gurudesh/pytracebugs huggingface dataset:
# Buggy code
def main():
    args = _options.options.parse_args()

    if args.help:
        _options.options.print_help()
        return

    if args.version:
        dist = pkg_resources.get_distribution("nox")
        print(dist.version, file=sys.stderr)
        return

    setup_logging(color=args.color, verbose=args.verbose)

    # Execute the appropriate tasks.
    exit_code = workflow.execute(
        global_config=args,
        workflow=(
            tasks.load_nox_module,
            tasks.merge_noxfile_options,
            tasks.discover_manifest,
            tasks.filter_manifest,
            tasks.honor_list_request,
            tasks.verify_manifest_nonempty,
            tasks.run_manifest,
            tasks.print_summary,
            tasks.create_report,
            tasks.final_reduce,
        ),
    )

    # Done; exit.
    sys.exit(exit_code)


# Traceback (ModuleNotFoundError)
nox --help
Traceback (most recent call last):
File "...\python38\lib\runpy.py", line 193, in _run_module_as_main
return _run_code(code, main_globals, None,
File "...\python38\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "...\AppData\Roaming\Python\Python38\Scripts\nox.exe\__main__.py", line 5, in <module>
File "...\AppData\Roaming\Python\Python38\site-packages\nox\__main__.py", line 24, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
pip install setuptools
Collecting setuptools
...
Successfully installed setuptools-44.0.0
nox --help
usage: nox [-h] [--version] [-l] [-s [SESSIONS [SESSIONS ...]]] [-k KEYWORDS] [-v] [-r] [--no-reuse-existing-virtualenvs] [-f NOXFILE] [--envdir ENVDIR]
[-x] [--no-stop-on-first-error] [--error-on-missing-interpreters] [--no-error-on-missing-interpreters] [--error-on-external-run]
[--no-error-on-external-run] [--install-only] [--report REPORT] [--non-interactive] [--nocolor] [--forcecolor]
...

Nox is a Python automation toolkit.

# Fixed code
def main():
    args = _options.options.parse_args()

    if args.help:
        _options.options.print_help()
        return

    if args.version:
        print(metadata.version("nox"), file=sys.stderr)
        return

    setup_logging(color=args.color, verbose=args.verbose)

    # Execute the appropriate tasks.
    exit_code = workflow.execute(
        global_config=args,
        workflow=(
            tasks.load_nox_module,
            tasks.merge_noxfile_options,
            tasks.discover_manifest,
            tasks.filter_manifest,
            tasks.honor_list_request,
            tasks.verify_manifest_nonempty,
            tasks.run_manifest,
            tasks.print_summary,
            tasks.create_report,
            tasks.final_reduce,
        ),
    )

    # Done; exit.
    sys.exit(exit_code)
# Buggy code
def check_connections(gd):
    """
    Given a graph, checks that all
     - inputs/outputs are symmetric
     - control_inputs/control_outputs are symmetric
     - The graph does not reference vertices outside of the graph

    Takes a graph in "dict{str, ParsedNode}" form. Does not return,
    asserts false on failure.
    """
    # check that inputs and outputs line up
    for k, v in gd.items():
        for i in v.inputs:
            assert k in gd[i].outputs
        for i in v.outputs:
            assert k in gd[i].inputs
        for i in v.control_inputs:
            assert k in gd[i].control_outputs
        for i in v.control_outputs:
            assert k in gd[i].control_inputs


# Traceback (AssertionError)
0 assert nodes deleted
5 nodes deleted
0 nodes deleted
0 nodes deleted
[Op Fusion] fuse_bias_add() deleted 4 nodes.
1 identity nodes deleted
2 disconnected nodes deleted
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
~/.pyenv/versions/3.6.8/envs/fritz-models-private/src/coremltools/coremltools/converters/tensorflow/_tf_converter.py in convert(filename, inputs, outputs, image_input_names, is_bgr, red_bias, green_bias, blue_bias, gray_bias, image_scale, class_labels, predicted_feature_name, predicted_probabilities_output, add_custom_layers, custom_conversion_functions, custom_shape_functions, **kwargs)
94                                  custom_shape_functions=custom_shape_functions,
---> 95                                  optional_inputs=optional_inputs)
96     except ImportError as e:

~/.pyenv/versions/3.6.8/envs/fritz-models-private/src/coremltools/coremltools/converters/nnssa/coreml/ssa_converter.py in ssa_convert(ssa, top_func, inputs, outputs, image_input_names, is_bgr, red_bias, green_bias, blue_bias, gray_bias, image_scale, class_labels, predicted_feature_name, predicted_probabilities_output, add_custom_layers, custom_conversion_functions, custom_shape_functions, optional_inputs)
132     for f in list(ssa.functions.values()):
--> 133         check_connections(f.graph)
134

~/.pyenv/versions/3.6.8/envs/fritz-models-private/src/coremltools/coremltools/converters/nnssa/commons/basic_graph_ops.py in check_connections(gd)
152             try:
--> 153                 assert (k in gd[i].control_inputs)
154             except Exception:

# Fixed code
def check_connections(gd):
    """
    Given a graph, checks that all
     - inputs/outputs are symmetric
     - control_inputs/control_outputs are symmetric
     - The graph does not reference vertices outside of the graph

