gurudesh/pytracebugs huggingface dataset:
# Buggy code
def wrapper(self, *args, **kwargs):
    if self.is_remote:
        if hasattr(self.remote_object, func.__name__):
            return getattr(self.remote_object, func.__name__)(*args, **kwargs)
    return func(self, *args, **kwargs)


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def wrapper(self, *args, **kwargs):
    iocache = self.rule.workflow.iocache
    if not iocache.active or self.inventory_path is None:
        return func(self, *args, **kwargs)

    cache = getattr(iocache, func.__name__)
    # first check if file is present in cache
    if self.inventory_path in cache:
        res = cache[self.inventory_path]
    # check if the folder was cached
    elif iocache.in_inventory(self.inventory_root):
        # as the folder was cached, we do know that the file does not exist
        if raise_error:
            # make sure that the cache behaves the same as non-cached results
            raise FileNotFoundError("No such file or directory: {}".format(self.file))
        else:
            return False
    elif self._is_function:
        raise ValueError(
            "This IOFile is specified as a function and may not be used directly."
        )
    else:
        res = IOCACHE_DEFERRED

    if res is IOCACHE_DEFERRED:
        # determine values that are not yet cached
        self._add_to_inventory(func.__name__)
        res = cache[self.inventory_path]

    # makes sure that cache behaves same as non-cached results
    if res is IOCACHE_BROKENSYMLINK:
        raise WorkflowError("File {} seems to be a broken symlink.".format(self.file))
    elif res is IOCACHE_NOTEXIST:
        raise FileNotFoundError("File {} does not exist.".format(self.file))
    elif res is IOCACHE_NOPERMISSION:
        raise PermissionError(
            "File {} does not have the required permissions.".format(self.file)
        )
    return res
# Buggy code
def __contains__(self, path):
    # if already in inventory, always return True.
    return self.cache.in_inventory(path) or super().__contains__(path)


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def __contains__(self, path):
    if super().__contains__(path):
        return True
    return path in self.passthroughdict
# Buggy code
def inventory(self, cache: snakemake.io.IOCache):
    """From this file, try to find as much existence and modification date
    information as possible.
    """
    # If this is implemented in a remote object, results have to be stored in
    # the given IOCache object.
    pass


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def inventory(self, cache: snakemake.io.IOCache):
    """From this file, try to find as much existence and modification date
    information as possible for files in the same folder.
    """
    # If this is implemented in a remote object, results have to be stored in
    # the given IOCache object.
    pass
# Buggy code
def init(self, progress=False):
    """Initialise the DAG."""
    for job in map(self.rule2job, self.targetrules):
        job = self.update([job], progress=progress)
        self.targetjobs.add(job)

    for file in self.targetfiles:
        job = self.update(self.file2jobs(file), file=file, progress=progress)
        self.targetjobs.add(job)

    self.cleanup()

    self.update_needrun()
    self.set_until_jobs()
    self.delete_omitfrom_jobs()
    self.update_jobids()

    self.check_directory_outputs()

    # check if remaining jobs are valid
    for i, job in enumerate(self.jobs):
        job.is_valid()


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def init(self, progress=False):
    """Initialise the DAG."""
    for job in map(self.rule2job, self.targetrules):
        job = self.update([job], progress=progress, create_inventory=True)
        self.targetjobs.add(job)

    for file in self.targetfiles:
        job = self.update(
            self.file2jobs(file),
            file=file,
            progress=progress,
            create_inventory=True,
        )
        self.targetjobs.add(job)

    self.cleanup()

    self.update_needrun(create_inventory=True)
    self.set_until_jobs()
    self.delete_omitfrom_jobs()
    self.update_jobids()

    self.check_directory_outputs()

    # check if remaining jobs are valid
    for i, job in enumerate(self.jobs):
        job.is_valid()
# Buggy code
def __init__(self, cache):
    super().__init__()
    self.cache = cache


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def __init__(self, cache):
    super().__init__()
    self.cache = cache
    self.has_inventory = set()
# Buggy code
def mtime(self):
    return self.mtime_local


