fit2["mu"])
File "<redacted>/lib/python3.7/site-packages/stan/fit.py", line 131, in __getitem__
raise RuntimeError("Still collecting draws for fit.")
RuntimeError: Still collecting draws for fit.

# Fixed code
def __getitem__(self, param):
    """Returns array with shape (stan_dimensions, num_chains * num_samples)"""
    assert param.endswith("__") or param in self.param_names, param
    param_indexes = self._parameter_indexes(param)
    param_dim = (
        []
        if param in self.sample_and_sampler_param_names
        else self.dims[self.param_names.index(param)]
    )
    # fmt: off
    num_samples_saved = (self.num_samples + self.num_warmup * self.save_warmup) // self.num_thin
    assert self._draws.shape == (len(self.sample_and_sampler_param_names) + len(self.constrained_param_names), num_samples_saved, self.num_chains)
    # fmt: on
    # Stack chains together. Parameter is still stored flat.
    view = self._draws[param_indexes, :, :].reshape(len(param_indexes), -1).view()
    assert view.shape == (len(param_indexes), num_samples_saved * self.num_chains)
    # reshape must yield something with least two dimensions
    reshape_args = param_dim + [-1] if param_dim else (1, -1)
    # reshape, recover the shape of the stan parameter
    return view.reshape(*reshape_args, order="F")
# Buggy code
def __repr__(self) -> str:
    # inspired by xarray
    parts = [f"<stan.{type(self).__name__}>"]

    def summarize_param(param_name, dims):
        return f"    {param_name}: {tuple(dims)}"

    if self.param_names:
        parts.append("Parameters:")
    for param_name, dims in zip(self.param_names, self.dims):
        parts.append(summarize_param(param_name, dims))
    if self._finished:
        # total draws is num_draws (per-chain) times num_chains
        parts.append(f"Draws: {self._draws.shape[-2] * self._draws.shape[-1]}")
    return "\n".join(parts)


# Traceback (RuntimeError)
Traceback (most recent call last):
File "scripts/pickle_error.py", line 45, in <module>
print(fit2["mu"])
File "<redacted>/lib/python3.7/site-packages/stan/fit.py", line 131, in __getitem__
raise RuntimeError("Still collecting draws for fit.")
RuntimeError: Still collecting draws for fit.

# Fixed code
def __repr__(self) -> str:
    # inspired by xarray
    parts = [f"<stan.{type(self).__name__}>"]

    def summarize_param(param_name, dims):
        return f"    {param_name}: {tuple(dims)}"

    if self.param_names:
        parts.append("Parameters:")
    for param_name, dims in zip(self.param_names, self.dims):
        parts.append(summarize_param(param_name, dims))

    # total draws is num_draws (per-chain) times num_chains
    parts.append(f"Draws: {self._draws.shape[-2] * self._draws.shape[-1]}")
    return "\n".join(parts)
# Buggy code
def _map_bivariate(self, func, indices, **kwargs):
    """Draw a bivariate plot on the indicated axes."""
    # This is a hack to handle the fact that new distribution plots don't add
    # their artists onto the axes. This is probably superior in general, but
    # we'll need a better way to handle it in the axisgrid functions.
    from .distributions import histplot, kdeplot

    if func is histplot or func is kdeplot:
        self._extract_legend_handles = True

    kws = kwargs.copy()  # Use copy as we insert other kwargs
    for i, j in indices:
        x_var = self.x_vars[j]
        y_var = self.y_vars[i]
        ax = self.axes[i, j]
        self._plot_bivariate(x_var, y_var, ax, func, **kws)
    self._add_axis_labels()

    if "hue" in signature(func).parameters:
        self.hue_names = list(self._legend_data)


# Traceback (AttributeError)
Traceback (most recent call last):

File "<ipython-input-87-23324450a106>", line 1, in <module>
sns.pairplot(p, diag_kind=None, corner=True)

File "c:\program files\python38\lib\site-packages\seaborn\_decorators.py", line 46, in inner_f
return f(**kwargs)