    Takes a graph in "dict{str, ParsedNode}" form. Does not return,
    asserts false on failure.
    """
    # check that inputs and outputs line up
    for k, v in gd.items():
        for i in v.inputs:
            assert k in gd[i].outputs
        for i in v.outputs:
            assert k in gd[i].inputs
        for i in v.control_inputs:
            assert k in gd[i].control_outputs
        for i in v.control_outputs:
            message = f"Node {k} not in {i} control_inputs"
            assert k in gd[i].control_inputs, message
# Buggy code
def __init__(self, tfnode=None):
    ParsedNode.__init__(self)
    self.original_node = tfnode
    if tfnode is not None:
        from .parse import parse_attr

        self.name = tfnode.name
        if tfnode.op == "PlaceholderWithDefault":
            self.op = "Placeholder"
        else:
            self.op = tfnode.op
        self.inputs = [x for x in tfnode.input if not x.startswith("^")]
        self.control_inputs = [x[1:] for x in tfnode.input if x.startswith("^")]
        self.attr = {k: parse_attr(v) for k, v in tfnode.attr.items()}


# Traceback (AssertionError)
0 assert nodes deleted
5 nodes deleted
0 nodes deleted
0 nodes deleted
[Op Fusion] fuse_bias_add() deleted 4 nodes.
1 identity nodes deleted
2 disconnected nodes deleted
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
~/.pyenv/versions/3.6.8/envs/fritz-models-private/src/coremltools/coremltools/converters/tensorflow/_tf_converter.py in convert(filename, inputs, outputs, image_input_names, is_bgr, red_bias, green_bias, blue_bias, gray_bias, image_scale, class_labels, predicted_feature_name, predicted_probabilities_output, add_custom_layers, custom_conversion_functions, custom_shape_functions, **kwargs)
94                                  custom_shape_functions=custom_shape_functions,
---> 95                                  optional_inputs=optional_inputs)
96     except ImportError as e:

~/.pyenv/versions/3.6.8/envs/fritz-models-private/src/coremltools/coremltools/converters/nnssa/coreml/ssa_converter.py in ssa_convert(ssa, top_func, inputs, outputs, image_input_names, is_bgr, red_bias, green_bias, blue_bias, gray_bias, image_scale, class_labels, predicted_feature_name, predicted_probabilities_output, add_custom_layers, custom_conversion_functions, custom_shape_functions, optional_inputs)
132     for f in list(ssa.functions.values()):
--> 133         check_connections(f.graph)
134

~/.pyenv/versions/3.6.8/envs/fritz-models-private/src/coremltools/coremltools/converters/nnssa/commons/basic_graph_ops.py in check_connections(gd)
152             try:
--> 153                 assert (k in gd[i].control_inputs)
154             except Exception:

# Fixed code
def __init__(self, tfnode=None):
    super(ParsedTFNode, self).__init__()
    self.original_node = tfnode

    if tfnode is not None:
        from .parse import parse_attr

        self.name = tfnode.name
        if tfnode.op == "PlaceholderWithDefault":
            self.op = "Placeholder"
        else:
            self.op = tfnode.op
        self.inputs = [x for x in tfnode.input if not x.startswith("^")]
        self.control_inputs = [x[1:] for x in tfnode.input if x.startswith("^")]
        self.attr = {k: parse_attr(v) for k, v in tfnode.attr.items()}
# Buggy code
def verify_executables(self):
    """Raise an error if any of the compiler executables is not valid.

    This method confirms that for all of the compilers (cc, cxx, f77, fc)
    that have paths, those paths exist and are executable by the current
    user.
    Raises a CompilerAccessError if any of the non-null paths for the
    compiler are not accessible.
    """
    missing = [
        cmp
        for cmp in (self.cc, self.cxx, self.f77, self.fc)
        if cmp and not (os.path.isfile(cmp) and os.access(cmp, os.X_OK))
    ]
    if missing:
        raise CompilerAccessError(self, missing)


# Traceback (spack.compiler.CompilerAccessError)
$> spack install zlib%gcc@8.3.0 arch=cray-cnl7-haswell
...
==> Error: Failed to install zlib due to ChildError: CompilerAccessError: Compiler 'gcc@8.3.0' has executables that are missing or are not executable: ['cc', 'CC', 'ftn', 'ftn']
/global/u1/l/lpeyrala/spack-greg-test/lib/spack/spack/build_environment.py:854, in child_process:
851            tb_string = traceback.format_exc()
852
853            # build up some context from the offending package so we can
>>    854            # show that, too.
855            package_context = get_package_context(tb)
856
857            build_log = None

Traceback (most recent call last):
File "/global/u1/l/lpeyrala/spack-greg-test/lib/spack/spack/build_environment.py", line 837, in child_process
setup_package(pkg, dirty=dirty)
File "/global/u1/l/lpeyrala/spack-greg-test/lib/spack/spack/build_environment.py", line 712, in setup_package
set_compiler_environment_variables(pkg, build_env)
File "/global/u1/l/lpeyrala/spack-greg-test/lib/spack/spack/build_environment.py", line 202, in set_compiler_environment_variables
compiler.verify_executables()
File "/global/u1/l/lpeyrala/spack-greg-test/lib/spack/spack/compiler.py", line 304, in verify_executables
raise CompilerAccessError(self, missing)
spack.compiler.CompilerAccessError: Compiler 'gcc@8.3.0' has executables that are missing or are not executable: ['cc', 'CC', 'ftn', 'ftn']

