code stringlengths 66 870k | docstring stringlengths 19 26.7k | func_name stringlengths 1 138 | language stringclasses 1
value | repo stringlengths 7 68 | path stringlengths 5 324 | url stringlengths 46 389 | license stringclasses 7
values |
|---|---|---|---|---|---|---|---|
def cwl(
path,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
use_singularity,
bench_record,
jobid,
sourcecache_path,
runtime_sourcecache_path,
):
"""
Load cwl from the given basedir + path and execute it.
... |
Load cwl from the given basedir + path and execute it.
| cwl | python | snakemake/snakemake | src/snakemake/cwl.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/cwl.py | MIT |
def job_to_cwl(job, dag, outputs, inputs):
"""Convert a job with its dependencies to a CWL workflow step."""
for f in job.output:
if os.path.isabs(f):
raise WorkflowError(
"All output files have to be relative to the working directory."
)
get_output_id = lamb... | Convert a job with its dependencies to a CWL workflow step. | job_to_cwl | python | snakemake/snakemake | src/snakemake/cwl.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/cwl.py | MIT |
def dag_to_cwl(dag):
"""Convert a given DAG to a CWL workflow, which is returned as a JSON object."""
snakemake_cwl = {
"class": "CommandLineTool",
"id": "#snakemake-job",
"label": "Snakemake job executor",
"hints": [{"dockerPull": get_container_image(), "class": "DockerRequireme... | Convert a given DAG to a CWL workflow, which is returned as a JSON object. | dag_to_cwl | python | snakemake/snakemake | src/snakemake/cwl.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/cwl.py | MIT |
def check_directory_outputs(self):
"""Check that no output file is contained in a directory output of the same or another rule."""
outputs = sorted(
{(os.path.abspath(f), job) for job in self.jobs for f in job.output}
)
for i in range(len(outputs) - 1):
(a, job_a)... | Check that no output file is contained in a directory output of the same or another rule. | check_directory_outputs | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def sanitize_local_storage_copies(self):
"""Remove local copies of storage files that will be recreated in this run."""
async with asyncio.TaskGroup() as tg:
for job in self.needrun_jobs():
if not self.finished(job):
for f in job.output:
... | Remove local copies of storage files that will be recreated in this run. | sanitize_local_storage_copies | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def check_incomplete(self):
"""Check if any output files are incomplete. This is done by looking up
markers in the persistence module."""
if not self.ignore_incomplete:
incomplete_files = await self.incomplete_files()
if any(incomplete_files):
if sel... | Check if any output files are incomplete. This is done by looking up
markers in the persistence module. | check_incomplete | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def incomplete_external_jobid(self, job) -> Optional[str]:
"""Return the external jobid of the job if it is marked as incomplete.
Returns None, if job is not incomplete, or if no external jobid has been
registered or if force_incomplete is True.
"""
if self.workflow.dag_settings... | Return the external jobid of the job if it is marked as incomplete.
Returns None, if job is not incomplete, or if no external jobid has been
registered or if force_incomplete is True.
| incomplete_external_jobid | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def needrun_jobs(self, exclude_finished=True):
"""Jobs that need to be executed."""
if exclude_finished:
return filterfalse(self.finished, self._needrun)
else:
return iter(self._needrun) | Jobs that need to be executed. | needrun_jobs | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def newversion_files(self):
"""Return list of files where the current version is newer than the
recorded version.
"""
return list(
chain(
*(
job.output
for job in filter(self.workflow.persistence.newversion, self.jobs)
... | Return list of files where the current version is newer than the
recorded version.
| newversion_files | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def check_and_touch_output(
self,
job: Job,
wait: int = 3,
ignore_missing_output: Union[List[_IOFile], bool] = False,
no_touch: bool = False,
wait_for_local: bool = True,
check_output_mtime: bool = True,
):
"""Raise exception if output files of j... | Raise exception if output files of job are missing. | check_and_touch_output | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def correctly_flagged_with_dir(f):
"""Check that files flagged as directories are in fact directories
In ambiguous cases, such as when f is managed by a storage backend, or f
doesn't exist and
ignore_missing_output is true, always return True
"""
... | Check that files flagged as directories are in fact directories
In ambiguous cases, such as when f is managed by a storage backend, or f
doesn't exist and
ignore_missing_output is true, always return True
| correctly_flagged_with_dir | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def unshadow_output(self, job, only_log=False, keep_shadow_dir=False):
"""Move files from shadow directory to real output paths."""