File "c:\program files\python38\lib\site-packages\seaborn\axisgrid.py", line 1974, in pairplot
plotter(scatterplot, **plot_kws)

File "c:\program files\python38\lib\site-packages\seaborn\axisgrid.py", line 1250, in map
self._map_bivariate(func, indices, **kwargs)

File "c:\program files\python38\lib\site-packages\seaborn\axisgrid.py", line 1434, in _map_bivariate
self._plot_bivariate(x_var, y_var, ax, func, **kws)

File "c:\program files\python38\lib\site-packages\seaborn\axisgrid.py", line 1446, in _plot_bivariate
plt.sca(ax)

File "C:\Users\tgentils\AppData\Roaming\Python\Python38\site-packages\matplotlib\pyplot.py", line 982, in sca
if not hasattr(ax.figure.canvas, "manager"):

AttributeError: 'NoneType' object has no attribute 'figure'

# Fixed code
def _map_bivariate(self, func, indices, **kwargs):
    """Draw a bivariate plot on the indicated axes."""
    # This is a hack to handle the fact that new distribution plots don't add
    # their artists onto the axes. This is probably superior in general, but
    # we'll need a better way to handle it in the axisgrid functions.
    from .distributions import histplot, kdeplot

    if func is histplot or func is kdeplot:
        self._extract_legend_handles = True

    kws = kwargs.copy()  # Use copy as we insert other kwargs
    for i, j in indices:
        x_var = self.x_vars[j]
        y_var = self.y_vars[i]
        ax = self.axes[i, j]
        if ax is None:  # i.e. we are in corner mode
            continue
        self._plot_bivariate(x_var, y_var, ax, func, **kws)
    self._add_axis_labels()

    if "hue" in signature(func).parameters:
        self.hue_names = list(self._legend_data)
# Buggy code
def set(self, **kwargs):
    """Set attributes on each subplot Axes."""
    for ax in self.axes.flat:
        ax.set(**kwargs)
    return self


# Traceback (AttributeError)
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-23-b993ffaa9ada> in <module>
4                   line_kws=dict(color='r'),
5                   scatter_kws=dict(alpha=0.1, marker='.'))
----> 6 g.set(xlim=(0, 1), ylim=(0, 1))

~/miniconda3/envs/py37/lib/python3.7/site-packages/seaborn/axisgrid.py in set(self, **kwargs)
26         """Set attributes on each subplot Axes."""
27         for ax in self.axes.flat:
---> 28             ax.set(**kwargs)
29         return self
30

AttributeError: 'NoneType' object has no attribute 'set'

# Fixed code
def set(self, **kwargs):
    """Set attributes on each subplot Axes."""
    for ax in self.axes.flat:
        if ax is not None:  # Handle removed axes
            ax.set(**kwargs)
    return self
# Buggy code
def establish_variables(self, data, **kws):
    """Extract variables from data or use directly."""
    self.data = data

    # Validate the inputs
    any_strings = any([isinstance(v, string_types) for v in kws.values()])
    if any_strings and data is None:
        raise ValueError("Must pass `data` if using named variables.")

    # Set the variables
    for var, val in kws.items():
        if isinstance(val, string_types):
            setattr(self, var, data[val])
        else:
            setattr(self, var, val)


# Traceback (TypeError)
<matplotlib.figure.Figure object at 0xbdb0b6c>
Traceback (most recent call last):

File "<ipython-input-4-48c88ed4333f>", line 1, in <module>
sns.regplot(x, y)

File ".../seaborn/plotobjs.py", line 742, in regplot
boots = moss.bootstrap(x, y, func=_bootstrap_reg)

File ".../lib/python2.7/site-packages/moss/statistical.py", line 61, in bootstrap
sample = [a[resampler] for a in args]

TypeError: only integer arrays with one element can be converted to an index

# Fixed code
def establish_variables(self, data, **kws):
    """Extract variables from data or use directly."""
    self.data = data

    # Validate the inputs
    any_strings = any([isinstance(v, string_types) for v in kws.values()])
    if any_strings and data is None:
        raise ValueError("Must pass `data` if using named variables.")