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def mtime(self):
    return self.mtime_uncached
# Buggy code
def local(value):
    """Mark a file as local file. This disables application of a default remote
    provider.
    """
    if is_flagged(value, "remote"):
        raise SyntaxError("Remote and local flags are mutually exclusive.")
    return flag(value, "local")


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def local(self, follow_symlinks=False):
    if follow_symlinks and self._local_target is not None:
        return self._local_target
    return self._local
# Buggy code
def output_mintime(self):
    """Return oldest output file."""

    existing = [f.mtime for f in self.expanded_output if f.exists]
    if self.benchmark and self.benchmark.exists:
        existing.append(self.benchmark.mtime)
    if existing:
        return min(existing)
    return None


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def output_mintime(self):
    """Return oldest output file."""
    try:
        mintime = min(
            f.mtime.local_or_remote() for f in self.expanded_output if f.exists
        )
    except ValueError:
        # no existing output
        mintime = None

    if self.benchmark and self.benchmark.exists:
        mintime_benchmark = self.benchmark.mtime.local_or_remote()
        if mintime is not None:
            return min(mintime, mintime_benchmark)
        else:
            return mintime_benchmark

    return mintime
# Buggy code
def remote_input_newer_than_local(self):
    files = set()
    for f in self.remote_input:
        if (f.exists_remote and f.exists_local) and (f.mtime > f.mtime_local):
            files.add(f)
    return files


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def remote_input_newer_than_local(self):
    files = set()
    for f in self.remote_input:
        if (f.exists_remote and f.exists_local) and (
            f.mtime.remote() > f.mtime.local(follow_symlinks=True)
        ):
            files.add(f)
    return files
# Buggy code
def remote_input_older_than_local(self):
    files = set()
    for f in self.remote_input:
        if (f.exists_remote and f.exists_local) and (f.mtime < f.mtime_local):
            files.add(f)
    return files


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def remote_input_older_than_local(self):
    files = set()
    for f in self.remote_input:
        if (f.exists_remote and f.exists_local) and (
            f.mtime.remote() < f.mtime.local(follow_symlinks=True)
        ):
            files.add(f)
    return files
# Buggy code
def remote_output_newer_than_local(self):
    files = set()
    for f in self.remote_output:
        if (f.exists_remote and f.exists_local) and (f.mtime > f.mtime_local):
            files.add(f)
    return files


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def remote_output_newer_than_local(self):
    files = set()
    for f in self.remote_output:
        if (f.exists_remote and f.exists_local) and (
            f.mtime.remote() > f.mtime.local(follow_symlinks=True)
        ):
            files.add(f)
    return files
# Buggy code
def remote_output_older_than_local(self):
    files = set()
    for f in self.remote_output:
        if (f.exists_remote and f.exists_local) and (f.mtime < f.mtime_local):
            files.add(f)
    return files


# Traceback (FileNotFoundError)
Building DAG of jobs...
Traceback (most recent call last):
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/__init__.py", line 709, in snakemake
keepincomplete=keep_incomplete,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/workflow.py", line 670, in execute
dag.init()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 177, in init
job = self.update(self.file2jobs(file), file=file, progress=progress)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 715, in update
progress=progress,
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/dag.py", line 792, in update_
file.inventory()
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 210, in inventory
self._local_inventory(cache)
File "<base_path>/software/miniconda/envs/snakemake/lib/python3.7/site-packages/snakemake/io.py", line 224, in _local_inventory
with os.scandir(path) as scan:
FileNotFoundError: [Errno 2] No such file or directory: '<analysis_patch>/tmp_batch113/codons'

# Fixed code
def remote_output_older_than_local(self):
    files = set()
    for f in self.remote_output:
        if (f.exists_remote and f.exists_local) and (
            f.mtime.remote() < f.mtime.local(follow_symlinks=True)
        ):
            files.add(f)
    return files
# Buggy code
def sleep():
    # do not sleep on CI. In that case we just want to quickly test everything.
    if os.environ.get("CIRCLECI") != "true":
        time.sleep(10)