# Fixed code
def verify_executables(self):
    """Raise an error if any of the compiler executables is not valid.

    This method confirms that for all of the compilers (cc, cxx, f77, fc)
    that have paths, those paths exist and are executable by the current
    user.
    Raises a CompilerAccessError if any of the non-null paths for the
    compiler are not accessible.
    """

    def accessible_exe(exe):
        # compilers may contain executable names (on Cray or user edited)
        if not os.path.isabs(exe):
            exe = spack.util.executable.which_string(exe)
            if not exe:
                return False
        return os.path.isfile(exe) and os.access(exe, os.X_OK)

    # setup environment before verifying in case we have executable names
    # instead of absolute paths
    with self._compiler_environment():
        missing = [
            cmp
            for cmp in (self.cc, self.cxx, self.f77, self.fc)
            if cmp and not accessible_exe(cmp)
        ]
        if missing:
            raise CompilerAccessError(self, missing)
# Buggy code
def _is_background_tty():
    """Return True iff this process is backgrounded and stdout is a tty"""
    if sys.stdout.isatty():
        return os.getpgrp() != os.tcgetpgrp(sys.stdout.fileno())
    return False  # not writing to tty, not background


# Traceback (KeyError)
Traceback (most recent call last):
File "/u/sciteam/stewart1/spack/bin/spack", line 64, in <module>
sys.exit(spack.main.main())
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/main.py", line 770, in main
if spack.config.get('config:debug'):
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 671, in get
return config.get(path, default, scope)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 552, in __getattr__
return getattr(self.instance, name)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 548, in instance
self._instance = self.factory()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 653, in _config
_add_platform_scope(cfg, ConfigScope, name, path)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 606, in _add_platform_scope
platform = spack.architecture.platform().name
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 178, in _memoized_function
func.cache[args] = func(*args)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/architecture.py", line 516, in platform
return platform_cls()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/platforms/cray.py", line 63, in __init__
_target = self._default_target_from_env()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/platforms/cray.py", line 121, in _default_target_from_env
env={'TERM': os.environ['TERM']},
File "/usr/lib64/python2.6/UserDict.py", line 22, in __getitem__
raise KeyError(key)
KeyError: 'TERM'

# Fixed code
def _is_background_tty(stream):
    """True if the stream is a tty and calling process is in the background."""
    return stream.isatty() and os.getpgrp() != os.tcgetpgrp(stream.fileno())
# Buggy code
def force_echo(self):
    """Context manager to force local echo, even if echo is off."""
    if not self._active:
        raise RuntimeError("Can't call force_echo() outside log_output region!")

    # This uses the xon/xoff to highlight regions to be echoed in the
    # output. We us these control characters rather than, say, a
    # separate pipe, because they're in-band and assured to appear
    # exactly before and after the text we want to echo.
    sys.stdout.write(xon)
    sys.stdout.flush()
    yield
    sys.stdout.write(xoff)
    sys.stdout.flush()


# Traceback (KeyError)
Traceback (most recent call last):
File "/u/sciteam/stewart1/spack/bin/spack", line 64, in <module>
sys.exit(spack.main.main())
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/main.py", line 770, in main
if spack.config.get('config:debug'):
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 671, in get
return config.get(path, default, scope)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 552, in __getattr__
return getattr(self.instance, name)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 548, in instance
self._instance = self.factory()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 653, in _config
_add_platform_scope(cfg, ConfigScope, name, path)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 606, in _add_platform_scope
platform = spack.architecture.platform().name
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 178, in _memoized_function
func.cache[args] = func(*args)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/architecture.py", line 516, in platform
return platform_cls()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/platforms/cray.py", line 63, in __init__
_target = self._default_target_from_env()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/platforms/cray.py", line 121, in _default_target_from_env
env={'TERM': os.environ['TERM']},
File "/usr/lib64/python2.6/UserDict.py", line 22, in __getitem__
raise KeyError(key)
KeyError: 'TERM'

# Fixed code
def force_echo(self):
    """Context manager to force local echo, even if echo is off."""
    if not self._active:
        raise RuntimeError("Can't call force_echo() outside log_output region!")

    # This uses the xon/xoff to highlight regions to be echoed in the
    # output. We us these control characters rather than, say, a
    # separate pipe, because they're in-band and assured to appear
    # exactly before and after the text we want to echo.
    sys.stdout.write(xon)
    sys.stdout.flush()
    try:
        yield
    finally:
        sys.stdout.write(xoff)
        sys.stdout.flush()
# Buggy code
def add_default_view_to_shell(self, shell):
    env_mod = spack.util.environment.EnvironmentModifications()

    if default_view_name not in self.views:
        # No default view to add to shell
        return env_mod.shell_modifications(shell)

    env_mod.extend(self.unconditional_environment_modifications(self.default_view))

    for _, spec in self.concretized_specs():
        if spec in self.default_view:
            env_mod.extend(
                self.environment_modifications_for_spec(spec, self.default_view)
            )

    # deduplicate paths from specs mapped to the same location
    for env_var in env_mod.group_by_name():
        env_mod.prune_duplicate_paths(env_var)

    return env_mod.shell_modifications(shell)