"""If shadow directory is kept, returns the path of it."""
if not job.shadow_dir or not job.output:
return
files = job.log if only_log else cha... | Move files from shadow directory to real output paths. | unshadow_output | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def check_periodic_wildcards(self, job):
"""Raise an exception if a wildcard of the given job appears to be periodic,
indicating a cyclic dependency."""
for wildcard, value in job.wildcards_dict.items():
periodic_substring = self.periodic_wildcard_detector.is_periodic(value)
... | Raise an exception if a wildcard of the given job appears to be periodic,
indicating a cyclic dependency. | check_periodic_wildcards | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def handle_protected(self, job):
"""Write-protect output files that are marked with protected()."""
for f in job.output:
if f in job.protected_output:
logger.info(f"Write-protecting output file {fmt_iofile(f)}.")
f.protect() | Write-protect output files that are marked with protected(). | handle_protected | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def handle_touch(self, job):
"""Touches those output files that are marked for touching."""
for f in job.output:
if f in job.touch_output:
f = job.shadowed_path(f)
logger.info(f"Touching output file {fmt_iofile(f)}.")
f.touch_or_create()
... | Touches those output files that are marked for touching. | handle_touch | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def temp_size(self, job):
"""Return the total size of temporary input files of the job.
If none, return 0.
"""
return sum([await f.size() for f in self.temp_input(job)]) | Return the total size of temporary input files of the job.
If none, return 0.
| temp_size | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def handle_temp(self, job):
"""Remove temp files if they are no longer needed. Update temp_mtimes."""
if self.workflow.storage_settings.notemp:
return
if job.is_group():
for j in job:
await self.handle_temp(j)
return
is_temp = l... | Remove temp files if they are no longer needed. Update temp_mtimes. | handle_temp | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def handle_storage(self, job, store_in_storage=True, store_only_log=False):
"""Remove local files if they are no longer needed and upload."""
if store_in_storage and (
self.workflow.remote_exec or self.workflow.is_main_process
):
# handle output files
fi... | Remove local files if they are no longer needed and upload. | handle_storage | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def jobid(self, job):
"""Return job id of given job."""
if job.is_group():
return job.jobid
else:
return self._jobid[job] | Return job id of given job. | jobid | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def update(
self,
jobs,
file=None,
visited=None,
known_producers=None,
progress=False,
create_inventory=False,
):
"""Update the DAG by adding given jobs and their dependencies."""
if visited is None:
visited = set()
if... | Update the DAG by adding given jobs and their dependencies. | update | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def update_(
self,
job,
visited=None,
known_producers=None,
progress=False,
create_inventory=False,
):
"""Update the DAG by adding the given job and its dependencies."""
if job in self._dependencies:
return
if visited is None:... | Update the DAG by adding the given job and its dependencies. | update_ | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def update_needrun(self, create_inventory=False):
"""Update the information whether a job needs to be executed."""
if create_inventory and self.workflow.is_main_process:
# Concurrently collect mtimes of all existing files.
await self.workflow.iocache.mtime_inventory(self.j... | Update the information whether a job needs to be executed. | update_needrun | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def _check_groups(self):
"""Check whether all groups are valid."""
# find paths of jobs that leave a group and then enter it again
# this is not allowed since then the group depends on itself
def dfs(job, group, visited, outside_jobs, outside_jobs_all, skip_this):
"""Inner f... | Check whether all groups are valid. | _check_groups | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def update_incomplete_input_expand_jobs(self):
"""Update (re-evaluate) all jobs which have incomplete input file expansions.
only filled in the second pass of postprocessing.
"""
updated = False
for job in list(self.jobs):
if job.incomplete_input_expand:
... | Update (re-evaluate) all jobs which have incomplete input file expansions.
only filled in the second pass of postprocessing.
| update_incomplete_input_expand_jobs | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def update_ready(self, jobs=None):
"""Update information whether a job is ready to execute.
Given jobs must be needrun jobs!
"""
if jobs is None:
jobs = self.needrun_jobs()
potential_new_ready_jobs = False
candidate_groups = set()
for job in jobs:
... | Update information whether a job is ready to execute.