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def sleep():
    # do not sleep on CI. In that case we just want to quickly test everything.
    if os.environ.get("CI") != "true":
        time.sleep(10)
# Buggy code
def job_args_and_prepare(self, job):
    job.prepare()

    conda_env = job.conda_env_path
    singularity_img = job.singularity_img_path

    benchmark = None
    benchmark_repeats = job.benchmark_repeats or 1
    if job.benchmark is not None:
        benchmark = str(job.benchmark)
    return (
        job.rule,
        job.input.plainstrings(),
        job.output.plainstrings(),
        job.params,
        job.wildcards,
        job.threads,
        job.resources,
        job.log.plainstrings(),
        benchmark,
        benchmark_repeats,
        conda_env,
        singularity_img,
        self.workflow.singularity_args,
        self.workflow.use_singularity,
        self.workflow.linemaps,
        self.workflow.debug,
        self.workflow.cleanup_scripts,
        job.shadow_dir,
        job.jobid,
    )


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def job_args_and_prepare(self, job):
    job.prepare()

    conda_env = job.conda_env_path
    singularity_img = job.singularity_img_path

    benchmark = None
    benchmark_repeats = job.benchmark_repeats or 1
    if job.benchmark is not None:
        benchmark = str(job.benchmark)
    return (
        job.rule,
        job.input._plainstrings(),
        job.output._plainstrings(),
        job.params,
        job.wildcards,
        job.threads,
        job.resources,
        job.log._plainstrings(),
        benchmark,
        benchmark_repeats,
        conda_env,
        singularity_img,
        self.workflow.singularity_args,
        self.workflow.use_singularity,
        self.workflow.linemaps,
        self.workflow.debug,
        self.workflow.cleanup_scripts,
        job.shadow_dir,
        job.jobid,
    )
# Buggy code
def __init__(
    self,
    toclone=None,
    fromdict=None,
    plainstr=False,
    strip_constraints=False,
    custom_map=None,
):
    """
    Create the object.

    Arguments
    toclone  -- another Namedlist that shall be cloned
    fromdict -- a dict that shall be converted to a
        Namedlist (keys become names)
    """
    list.__init__(self)
    self._names = dict()

    if toclone:
        if custom_map is not None:
            self.extend(map(custom_map, toclone))
        elif plainstr:
            self.extend(map(str, toclone))
        elif strip_constraints:
            self.extend(map(strip_wildcard_constraints, toclone))
        else:
            self.extend(toclone)
        if isinstance(toclone, Namedlist):
            self.take_names(toclone.get_names())
    if fromdict:
        for key, item in fromdict.items():
            self.append(item)
            self.add_name(key)


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def __init__(
    self,
    toclone=None,
    fromdict=None,
    plainstr=False,
    strip_constraints=False,
    custom_map=None,
):
    """
    Create the object.

    Arguments
    toclone  -- another Namedlist that shall be cloned
    fromdict -- a dict that shall be converted to a
        Namedlist (keys become names)
    """
    list.__init__(self)
    self._names = dict()

    if toclone:
        if custom_map is not None:
            self.extend(map(custom_map, toclone))
        elif plainstr:
            self.extend(map(str, toclone))
        elif strip_constraints:
            self.extend(map(strip_wildcard_constraints, toclone))
        else:
            self.extend(toclone)
        if isinstance(toclone, Namedlist):
            self._take_names(toclone._get_names())
    if fromdict:
        for key, item in fromdict.items():
            self.append(item)
            self._add_name(key)
# Buggy code
def keys(self):
    return self._names


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def keys(self):
    return self._names.keys()
# Buggy code
def format_dict(dict, omit_keys=[], omit_values=[]):
    return ", ".join(
        "{}={}".format(name, str(value))
        for name, value in dict.items()
        if name not in omit_keys and value not in omit_values
    )


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def format_dict(dict_like, omit_keys=[], omit_values=[]):
    from snakemake.io import Namedlist

    if isinstance(dict_like, Namedlist):
        items = dict_like.items()
    elif isinstance(dict_like, dict):
        items = dict_like.items()
    else:
        raise ValueError(
            "bug: format_dict applied to something neither a dict nor a Namedlist"
        )
    return ", ".join(
        "{}={}".format(name, str(value))
        for name, value in items
        if name not in omit_keys and value not in omit_values
    )
# Buggy code
def check_output_duplicates(self):
    """Check ``Namedlist`` for duplicate entries and raise a ``WorkflowError``
    on problems.
    """
    seen = dict()
    idx = None
    for name, value in self.output.allitems():
        if name is None:
            if idx is None:
                idx = 0
            else:
                idx += 1
        if value in seen:
            raise WorkflowError(
                "Duplicate output file pattern in rule {}. First two "
                "duplicate for entries {} and {}".format(
                    self.name, seen[value], name or idx
                )
            )
        seen[value] = name or idx