# Traceback (RuntimeError)
Traceback (most recent call last):
File "./atdm-spack/spack/bin/spack", line 64, in <module>
sys.exit(spack.main.main())
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/main.py", line 653, in main
ev.activate(env, args.use_env_repo)
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/environment.py", line 163, in activate
cmds += env.add_default_view_to_shell(shell)
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/environment.py", line 1074, in add_default_view_to_shell
spec, self.default_view))
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/environment.py", line 1055, in environment_modifications_for_spec
spec, context='run'
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/build_environment.py", line 759, in modifications_from_dependencies
dpkg.setup_dependent_package(pkg.module, spec)
File "/home/rabartl/Spack.base4/atdm-spack/spack/var/spack/repos/builtin/packages/python/package.py", line 729, in setup_dependent_package
module.setup_py = Executable(
File "/home/rabartl/Spack.base4/atdm-spack/spack/var/spack/repos/builtin/packages/python/package.py", line 526, in command

RuntimeError: Unable to locate python command in /home/rabartl/Spack.base4/atdm-spack/spack/opt/spack/linux-rhel6-x86_64/gcc-7.2.0/python-2.7.15-bfndwzimloeo5odtb656tkcsid4jzg42/bin

# Fixed code
def add_default_view_to_shell(self, shell):
    env_mod = spack.util.environment.EnvironmentModifications()

    if default_view_name not in self.views:
        # No default view to add to shell
        return env_mod.shell_modifications(shell)

    env_mod.extend(self.unconditional_environment_modifications(self.default_view))

    for _, spec in self.concretized_specs():
        if spec in self.default_view and spec.package.installed:
            env_mod.extend(
                self.environment_modifications_for_spec(spec, self.default_view)
            )

    # deduplicate paths from specs mapped to the same location
    for env_var in env_mod.group_by_name():
        env_mod.prune_duplicate_paths(env_var)

    return env_mod.shell_modifications(shell)
# Buggy code
def rm_default_view_from_shell(self, shell):
    env_mod = spack.util.environment.EnvironmentModifications()

    if default_view_name not in self.views:
        # No default view to add to shell
        return env_mod.shell_modifications(shell)

    env_mod.extend(
        self.unconditional_environment_modifications(self.default_view).reversed()
    )

    for _, spec in self.concretized_specs():
        if spec in self.default_view:
            env_mod.extend(
                self.environment_modifications_for_spec(
                    spec, self.default_view
                ).reversed()
            )
    return env_mod.shell_modifications(shell)


# Traceback (RuntimeError)
Traceback (most recent call last):
File "./atdm-spack/spack/bin/spack", line 64, in <module>
sys.exit(spack.main.main())
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/main.py", line 653, in main
ev.activate(env, args.use_env_repo)
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/environment.py", line 163, in activate
cmds += env.add_default_view_to_shell(shell)
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/environment.py", line 1074, in add_default_view_to_shell
spec, self.default_view))
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/environment.py", line 1055, in environment_modifications_for_spec
spec, context='run'
File "/home/rabartl/Spack.base4/atdm-spack/spack/lib/spack/spack/build_environment.py", line 759, in modifications_from_dependencies
dpkg.setup_dependent_package(pkg.module, spec)
File "/home/rabartl/Spack.base4/atdm-spack/spack/var/spack/repos/builtin/packages/python/package.py", line 729, in setup_dependent_package
module.setup_py = Executable(
File "/home/rabartl/Spack.base4/atdm-spack/spack/var/spack/repos/builtin/packages/python/package.py", line 526, in command

RuntimeError: Unable to locate python command in /home/rabartl/Spack.base4/atdm-spack/spack/opt/spack/linux-rhel6-x86_64/gcc-7.2.0/python-2.7.15-bfndwzimloeo5odtb656tkcsid4jzg42/bin

# Fixed code
def rm_default_view_from_shell(self, shell):
    env_mod = spack.util.environment.EnvironmentModifications()

    if default_view_name not in self.views:
        # No default view to add to shell
        return env_mod.shell_modifications(shell)

    env_mod.extend(
        self.unconditional_environment_modifications(self.default_view).reversed()
    )

    for _, spec in self.concretized_specs():
        if spec in self.default_view and spec.package.installed:
            env_mod.extend(
                self.environment_modifications_for_spec(
                    spec, self.default_view
                ).reversed()
            )
    return env_mod.shell_modifications(shell)
# Buggy code
def _detect_crayos_version(cls):
    release_attrs = read_cle_release_file()
    v = spack.version.Version(release_attrs["RELEASE"])
    return v[0]


# Traceback (IOError)
Traceback (most recent call last):
File "/u/sciteam/stewart1/spack/bin/spack", line 48, in <module>
sys.exit(spack.main.main())
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/main.py", line 704, in main
if spack.config.get('config:debug'):
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 627, in get
return config.get(path, default, scope)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 558, in __getattr__
return getattr(self.instance, name)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 554, in instance
self._instance = self.factory()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 609, in _config
_add_platform_scope(cfg, ConfigScope, name, path)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/config.py", line 562, in _add_platform_scope
platform = spack.architecture.platform().name
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/llnl/util/lang.py", line 184, in _memoized_function
func.cache[args] = func(*args)
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/architecture.py", line 388, in platform
return platform_cls()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/platforms/cray.py", line 76, in __init__
back_distro = Cnl()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/operating_systems/cnl.py", line 57, in __init__
version = self._detect_crayos_version()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/operating_systems/cnl.py", line 66, in _detect_crayos_version
release_attrs = read_cle_release_file()
File "/mnt/a/u/sciteam/stewart1/spack/lib/spack/spack/operating_systems/cnl.py", line 37, in read_cle_release_file
with open(_cle_release_file) as release_file:
IOError: [Errno 2] No such file or directory: '/etc/opt/cray/release/cle-release'