Given jobs must be needrun jobs!
| update_ready | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def postprocess(
self,
update_needrun=True,
update_incomplete_input_expand_jobs=True,
check_initial=False,
):
"""Postprocess the DAG. This has to be invoked after any change to the
DAG topology."""
self.cleanup()
self.update_jobids()
if u... | Postprocess the DAG. This has to be invoked after any change to the
DAG topology. | postprocess | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def handle_pipes_and_services(self):
"""Use pipes and services to determine job groups. Check if every pipe has exactly
one consumer"""
visited = set()
for job in self.needrun_jobs():
candidate_groups = set()
user_groups = set()
if job.pipe_group is n... | Use pipes and services to determine job groups. Check if every pipe has exactly
one consumer | handle_pipes_and_services | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def _ready(self, job):
"""Return whether the given job is ready to execute."""
group = self._group.get(job, None)
if group is None:
return self._n_until_ready[job] == 0
else:
n_internal_deps = lambda job: sum(
self._group.get(dep) == group for dep... | Return whether the given job is ready to execute. | _ready | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def finish(self, job, update_checkpoint_dependencies=True):
"""Finish a given job (e.g. remove from ready jobs, mark depending jobs
as ready)."""
self._running.remove(job)
# turn off this job's Reason
if job.is_group():
for j in job:
self.reaso... | Finish a given job (e.g. remove from ready jobs, mark depending jobs
as ready). | finish | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def new_job(
self, rule, targetfile=None, format_wildcards=None, wildcards_dict=None
):
"""Create new job for given rule and (optional) targetfile.
This will reuse existing jobs with the same wildcards."""
product = rule.get_some_product()
if targetfile is None and wild... | Create new job for given rule and (optional) targetfile.
This will reuse existing jobs with the same wildcards. | new_job | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def replace_job(self, job, newjob, recursive=True):
"""Replace given job with new job."""
add_to_targetjobs = job in self.targetjobs
try:
jobid = self.jobid(job)
except KeyError:
# Job has been added while updating another checkpoint,
# jobid is ... | Replace given job with new job. | replace_job | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def collect_potential_dependencies(self, job, known_producers):
"""Collect all potential dependencies of a job. These might contain
ambiguities. The keys of the returned dict represent the files to be considered.
"""
# use a set to circumvent multiple jobs for the same file
... | Collect all potential dependencies of a job. These might contain
ambiguities. The keys of the returned dict represent the files to be considered.
| collect_potential_dependencies | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def bfs(self, direction, *jobs, stop=lambda job: False):
"""Perform a breadth-first traversal of the DAG."""
queue = deque(jobs)
visited = set(queue)
while queue:
job = queue.popleft()
if stop(job):
# stop criterion reached for this node
... | Perform a breadth-first traversal of the DAG. | bfs | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def level_bfs(self, direction, *jobs, stop=lambda job: False):
"""Perform a breadth-first traversal of the DAG, but also yield the
level together with each job."""
queue = [(job, 0) for job in jobs]
visited = set(jobs)
while queue:
job, level = queue.pop(0)
... | Perform a breadth-first traversal of the DAG, but also yield the
level together with each job. | level_bfs | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def dfs(self, direction, *jobs, stop=lambda job: False, post=True):
"""Perform depth-first traversal of the DAG."""
visited = set()
def _dfs(job):
"""Inner function for DFS traversal."""
if stop(job):
return
if not post:
yield ... | Perform depth-first traversal of the DAG. | dfs | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def new_wildcards(self, job):
"""Return wildcards that are newly introduced in this job,
compared to its ancestors."""
new_wildcards = set(job.wildcards.items())
for job_ in self._dependencies[job]:
if not new_wildcards:
return set()
for wildcard i... | Return wildcards that are newly introduced in this job,
compared to its ancestors. | new_wildcards | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def rule2job(self, targetrule):
"""Generate a new job from a given rule."""
if targetrule.has_wildcards():
raise WorkflowError(
"Target rules may not contain wildcards. "
"Please specify concrete files or a rule without wildcards at the command line, "
... | Generate a new job from a given rule. | rule2job | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def hsv_to_htmlhexrgb(h, s, v):
"""Convert hsv colors to hex-encoded rgb colors usable by html."""
import colorsys
hex_r, hex_g, hex_b = (round(255 * x) for x in colorsys.hsv_to_rgb(h, s, v))
return "#{hex_r:0>2X}{hex_g:0>2X}{hex_b:0>2X}".format(
hex_r=he... | Convert hsv colors to hex-encoded rgb colors usable by html. | hsv_to_htmlhexrgb | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def resolve_input_functions(input_files):
"""Iterate over all input files and replace input functions
with a fixed string.