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def check_output_duplicates(self):
    """Check ``Namedlist`` for duplicate entries and raise a ``WorkflowError``
    on problems.
    """
    seen = dict()
    idx = None
    for name, value in self.output._allitems():
        if name is None:
            if idx is None:
                idx = 0
            else:
                idx += 1
        if value in seen:
            raise WorkflowError(
                "Duplicate output file pattern in rule {}. First two "
                "duplicate for entries {} and {}".format(
                    self.name, seen[value], name or idx
                )
            )
        seen[value] = name or idx
# Buggy code
def _set_params_item(self, item, name=None):
    self.params.append(item)
    if name:
        self.params.add_name(name)


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def _set_params_item(self, item, name=None):
    self.params.append(item)
    if name:
        self.params._add_name(name)
# Buggy code
def _set_log_item(self, item, name=None):
    # Pathlib compatibility
    if isinstance(item, Path):
        item = str(item)
    if isinstance(item, str) or callable(item):
        if not callable(item):
            item = self.apply_default_remote(item)
            item = self._update_item_wildcard_constraints(item)

        self.log.append(IOFile(item, rule=self) if isinstance(item, str) else item)
        if name:
            self.log.add_name(name)
    else:
        try:
            start = len(self.log)
            for i in item:
                self._set_log_item(i)
            if name:
                self.log.set_name(name, start, end=len(self.log))
        except TypeError:
            raise SyntaxError("Log files have to be specified as strings.")


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def _set_log_item(self, item, name=None):
    # Pathlib compatibility
    if isinstance(item, Path):
        item = str(item)
    if isinstance(item, str) or callable(item):
        if not callable(item):
            item = self.apply_default_remote(item)
            item = self._update_item_wildcard_constraints(item)

        self.log.append(IOFile(item, rule=self) if isinstance(item, str) else item)
        if name:
            self.log._add_name(name)
    else:
        try:
            start = len(self.log)
            for i in item:
                self._set_log_item(i)
            if name:
                self.log._set_name(name, start, end=len(self.log))
        except TypeError:
            raise SyntaxError("Log files have to be specified as strings.")
# Buggy code
def expand_output(self, wildcards):
    output = OutputFiles(o.apply_wildcards(wildcards) for o in self.output)
    output.take_names(self.output.get_names())
    mapping = {f: f_ for f, f_ in zip(output, self.output)}

    for f in output:
        f.check()

    # Note that we do not need to check for duplicate file names after
    # expansion as all output patterns have contain all wildcards anyway.

    return output, mapping


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def expand_output(self, wildcards):
    output = OutputFiles(o.apply_wildcards(wildcards) for o in self.output)
    output._take_names(self.output._get_names())
    mapping = {f: f_ for f, f_ in zip(output, self.output)}

    for f in output:
        f.check()

    # Note that we do not need to check for duplicate file names after
    # expansion as all output patterns have contain all wildcards anyway.

    return output, mapping
# Buggy code
def input(self):
    return self.rule.input.stripped_constraints()


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def input(self):
    return self.rule.input._stripped_constraints()
# Buggy code
def params(self):
    return self.rule.params.clone()


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def params(self):
    return self.rule.params._clone()
# Buggy code
def __init__(
    self,
    input,
    output,
    params,
    wildcards,
    threads,
    resources,
    log,
    config,
    rulename,
    bench_iteration,
    scriptdir=None,
):
    # convert input and output to plain strings as some remote objects cannot
    # be pickled
    self.input = input.plainstrings()
    self.output = output.plainstrings()
    self.params = params
    self.wildcards = wildcards
    self.threads = threads
    self.resources = resources
    self.log = log.plainstrings()
    self.config = config
    self.rule = rulename
    self.bench_iteration = bench_iteration
    self.scriptdir = scriptdir