# Fixed code
def _detect_crayos_version(cls):
    if os.path.isfile(_cle_release_file):
        release_attrs = read_cle_release_file()
        v = spack.version.Version(release_attrs["RELEASE"])
        return v[0]
    elif os.path.isfile(_clerelease_file):
        v = read_clerelease_file()
        return spack.version.Version(v)[0]
    else:
        raise spack.error.UnsupportedPlatformError("Unable to detect Cray OS version")
# Buggy code
def setup_dependent_package(self, module, dependent_spec):
    """Called before perl modules' install() methods.
    In most cases, extensions will only need to have one line:
    perl('Makefile.PL','INSTALL_BASE=%s' % self.prefix)
    """

    # perl extension builds can have a global perl executable function
    module.perl = self.spec["perl"].command

    # Add variables for library directory
    module.perl_lib_dir = dependent_spec.prefix.lib.perl5

    # Make the site packages directory for extensions,
    # if it does not exist already.
    if dependent_spec.package.is_extension:
        mkdirp(module.perl_lib_dir)


# Traceback (RuntimeError)
==> [2019-03-28-09:45:40.882685] Error: RuntimeError: Unable to locate perl command in None/bin

/scratch/gartung/work/spack/var/spack/repos/builtin/packages/perl/package.py:194, in setup_dependent_package:
191        """
192
193        # perl extension builds can have a global perl executable function
>>    194        module.perl = self.spec['perl'].command
195
196        # Add variables for library directory
197        module.perl_lib_dir = dependent_spec.prefix.lib.perl5


Traceback (most recent call last):
File "/scratch/gartung/work/spack/lib/spack/spack/build_environment.py", line 766, in child_process
setup_package(pkg, dirty=dirty)
File "/scratch/gartung/work/spack/lib/spack/spack/build_environment.py", line 687, in setup_package
dpkg.setup_dependent_package(pkg.module, spec)
File "/scratch/gartung/work/spack/var/spack/repos/builtin/packages/perl/package.py", line 195, in setup_dependent_package
File "/scratch/gartung/work/spack/lib/spack/spack/spec.py", line 810, in __get__
value = f()
File "/scratch/gartung/work/spack/lib/spack/spack/spec.py", line 802, in <lambda>
callbacks_chain.append(lambda: self.default(self, instance, cls))
File "/scratch/gartung/work/spack/lib/spack/spack/spec.py", line 654, in _command_default_handler
raise RuntimeError(msg.format(spec.name, spec.prefix.bin))
RuntimeError: Unable to locate perl command in None/bin

# Fixed code
def setup_dependent_package(self, module, dependent_spec):
    """Called before perl modules' install() methods.
    In most cases, extensions will only need to have one line:
    perl('Makefile.PL','INSTALL_BASE=%s' % self.prefix)
    """

    # If system perl is used through packages.yaml
    # there cannot be extensions.
    if dependent_spec.package.is_extension:
        # perl extension builds can have a global perl
        # executable function
        module.perl = self.spec["perl"].command

        # Add variables for library directory
        module.perl_lib_dir = dependent_spec.prefix.lib.perl5

        # Make the site packages directory for extensions,
        # if it does not exist already.
        mkdirp(module.perl_lib_dir)
# Buggy code
def get_number(prompt, **kwargs):
    default = kwargs.get("default", None)
    abort = kwargs.get("abort", None)

    if default is not None and abort is not None:
        prompt += " (default is %s, %s to abort) " % (default, abort)
    elif default is not None:
        prompt += " (default is %s) " % default
    elif abort is not None:
        prompt += " (%s to abort) " % abort

    number = None
    while number is None:
        msg(prompt, newline=False)
        ans = raw_input()
        if ans == str(abort):
            return None

        if ans:
            try:
                number = int(ans)
                if number < 1:
                    msg("Please enter a valid number.")
                    number = None
            except ValueError:
                msg("Please enter a valid number.")
        elif default is not None:
            number = default
    return number


# Traceback (NameError)
$ spack uninstall --all
...
==> Do you want to proceed? [y/N] Traceback (most recent call last):
File "/home/christoph/spack/bin/spack", line 220, in <module>
main(sys.argv)
File "/home/christoph/spack/bin/spack", line 216, in main
_main(args, unknown)
File "/home/christoph/spack/bin/spack", line 183, in _main
return_val = command(parser, args)
File "/home/christoph/spack/lib/spack/spack/cmd/uninstall.py", line 213, in uninstall
answer = tty.get_yes_or_no('Do you want to proceed?', default=False)
File "/home/christoph/spack/lib/spack/llnl/util/tty/__init__.py", line 200, in get_yes_or_no
ans = raw_input().lower()
NameError: name 'raw_input' is not defined

# Fixed code
def get_number(prompt, **kwargs):
    default = kwargs.get("default", None)
    abort = kwargs.get("abort", None)

    if default is not None and abort is not None:
        prompt += " (default is %s, %s to abort) " % (default, abort)
    elif default is not None:
        prompt += " (default is %s) " % default
    elif abort is not None:
        prompt += " (%s to abort) " % abort

    number = None
    while number is None:
        msg(prompt, newline=False)
        ans = input()
        if ans == str(abort):
            return None

        if ans:
            try:
                number = int(ans)
                if number < 1:
                    msg("Please enter a valid number.")
                    number = None
            except ValueError:
                msg("Please enter a valid number.")
        elif default is not None:
            number = default
    return number
# Buggy code
def get_yes_or_no(prompt, **kwargs):
    default_value = kwargs.get("default", None)

    if default_value is None:
        prompt += " [y/n] "
    elif default_value is True:
        prompt += " [Y/n] "
    elif default_value is False:
        prompt += " [y/N] "
    else:
        raise ValueError("default for get_yes_no() must be True, False, or None.")