"""
files = []
for f in input_files:
if callable(f):
files.append("<input function>")
... | Iterate over all input files and replace input functions
with a fixed string.
| resolve_input_functions | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def html_node(node_id, node, color):
"""Assemble a html style node for graphviz"""
input_files = resolve_input_functions(node._input)
output_files = [repr(f).strip("'") for f in node._output]
input_header = (
'<b><font point-size="14">↪ input</font><... | Assemble a html style node for graphviz | html_node | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def archive(self, path: Path):
"""Archives workflow such that it can be re-run on a different system.
Archiving includes git versioned files (i.e. Snakefiles, config files, ...),
ancestral input files and conda environments.
"""
if path.suffix == ".tar":
mode = "x"
... | Archives workflow such that it can be re-run on a different system.
Archiving includes git versioned files (i.e. Snakefiles, config files, ...),
ancestral input files and conda environments.
| archive | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def is_external_input(self, file, job, not_needrun_is_external=False):
"""Return True if the given file is an external input for the given job."""
consider = lambda job: True
if not_needrun_is_external:
consider = lambda job: self.needrun(job)
return not any(
file... | Return True if the given file is an external input for the given job. | is_external_input | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
async def clean(self, only_temp=False, dryrun=False):
"""Removes files generated by the workflow."""
for job in self.jobs:
for f in job.output:
if not only_temp or is_flagged(f, "temp"):
# The reason for the second check is that dangling
... | Removes files generated by the workflow. | clean | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def list_untracked(self):
"""List files in the workdir that are not in the dag."""
used_files = set()
files_in_cwd = set()
for job in self.jobs:
used_files.update(
os.path.relpath(file)
for file in chain(job.local_input, job.local_output, job.l... | List files in the workdir that are not in the dag. | list_untracked | python | snakemake/snakemake | src/snakemake/dag.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/dag.py | MIT |
def format_exception_to_string(ex, linemaps=None):
"""
Returns the error message for a given exception as a string.
Arguments
ex -- the exception
linemaps -- a dict of a dict that maps for each snakefile
the compiled lines to source code lines in the snakefile.
"""
if isinstance(ex,... |
Returns the error message for a given exception as a string.
Arguments
ex -- the exception
linemaps -- a dict of a dict that maps for each snakefile
the compiled lines to source code lines in the snakefile.
| format_exception_to_string | python | snakemake/snakemake | src/snakemake/exceptions.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/exceptions.py | MIT |
def print_exception_warning(ex, linemaps=None, footer_message=""):
"""
Print an error message for a given exception using logger warning.
Arguments
ex -- the exception
linemaps -- a dict of a dict that maps for each snakefile
the compiled lines to source code lines in the snakefile.
"""... |
Print an error message for a given exception using logger warning.
Arguments
ex -- the exception
linemaps -- a dict of a dict that maps for each snakefile
the compiled lines to source code lines in the snakefile.
| print_exception_warning | python | snakemake/snakemake | src/snakemake/exceptions.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/exceptions.py | MIT |
def print_exception(ex, linemaps=None):
"""
Print an error message for a given exception.
Arguments
ex -- the exception
linemaps -- a dict of a dict that maps for each snakefile
the compiled lines to source code lines in the snakefile.
"""
from snakemake.logging import logger
l... |
Print an error message for a given exception.
Arguments
ex -- the exception
linemaps -- a dict of a dict that maps for each snakefile
the compiled lines to source code lines in the snakefile.
| print_exception | python | snakemake/snakemake | src/snakemake/exceptions.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/exceptions.py | MIT |
def __init__(
self, message=None, include=None, lineno=None, snakefile=None, rule=None
):
"""
Creates a new instance of RuleException.
Arguments
message -- the exception message
include -- iterable of other exceptions to be included
lineno -- the line the exc... |
Creates a new instance of RuleException.