# Traceback (TypeError)
snakemake  --report
Building DAG of jobs...
Creating report...
Adding foo.rst (0 MB).
Could not detect mimetype for foo.rst, assuming text/plain.
Traceback (most recent call last):
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/__init__.py", line 618, in snakemake
batch=batch,
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/workflow.py", line 617, in execute
auto_report(dag, report)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 552, in auto_report
FileRecord(f, job, report_obj.caption, env, category)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/report/__init__.py", line 326, in __init__
self.params = logging.format_dict(job.params)
File "/mnt/work/Qc.py375.venv/lib/python3.7/site-packages/snakemake/logging.py", line 384, in format_dict
for name, value in dict.items()
TypeError: 'str' object is not callable

# Fixed code
def __init__(
    self,
    input,
    output,
    params,
    wildcards,
    threads,
    resources,
    log,
    config,
    rulename,
    bench_iteration,
    scriptdir=None,
):
    # convert input and output to plain strings as some remote objects cannot
    # be pickled
    self.input = input._plainstrings()
    self.output = output._plainstrings()
    self.params = params
    self.wildcards = wildcards
    self.threads = threads
    self.resources = resources
    self.log = log._plainstrings()
    self.config = config
    self.rule = rulename
    self.bench_iteration = bench_iteration
    self.scriptdir = scriptdir
# Buggy code
def __init__(self, *args, stay_on_remote=False, **kwargs):
    super(RemoteProvider, self).__init__(*args, stay_on_remote=stay_on_remote, **kwargs)

    self._as = AzureStorageHelper(*args, **kwargs)


# Traceback (TypeError)
snakemake --tibanna --default-remote-prefix=tibanna/run_1
Traceback (most recent call last):
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/snakemake/__init__.py", line 421, in snakemake
keep_local=True, is_default=True
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/snakemake/remote/S3.py", line 41, in __init__
self._s3c = S3Helper(*args, **kwargs)  # _private variable by convention
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/snakemake/remote/S3.py", line 167, in __init__
self.s3 = boto3.resource("s3", **kwargs)
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/boto3/__init__.py", line 100, in resource
return _get_default_session().resource(*args, **kwargs)
TypeError: resource() got an unexpected keyword argument 'keep_local'

# Fixed code
def __init__(
    self, *args, keep_local=False, stay_on_remote=False, is_default=False, **kwargs
):
    super(RemoteProvider, self).__init__(
        *args,
        keep_local=keep_local,
        stay_on_remote=stay_on_remote,
        is_default=is_default,
        **kwargs,
    )

    self._as = AzureStorageHelper(*args, **kwargs)
# Buggy code
def __init__(
    self, *args, stay_on_remote=False, **kwargs
):  # this method is evaluated when instantiating this class
    super(RemoteProvider, self).__init__(
        *args, stay_on_remote=stay_on_remote, **kwargs
    )  # in addition to methods provided by AbstractRemoteProvider, we add these in

    self._s3c = S3Helper(*args, **kwargs)  # _private variable by convention


# Traceback (TypeError)
snakemake --tibanna --default-remote-prefix=tibanna/run_1
Traceback (most recent call last):
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/snakemake/__init__.py", line 421, in snakemake
keep_local=True, is_default=True
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/snakemake/remote/S3.py", line 41, in __init__
self._s3c = S3Helper(*args, **kwargs)  # _private variable by convention
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/snakemake/remote/S3.py", line 167, in __init__
self.s3 = boto3.resource("s3", **kwargs)
File "/tmp/tmp.1BY3tqvG9v/venv/lib/python3.6/site-packages/boto3/__init__.py", line 100, in resource
return _get_default_session().resource(*args, **kwargs)
TypeError: resource() got an unexpected keyword argument 'keep_local'

# Fixed code
def __init__(
    self, *args, keep_local=False, stay_on_remote=False, is_default=False, **kwargs
):
    super(RemoteProvider, self).__init__(
        *args,
        keep_local=keep_local,
        stay_on_remote=stay_on_remote,
        is_default=is_default,
        **kwargs,
    )  # in addition to methods provided by AbstractRemoteProvider, we add these in

    self._s3c = S3Helper(*args, **kwargs)  # _private variable by convention