    result = None
    while result is None:
        msg(prompt, newline=False)
        ans = raw_input().lower()
        if not ans:
            result = default_value
            if result is None:
                print("Please enter yes or no.")
        else:
            if ans == "y" or ans == "yes":
                result = True
            elif ans == "n" or ans == "no":
                result = False
    return result


# Traceback (NameError)
$ spack uninstall --all
...
==> Do you want to proceed? [y/N] Traceback (most recent call last):
File "/home/christoph/spack/bin/spack", line 220, in <module>
main(sys.argv)
File "/home/christoph/spack/bin/spack", line 216, in main
_main(args, unknown)
File "/home/christoph/spack/bin/spack", line 183, in _main
return_val = command(parser, args)
File "/home/christoph/spack/lib/spack/spack/cmd/uninstall.py", line 213, in uninstall
answer = tty.get_yes_or_no('Do you want to proceed?', default=False)
File "/home/christoph/spack/lib/spack/llnl/util/tty/__init__.py", line 200, in get_yes_or_no
ans = raw_input().lower()
NameError: name 'raw_input' is not defined

# Fixed code
def get_yes_or_no(prompt, **kwargs):
    default_value = kwargs.get("default", None)

    if default_value is None:
        prompt += " [y/n] "
    elif default_value is True:
        prompt += " [Y/n] "
    elif default_value is False:
        prompt += " [y/N] "
    else:
        raise ValueError("default for get_yes_no() must be True, False, or None.")

    result = None
    while result is None:
        msg(prompt, newline=False)
        ans = input().lower()
        if not ans:
            result = default_value
            if result is None:
                print("Please enter yes or no.")
        else:
            if ans == "y" or ans == "yes":
                result = True
            elif ans == "n" or ans == "no":
                result = False
    return result
# Buggy code
def install(self, spec, prefix):
    env["GEOS_DIR"] = spec["geos"].prefix
    setup_py("install", "--prefix=%s" % prefix)


# Traceback (ImportError)
import mpl_toolkits.basemap
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home2/rpfische/spack3/opt/spack/linux-centos7-x86_64/gcc-4.9.3/py-basemap-1.0.7-ruhltkr62akc3yp2llvsqupikvhkq5b5/lib/python3.5/site-packages/mpl_toolkits/basemap/__init__.py", line 31, in <module>
from mpl_toolkits.axes_grid1 import make_axes_locatable
ImportError: No module named 'mpl_toolkits.axes_grid1'

# Fixed code
def install(self, spec, prefix):
    env["GEOS_DIR"] = spec["geos"].prefix
    setup_py("install", "--prefix=%s" % prefix)

    # We are not sure if this fix is needed before Python 3.5.2.
    # If it is needed, this test should be changed.
    # See: https://github.com/LLNL/spack/pull/1964
    if spec["python"].version >= Version("3.5.2"):
        # Use symlinks to join the two mpl_toolkits/ directories into
        # one, inside of basemap.  This is because Basemap tries to
        # "add to" an existing package in Matplotlib, which is only
        # legal Python for "Implicit Namespace Packages":
        #     https://www.python.org/dev/peps/pep-0420/
        #     https://github.com/Homebrew/homebrew-python/issues/112
        # In practice, Python will see only the basemap version of
        # mpl_toolkits
        path_m = find_package_dir(spec["py-matplotlib"].prefix, "mpl_toolkits")
        path_b = find_package_dir(spec.prefix, "mpl_toolkits")
        link_dir(path_m, path_b)
# Buggy code
def create_db_tarball(args):
    tar = which("tar")
    tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
    tarball_path = os.path.abspath(tarball_name)

    base = os.path.basename(spack.install_path)
    transform_args = []
    if "GNU" in tar("--version", output=str):
        transform_args = ["--transform", "s/^%s/%s/" % (base, tarball_name)]
    else:
        transform_args = ["-s", "/^%s/%s/" % (base, tarball_name)]

    wd = os.path.dirname(spack.install_path)
    with working_dir(wd):
        files = [spack.installed_db._index_path]
        files += glob("%s/*/*/*/.spack/spec.yaml" % base)
        files = [os.path.relpath(f) for f in files]

        args = ["-czf", tarball_path]
        args += transform_args
        args += files
        tar(*args)

    tty.msg("Created %s" % tarball_name)