    # Set the variables
    for var, val in kws.items():
        if isinstance(val, string_types):
            setattr(self, var, data[val])
        elif isinstance(val, list):
            setattr(self, var, np.asarray(val))
        else:
            setattr(self, var, val)
# Buggy code
def get_headers(self, version="1.1", keep_alive=False, keep_alive_timeout=None):
    # This is all returned in a kind-of funky way
    # We tried to make this as fast as possible in pure python
    timeout_header = b""
    if keep_alive and keep_alive_timeout is not None:
        timeout_header = b"Keep-Alive: %d\r\n" % keep_alive_timeout

    self.headers["Transfer-Encoding"] = "chunked"
    self.headers.pop("Content-Length", None)
    self.headers["Content-Type"] = self.headers.get("Content-Type", self.content_type)

    headers = self._parse_headers()

    if self.status is 200:
        status = b"OK"
    else:
        status = http.STATUS_CODES.get(self.status)

    return (b"HTTP/%b %d %b\r\n%b%b\r\n") % (
        version.encode(),
        self.status,
        status,
        timeout_header,
        headers,
    )


# Traceback (ModuleNotFoundError)
Traceback (most recent call last):
File "/env/lib/python3.6/site-packages/sanic/__main__.py", line 4, in <module>
from sanic.log import logger
File "/env/lib/python3.6/site-packages/sanic/__init__.py", line 1, in <module>
from sanic.app import Sanic
File "/env/lib/python3.6/site-packages/sanic/app.py", line 21, in <module>
from sanic.server import serve, serve_multiple, HttpProtocol, Signal
File "/env/lib/python3.6/site-packages/sanic/server.py", line 31, in <module>
from sanic.request import Request
File "/env/lib/python3.6/site-packages/sanic/request.py", line 6, in <module>
from http.cookies import SimpleCookie
ModuleNotFoundError: No module named 'http.cookies'; 'http' is not a package

# Fixed code
def get_headers(self, version="1.1", keep_alive=False, keep_alive_timeout=None):
    # This is all returned in a kind-of funky way
    # We tried to make this as fast as possible in pure python
    timeout_header = b""
    if keep_alive and keep_alive_timeout is not None:
        timeout_header = b"Keep-Alive: %d\r\n" % keep_alive_timeout

    self.headers["Transfer-Encoding"] = "chunked"
    self.headers.pop("Content-Length", None)
    self.headers["Content-Type"] = self.headers.get("Content-Type", self.content_type)

    headers = self._parse_headers()

    if self.status is 200:
        status = b"OK"
    else:
        status = STATUS_CODES.get(self.status)

    return (b"HTTP/%b %d %b\r\n%b%b\r\n") % (
        version.encode(),
        self.status,
        status,
        timeout_header,
        headers,
    )
# Buggy code
def output(self, version="1.1", keep_alive=False, keep_alive_timeout=None):
    # This is all returned in a kind-of funky way
    # We tried to make this as fast as possible in pure python
    timeout_header = b""
    if keep_alive and keep_alive_timeout is not None:
        timeout_header = b"Keep-Alive: %d\r\n" % keep_alive_timeout

    body = b""
    if http.has_message_body(self.status):
        body = self.body
        self.headers["Content-Length"] = self.headers.get(
            "Content-Length", len(self.body)
        )

    self.headers["Content-Type"] = self.headers.get("Content-Type", self.content_type)

    if self.status in (304, 412):
        self.headers = http.remove_entity_headers(self.headers)

    headers = self._parse_headers()

    if self.status is 200:
        status = b"OK"
    else:
        status = http.STATUS_CODES.get(self.status, b"UNKNOWN RESPONSE")

    return (b"HTTP/%b %d %b\r\nConnection: %b\r\n%b%b\r\n%b") % (
        version.encode(),
        self.status,
        status,
        b"keep-alive" if keep_alive else b"close",
        timeout_header,
        headers,
        body,
    )