Arguments
message -- the exception message
include -- iterable of other exceptions to be included
lineno -- the line the exception originates
snakefile -- the file the exception originates
| __init__ | python | snakemake/snakemake | src/snakemake/exceptions.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/exceptions.py | MIT |
def logfile_suggestion(self, prefix: str) -> str:
"""Return a suggestion for the log file name given a prefix."""
return (
"/".join(
[prefix, self.rule.name]
+ [
f"{w}_{v}"
for w, v in sorted(
sel... | Return a suggestion for the log file name given a prefix. | logfile_suggestion | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
async def outputs_older_than_script_or_notebook(self):
"""return output that's older than script, i.e. script has changed"""
path = self.rule.script or self.rule.notebook
if not path:
return
path: SourceFile = self._path_to_source_file(path)
if isinstance(path, Loca... | return output that's older than script, i.e. script has changed | outputs_older_than_script_or_notebook | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def _get_resources_to_skip(self):
"""Return a set of resource names that are callable and depend on input files."""
return {
name
for name, val in self.rule.resources.items()
if is_callable(val) and "input" in get_function_params(val)
} | Return a set of resource names that are callable and depend on input files. | _get_resources_to_skip | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def archive_conda_env(self):
"""Archive a conda environment into a custom local channel."""
if self.conda_env_spec:
if self.conda_env.is_externally_managed:
raise WorkflowError(
"Workflow archives cannot be created for workflows using externally managed co... | Archive a conda environment into a custom local channel. | archive_conda_env | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
async def inputsize(self):
"""
Return the size of the input files.
Input files need to be present.
"""
if self._inputsize is None:
self._inputsize = sum([await f.size() for f in self.input])
return self._inputsize |
Return the size of the input files.
Input files need to be present.
| inputsize | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def message(self):
"""Return the message for this job."""
try:
return (
self.format_wildcards(self.rule.message) if self.rule.message else None
)
except AttributeError as ex:
raise RuleException(str(ex), rule=self.rule)
except KeyError ... | Return the message for this job. | message | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def _path_to_source_file(self, path: Union[str, Path]) -> SourceFile:
"""Return the path to source file referred by rule, while expanding
wildcards and params.
"""
if isinstance(path, Path):
path = str(path)
if self.wildcards is not None or self.params is not None:
... | Return the path to source file referred by rule, while expanding
wildcards and params.
| _path_to_source_file | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def shadowed_path(self, f):
"""Get the shadowed path of IOFile f."""
if not self.shadow_dir:
return f
f_ = IOFile(os.path.join(self.shadow_dir, f), self.rule)
# The shadowed path does not need the storage object, storage will be handled
# after shadowing.
f_.c... | Get the shadowed path of IOFile f. | shadowed_path | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
async def remove_existing_output(self):
"""Clean up output before rules actually run"""
for f, f_ in zip(self.output, self.rule.output):
if is_flagged(f, "update"):
# output files marked as to be updated are not removed
continue
try:
... | Clean up output before rules actually run | remove_existing_output | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
async def prepare(self):
"""
Prepare execution of job.
This includes creation of directories and deletion of previously
created files.
Creates a shadow directory for the job if specified.
"""
await self.check_protected_output()
unexpected_output = self.d... |
Prepare execution of job.
This includes creation of directories and deletion of previously
created files.
Creates a shadow directory for the job if specified.
| prepare | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def format_wildcards(self, string, **variables):
"""Format a string with variables from the job."""
_variables = dict()
_variables.update(self.rule.workflow.globals)
_variables.update(
dict(
input=self.input,
output=self.output,
... | Format a string with variables from the job. | format_wildcards | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def format_wildcards(self, string, **variables):
"""Format a string with variables from the job."""
_variables = dict()
_variables.update(self.dag.workflow.globals)
_variables.update(
dict(
input=self.input,
output=self.output,
... | Format a string with variables from the job. | format_wildcards | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def expanded_output(self):
"""Yields the entire expanded output of all jobs"""
for job in self.jobs:
yield from job.output | Yields the entire expanded output of all jobs | expanded_output | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def is_provenance_triggered(self):
"""Return True if reason is triggered by provenance information."""
return (
self.params_changed
or self.code_changed
or self.software_stack_changed
or self.input_changed
) | Return True if reason is triggered by provenance information. | is_provenance_triggered | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def mark_finished(self):
"called if the job has been run"
self.finished = True | called if the job has been run | mark_finished | python | snakemake/snakemake | src/snakemake/jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/jobs.py | MIT |
def format_percentage(done, total):
"""Format percentage from given fraction while avoiding superfluous precision."""
if done == total:
return "100%"
if done == 0:
return "0%"
precision = 0
fraction = done / total
fmt_precision = "{{:.{}%}}".format
def fmt(fraction):
... | Format percentage from given fraction while avoiding superfluous precision. | format_percentage | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def get_event_level(record: logging.LogRecord) -> tuple[LogEvent, str]:
"""
Gets snakemake log level from a log record. If there is no snakemake log level,
returns the log record's level name.