# Traceback (AssertionError)
$ spack install eigen
==> Installing eigen
==> metis is already installed in /blues/gpfs/home/software/spack-0.9.1/opt/spack/linux-centos6-x86_64/gcc-6.1.0/metis-5.1.0-k4pqzigdgdsuk2r3xls7eyhk6uwvxp46
Traceback (most recent call last):
File "/soft/spack-0.9.1/bin/spack", line 202, in <module>
main()
File "/soft/spack-0.9.1/bin/spack", line 179, in main
return_val = command(parser, args)
File "/blues/gpfs/home/software/spack-0.9.1/lib/spack/spack/cmd/install.py", line 117, in install
package.do_install(**kwargs)
File "/blues/gpfs/home/software/spack-0.9.1/lib/spack/spack/package.py", line 1183, in do_install
dirty=dirty)
File "/blues/gpfs/home/software/spack-0.9.1/lib/spack/spack/package.py", line 1160, in do_install
rec = spack.installed_db.get_record(self.spec)
File "/blues/gpfs/home/software/spack-0.9.1/lib/spack/spack/database.py", line 79, in converter
return function(self, spec_like, *args, **kwargs)
File "/blues/gpfs/home/software/spack-0.9.1/lib/spack/spack/database.py", line 527, in get_record
key = self._get_matching_spec_key(spec, **kwargs)
File "/blues/gpfs/home/software/spack-0.9.1/lib/spack/spack/database.py", line 519, in _get_matching_spec_key
match = self.query_one(spec, **kwargs)
File "/blues/gpfs/home/software/spack-0.9.1/lib/spack/spack/database.py", line 653, in query_one
assert len(concrete_specs) <= 1
AssertionError

# Fixed code
def create_db_tarball(args):
    tar = which("tar")
    tarball_name = "spack-db.%s.tar.gz" % _debug_tarball_suffix()
    tarball_path = os.path.abspath(tarball_name)

    base = os.path.basename(spack.store.root)
    transform_args = []
    if "GNU" in tar("--version", output=str):
        transform_args = ["--transform", "s/^%s/%s/" % (base, tarball_name)]
    else:
        transform_args = ["-s", "/^%s/%s/" % (base, tarball_name)]

    wd = os.path.dirname(spack.store.root)
    with working_dir(wd):
        files = [spack.store.db._index_path]
        files += glob("%s/*/*/*/.spack/spec.yaml" % base)
        files = [os.path.relpath(f) for f in files]

        args = ["-czf", tarball_path]
        args += transform_args
        args += files
        tar(*args)

    tty.msg("Created %s" % tarball_name)
# Buggy code
def graph(parser, args):
    concretize = not args.normalize
    if args.installed:
        if args.specs:
            tty.die("Can't specify specs with --installed")
        args.dot = True
        specs = spack.installed_db.query()

    else:
        specs = spack.cmd.parse_specs(args.specs, normalize=True, concretize=concretize)

    if not specs:
        setup_parser.parser.print_help()
        return 1

    deptype = nobuild
    if args.deptype:
        deptype = tuple(args.deptype.split(","))
        validate_deptype(deptype)
        deptype = canonical_deptype(deptype)

    if args.dot:  # Dot graph only if asked for.
        graph_dot(specs, static=args.static, deptype=deptype)

    elif specs:  # ascii is default: user doesn't need to provide it explicitly
        graph_ascii(specs[0], debug=spack.debug, deptype=deptype)
        for spec in specs[1:]:
            print  # extra line bt/w independent graphs
            graph_ascii(spec, debug=spack.debug)


# Traceback (AttributeError)
$ spack setup pism@dev
Traceback (most recent call last):
File "/home2/rpfische/spack4/bin/spack", line 203, in <module>
main()
File "/home2/rpfische/spack4/bin/spack", line 180, in main
return_val = command(parser, args)
File "/home2/rpfische/spack4/lib/spack/spack/cmd/setup.py", line 133, in setup
with spack.installed_db.write_transaction():
AttributeError: 'module' object has no attribute 'installed_db'

# Fixed code
def graph(parser, args):
    concretize = not args.normalize
    if args.installed:
        if args.specs:
            tty.die("Can't specify specs with --installed")
        args.dot = True
        specs = spack.store.db.query()

    else:
        specs = spack.cmd.parse_specs(args.specs, normalize=True, concretize=concretize)

    if not specs:
        setup_parser.parser.print_help()
        return 1

    deptype = nobuild
    if args.deptype:
        deptype = tuple(args.deptype.split(","))
        validate_deptype(deptype)
        deptype = canonical_deptype(deptype)

    if args.dot:  # Dot graph only if asked for.
        graph_dot(specs, static=args.static, deptype=deptype)

    elif specs:  # ascii is default: user doesn't need to provide it explicitly
        graph_ascii(specs[0], debug=spack.debug, deptype=deptype)
        for spec in specs[1:]:
            print  # extra line bt/w independent graphs
            graph_ascii(spec, debug=spack.debug)
# Buggy code
def find_working_dir(self):
    # type: () -> Optional[str]
    view = self._current_view()
    window = view.window() if view else None

    if view and view.file_name():
        file_dir = os.path.dirname(view.file_name())
        if os.path.isdir(file_dir):
            return file_dir

    if window:
        folders = window.folders()
        if folders and os.path.isdir(folders[0]):
            return folders[0]

    return None


# Traceback (AttributeError)
Traceback (most recent call last):
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 157, in git
working_dir = self.repo_path
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 437, in repo_path
return self.get_repo_path()
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 409, in get_repo_path
window = view.window()
AttributeError: 'NoneType' object has no attribute 'window'

# Fixed code
def find_working_dir(self):
    # type: () -> Optional[str]
    view = self._current_view()
    window = view.window() if view else None

    file_name = self._current_filename()
    if file_name:
        file_dir = os.path.dirname(file_name)
        if os.path.isdir(file_dir):
            return file_dir

    if window:
        folders = window.folders()
        if folders and os.path.isdir(folders[0]):
            return folders[0]

    return None
# Buggy code
def find_repo_path(self):
    # type: () -> Optional[str]
    """
    Similar to find_working_dir, except that it does not stop on the first
    directory found, rather on the first git repository found.
    """
    view = self._current_view()
    window = view.window() if view else None
    repo_path = None