# Traceback (ModuleNotFoundError)
Traceback (most recent call last):
File "/env/lib/python3.6/site-packages/sanic/__main__.py", line 4, in <module>
from sanic.log import logger
File "/env/lib/python3.6/site-packages/sanic/__init__.py", line 1, in <module>
from sanic.app import Sanic
File "/env/lib/python3.6/site-packages/sanic/app.py", line 21, in <module>
from sanic.server import serve, serve_multiple, HttpProtocol, Signal
File "/env/lib/python3.6/site-packages/sanic/server.py", line 31, in <module>
from sanic.request import Request
File "/env/lib/python3.6/site-packages/sanic/request.py", line 6, in <module>
from http.cookies import SimpleCookie
ModuleNotFoundError: No module named 'http.cookies'; 'http' is not a package

# Fixed code
def output(self, version="1.1", keep_alive=False, keep_alive_timeout=None):
    # This is all returned in a kind-of funky way
    # We tried to make this as fast as possible in pure python
    timeout_header = b""
    if keep_alive and keep_alive_timeout is not None:
        timeout_header = b"Keep-Alive: %d\r\n" % keep_alive_timeout

    body = b""
    if has_message_body(self.status):
        body = self.body
        self.headers["Content-Length"] = self.headers.get(
            "Content-Length", len(self.body)
        )

    self.headers["Content-Type"] = self.headers.get("Content-Type", self.content_type)

    if self.status in (304, 412):
        self.headers = remove_entity_headers(self.headers)

    headers = self._parse_headers()

    if self.status is 200:
        status = b"OK"
    else:
        status = STATUS_CODES.get(self.status, b"UNKNOWN RESPONSE")

    return (b"HTTP/%b %d %b\r\nConnection: %b\r\n%b%b\r\n%b") % (
        version.encode(),
        self.status,
        status,
        b"keep-alive" if keep_alive else b"close",
        timeout_header,
        headers,
        body,
    )
# Buggy code
def do_EI(self, obj):
    """End inline image object"""
    if "W" in obj and "H" in obj:
        iobjid = str(id(obj))
        self.device.begin_figure(iobjid, (0, 0, 1, 1), MATRIX_IDENTITY)
        self.device.render_image(iobjid, obj)
        self.device.end_figure(iobjid)
    return


# Traceback (TypeError)
Traceback (most recent call last):
File "pdf2txt.py", line 188, in <module>
sys.exit(main())
File "pdf2txt.py", line 182, in main
outfp = extract_text(**vars(A))
File "pdf2txt.py", line 56, in extract_text
pdfminer.high_level.extract_text_to_fp(fp, **locals())
File "***/lib/python3.6/site-packages/pdfminer/high_level.py", line 86, in extract_text_to_fp
interpreter.process_page(page)
File "***/lib/python3.6/site-packages/pdfminer/pdfinterp.py", line 895, in process_page
self.render_contents(page.resources, page.contents, ctm=ctm)
File "***/lib/python3.6/site-packages/pdfminer/pdfinterp.py", line 908, in render_contents
self.execute(list_value(streams))
File "***/lib/python3.6/site-packages/pdfminer/pdfinterp.py", line 933, in execute
func(*args)
File "***/lib/python3.6/site-packages/pdfminer/pdfinterp.py", line 840, in do_EI
if 'W' in obj and 'H' in obj:
TypeError: a bytes-like object is required, not 'str'

# Fixed code
def do_EI(self, obj):
    """End inline image object"""
    if isinstance(obj, PDFStream) and "W" in obj and "H" in obj:
        iobjid = str(id(obj))
        self.device.begin_figure(iobjid, (0, 0, 1, 1), MATRIX_IDENTITY)
        self.device.render_image(iobjid, obj)
        self.device.end_figure(iobjid)
    return
# Buggy code
def init_params(self):
    self.v = int_value(self.param.get("V", 0))
    self.r = int_value(self.param["R"])
    self.p = int_value(self.param["P"])
    self.o = str_value(self.param["O"])
    self.u = str_value(self.param["U"])
    self.length = int_value(self.param.get("Length", 40))
    return


# Traceback (struct.error)
Traceback (most recent call last):
File "/mnt/c/Users/aq4'july/Desktop/CleanTextAPI_withNewPdfAnalyser/PdfAnalyzer.py", line 108, in GetTextFromPdf
for page in PDFPage.get_pages(pdfFile):
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfpage.py", line 129, in get_pages
doc = PDFDocument(parser, password=password, caching=caching)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 577, in __init__
self._initialize_password(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 603, in _initialize_password
handler = factory(docid, param, password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 303, in __init__
self.init()
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 310, in init
self.init_key()
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 323, in init_key
self.key = self.authenticate(self.password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 372, in authenticate
key = self.authenticate_user_password(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 378, in authenticate_user_password
key = self.compute_encryption_key(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 357, in compute_encryption_key
hash.update(struct.pack('<l', self.p))  # 4
struct.error: 'l' format requires -2147483648 <= number <= 2147483647

# Fixed code
def init_params(self):
    self.v = int_value(self.param.get("V", 0))
    self.r = int_value(self.param["R"])
    self.p = uint_value(self.param["P"], 32)
    self.o = str_value(self.param["O"])
    self.u = str_value(self.param["U"])
    self.length = int_value(self.param.get("Length", 40))
    return
# Buggy code
def compute_encryption_key(self, password):
    # Algorithm 3.2
    password = (password + self.PASSWORD_PADDING)[:32]  # 1
    hash = md5.md5(password)  # 2
    hash.update(self.o)  # 3
    hash.update(struct.pack("<l", self.p))  # 4
    hash.update(self.docid[0])  # 5
    if self.r >= 4:
        if not self.encrypt_metadata:
            hash.update(b"\xff\xff\xff\xff")
    result = hash.digest()
    n = 5
    if self.r >= 3:
        n = self.length // 8
        for _ in range(50):
            result = md5.md5(result[:n]).digest()
    return result[:n]


# Traceback (struct.error)
Traceback (most recent call last):
File "/mnt/c/Users/aq4'july/Desktop/CleanTextAPI_withNewPdfAnalyser/PdfAnalyzer.py", line 108, in GetTextFromPdf
for page in PDFPage.get_pages(pdfFile):
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfpage.py", line 129, in get_pages
doc = PDFDocument(parser, password=password, caching=caching)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 577, in __init__
self._initialize_password(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 603, in _initialize_password
handler = factory(docid, param, password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 303, in __init__
self.init()
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 310, in init
self.init_key()
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 323, in init_key
self.key = self.authenticate(self.password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 372, in authenticate
key = self.authenticate_user_password(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 378, in authenticate_user_password
key = self.compute_encryption_key(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 357, in compute_encryption_key
hash.update(struct.pack('<l', self.p))  # 4
struct.error: 'l' format requires -2147483648 <= number <= 2147483647

# Fixed code
def compute_encryption_key(self, password):
    # Algorithm 3.2
    password = (password + self.PASSWORD_PADDING)[:32]  # 1
    hash = md5.md5(password)  # 2
    hash.update(self.o)  # 3
    # See https://github.com/pdfminer/pdfminer.six/issues/186
    hash.update(struct.pack("<L", self.p))  # 4
    hash.update(self.docid[0])  # 5
    if self.r >= 4:
        if not self.encrypt_metadata:
            hash.update(b"\xff\xff\xff\xff")
    result = hash.digest()
    n = 5
    if self.r >= 3:
        n = self.length // 8
        for _ in range(50):
            result = md5.md5(result[:n]).digest()
    return result[:n]
# Buggy code
def isnumber(x):
    return isinstance(x, ((int,), float))