    # try the current file first
    if view and view.file_name():
        file_dir = os.path.dirname(view.file_name())
        if os.path.isdir(file_dir):
            repo_path = self._find_git_toplevel(file_dir)

    # fallback: use the first folder if the current file is not inside a git repo
    if not repo_path:
        if window:
            folders = window.folders()
            if folders and os.path.isdir(folders[0]):
                repo_path = self._find_git_toplevel(folders[0])

    return os.path.realpath(repo_path) if repo_path else None


# Traceback (AttributeError)
Traceback (most recent call last):
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 157, in git
working_dir = self.repo_path
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 437, in repo_path
return self.get_repo_path()
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 409, in get_repo_path
window = view.window()
AttributeError: 'NoneType' object has no attribute 'window'

# Fixed code
def find_repo_path(self):
    # type: () -> Optional[str]
    """
    Similar to find_working_dir, except that it does not stop on the first
    directory found, rather on the first git repository found.
    """
    view = self._current_view()
    window = view.window() if view else None
    repo_path = None

    file_name = self._current_filename()
    if file_name:
        file_dir = os.path.dirname(file_name)
        if os.path.isdir(file_dir):
            repo_path = self._find_git_toplevel(file_dir)

    # fallback: use the first folder if the current file is not inside a git repo
    if not repo_path:
        if window:
            folders = window.folders()
            if folders and os.path.isdir(folders[0]):
                repo_path = self._find_git_toplevel(folders[0])

    return os.path.realpath(repo_path) if repo_path else None
# Buggy code
def __init__(self, parent=None):
    self.parent = parent
    self.global_settings = sublime.load_settings("GitSavvy.sublime-settings")


# Traceback (AttributeError)
Traceback (most recent call last):
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 220, in git
stdout, stderr = self.decode_stdout(stdout), self.decode_stdout(stderr)
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 277, in decode_stdout
fallback_encoding = self.savvy_settings.get("fallback_encoding")
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\settings.py", line 12, in get
project_savvy_settings = view.settings().get("GitSavvy", {}) or {}
AttributeError: 'NoneType' object has no attribute 'settings'

# Fixed code
def __init__(self, window=None):
    # type: (sublime.Window) -> None
    self._window = window or sublime.active_window()
    self._global_settings = get_global_settings()
# Buggy code
def get(self, key, default=None):
    window = sublime.active_window()
    view = window.active_view()
    project_savvy_settings = view.settings().get("GitSavvy", {}) or {}

    if key in project_savvy_settings:
        return project_savvy_settings[key]

    # fall back to old style project setting
    project_data = window.project_data()
    if project_data and "GitSavvy" in project_data:
        project_savvy_settings = project_data["GitSavvy"]
        if key in project_savvy_settings:
            return project_savvy_settings.get(key)

    return self.global_settings.get(key, default)


# Traceback (AttributeError)
Traceback (most recent call last):
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 220, in git
stdout, stderr = self.decode_stdout(stdout), self.decode_stdout(stderr)
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 277, in decode_stdout
fallback_encoding = self.savvy_settings.get("fallback_encoding")
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\settings.py", line 12, in get
project_savvy_settings = view.settings().get("GitSavvy", {}) or {}
AttributeError: 'NoneType' object has no attribute 'settings'

# Fixed code
def get(self, key, default=None):
    try:
        return get_project_settings(self._window)[key]
    except KeyError:
        return self._global_settings.get(key, default)
# Buggy code
def set(self, key, value):
    self.global_settings.set(key, value)


# Traceback (AttributeError)
Traceback (most recent call last):
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 220, in git
stdout, stderr = self.decode_stdout(stdout), self.decode_stdout(stderr)
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 277, in decode_stdout
fallback_encoding = self.savvy_settings.get("fallback_encoding")
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\settings.py", line 12, in get
project_savvy_settings = view.settings().get("GitSavvy", {}) or {}
AttributeError: 'NoneType' object has no attribute 'settings'

# Fixed code
def set(self, key, value):
    self._global_settings.set(key, value)
# Buggy code
def savvy_settings(self):
    if not self._savvy_settings:
        self._savvy_settings = GitSavvySettings(self)
    return self._savvy_settings


# Traceback (AttributeError)
Traceback (most recent call last):
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 220, in git
stdout, stderr = self.decode_stdout(stdout), self.decode_stdout(stderr)
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\git_command.py", line 277, in decode_stdout
fallback_encoding = self.savvy_settings.get("fallback_encoding")
File "C:\Users\c-flo\AppData\Roaming\Sublime Text 3\Packages\GitSavvy\core\settings.py", line 12, in get
project_savvy_settings = view.settings().get("GitSavvy", {}) or {}
AttributeError: 'NoneType' object has no attribute 'settings'

# Fixed code
def savvy_settings(self):
    if not self._savvy_settings:
        window = (
            maybe(lambda: self.window)  # type: ignore[attr-defined]
            or maybe(lambda: self.view.window())  # type: ignore[attr-defined]
            or sublime.active_window()
        )
        self._savvy_settings = GitSavvySettings(window)
    return self._savvy_settings