# Traceback (struct.error)
Traceback (most recent call last):
File "/mnt/c/Users/aq4'july/Desktop/CleanTextAPI_withNewPdfAnalyser/PdfAnalyzer.py", line 108, in GetTextFromPdf
for page in PDFPage.get_pages(pdfFile):
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfpage.py", line 129, in get_pages
doc = PDFDocument(parser, password=password, caching=caching)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 577, in __init__
self._initialize_password(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 603, in _initialize_password
handler = factory(docid, param, password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 303, in __init__
self.init()
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 310, in init
self.init_key()
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 323, in init_key
self.key = self.authenticate(self.password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 372, in authenticate
key = self.authenticate_user_password(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 378, in authenticate_user_password
key = self.compute_encryption_key(password)
File "/usr/local/lib/python3.5/dist-packages/pdfminer/pdfdocument.py", line 357, in compute_encryption_key
hash.update(struct.pack('<l', self.p))  # 4
struct.error: 'l' format requires -2147483648 <= number <= 2147483647

# Fixed code
def isnumber(x):
    return isinstance(x, (int, float))
# Buggy code
def getobj(self, objid):
    assert objid != 0
    if not self.xrefs:
        raise PDFException("PDFDocument is not initialized")
    log.debug("getobj: objid=%r", objid)
    if objid in self._cached_objs:
        (obj, genno) = self._cached_objs[objid]
    else:
        for xref in self.xrefs:
            try:
                (strmid, index, genno) = xref.get_pos(objid)
            except KeyError:
                continue
            try:
                if strmid is not None:
                    stream = stream_value(self.getobj(strmid))
                    obj = self._getobj_objstm(stream, index, objid)
                else:
                    obj = self._getobj_parse(index, objid)
                    if self.decipher:
                        obj = decipher_all(self.decipher, objid, genno, obj)

                if isinstance(obj, PDFStream):
                    obj.set_objid(objid, genno)
                break
            except (PSEOF, PDFSyntaxError):
                continue
        else:
            raise PDFObjectNotFound(objid)
        log.debug("register: objid=%r: %r", objid, obj)
        if self.caching:
            self._cached_objs[objid] = (obj, genno)
    return obj


# Traceback (AssertionError)
$ dumppdf -a invalid.pdf
<pdf>Traceback (most recent call last):
File "/usr/bin/dumppdf", line 268, in <module>
if __name__ == '__main__': sys.exit(main(sys.argv))
File "/usr/bin/dumppdf", line 265, in main
dumpall=dumpall, codec=codec, extractdir=extractdir)
File "/usr/bin/dumppdf", line 216, in dumppdf
dumpallobjs(outfp, doc, codec=codec)
File "/usr/bin/dumppdf", line 102, in dumpallobjs
obj = doc.getobj(objid)
File "/usr/local/lib/python2.7/dist-packages/pdfminer/pdfdocument.py", line 658, in getobj
assert objid != 0
AssertionError

# Fixed code
def getobj(self, objid):
    """Get object from PDF

    :raises PDFException if PDFDocument is not initialized
    :raises PDFObjectNotFound if objid does not exist in PDF
    """
    if not self.xrefs:
        raise PDFException("PDFDocument is not initialized")
    log.debug("getobj: objid=%r", objid)
    if objid in self._cached_objs:
        (obj, genno) = self._cached_objs[objid]
    else:
        for xref in self.xrefs:
            try:
                (strmid, index, genno) = xref.get_pos(objid)
            except KeyError:
                continue
            try:
                if strmid is not None:
                    stream = stream_value(self.getobj(strmid))
                    obj = self._getobj_objstm(stream, index, objid)
                else:
                    obj = self._getobj_parse(index, objid)
                    if self.decipher:
                        obj = decipher_all(self.decipher, objid, genno, obj)

                if isinstance(obj, PDFStream):
                    obj.set_objid(objid, genno)
                break
            except (PSEOF, PDFSyntaxError):
                continue
        else:
            raise PDFObjectNotFound(objid)
        log.debug("register: objid=%r: %r", objid, obj)
        if self.caching:
            self._cached_objs[objid] = (obj, genno)
    return obj