Args:
record (logging.LogRecord)
Returns:
tuple[LogEvent, str]
"""
event = record... |
Gets snakemake log level from a log record. If there is no snakemake log level,
returns the log record's level name.
Args:
record (logging.LogRecord)
Returns:
tuple[LogEvent, str]
| get_event_level | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def format(self, record):
"""
Override format method to format Snakemake-specific log messages.
"""
event, level = get_event_level(record)
record_dict = record.__dict__.copy()
def default_formatter(rd):
return rd["msg"]
formatters = {
Non... |
Override format method to format Snakemake-specific log messages.
| format | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def _format_job_info(self, msg):
"""Helper method to format job info details."""
def format_item(item, omit=None, valueformat=str):
value = msg[item]
if value != omit:
return f" {item}: {valueformat(value)}"
output = [
f"{'local' if msg['l... | Helper method to format job info details. | _format_job_info | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def _format_job_error(self, msg):
"""Helper method to format job error details."""
output = [f"Error in rule {msg['rule_name']}:"]
if msg["msg"]:
output.append(f" message: {msg['rule_msg']}")
output.append(f" jobid: {msg['jobid']}")
if msg["input"]:
... | Helper method to format job error details. | _format_job_error | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def _format_group_error(self, msg):
"""Helper method to format group error details."""
output = []
if msg["msg"]:
output.append(f" message: {msg['msg']}")
if msg["aux_logs"]:
output.append(
f" log: {', '.join(msg['aux_logs'])} (check log fil... | Helper method to format group error details. | _format_group_error | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def can_color_tty(self, mode):
"""
Colors are supported when:
1. Terminal is not "dumb"
2. Running in subprocess mode
3. Using a TTY on non-Windows systems
"""
from snakemake_interface_executor_plugins.settings import ExecMode
# Case 1: Check if terminal ... |
Colors are supported when:
1. Terminal is not "dumb"
2. Running in subprocess mode
3. Using a TTY on non-Windows systems
| can_color_tty | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def decorate(self, record, message):
"""
Add color to the log message based on its level.
"""
message = [message]
event, level = get_event_level(record)
if not self.nocolor and record.levelname in self.colors:
if level == "INFO" and event in self.yellow_info... |
Add color to the log message based on its level.
| decorate | python | snakemake/snakemake | src/snakemake/logging.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/logging.py | MIT |
def notebook(
path,
basedir,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
jobid,
bench_iteration,
cleanup_scripts,
s... |
Load a script from the given basedir + path and execute it.
| notebook | python | snakemake/snakemake | src/snakemake/notebook.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/notebook.py | MIT |
def match(self, targetfile: str) -> set[Rule]:
"""Returns all rules that match the given target file, considering only the prefix and suffix up to the
first wildcard.
To further verify the match, the returned rules should be checked with ``Rule.is_producer(targetfile)``.
"""
ret... | Returns all rules that match the given target file, considering only the prefix and suffix up to the
first wildcard.
To further verify the match, the returned rules should be checked with ``Rule.is_producer(targetfile)``.
| match | python | snakemake/snakemake | src/snakemake/output_index.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/output_index.py | MIT |
def parse_fstring(self, token: tokenize.TokenInfo):
"""
only for python >= 3.12, since then python changed the
parsing manner of f-string, see
[pep-0701](https://peps.python.org/pep-0701)
Here, we just read where the f-string start and end from tokens.
Luckily, each toke... |
only for python >= 3.12, since then python changed the
parsing manner of f-string, see
[pep-0701](https://peps.python.org/pep-0701)
Here, we just read where the f-string start and end from tokens.
Luckily, each token records the content of the line,
and we can just take... | parse_fstring | python | snakemake/snakemake | src/snakemake/parser.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/parser.py | MIT |
def apply_default_storage(self, path):
"""Apply the defined default remote provider to the given path and return the updated _IOFile.
Asserts that default remote provider is defined.
"""
from snakemake.storage import flag_with_storage_object
def is_annotated_callable(value):
... | Apply the defined default remote provider to the given path and return the updated _IOFile.
Asserts that default remote provider is defined.
| apply_default_storage | python | snakemake/snakemake | src/snakemake/path_modifier.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/path_modifier.py | MIT |
def input_checksums(self, job, input_path):
"""Return all checksums of the given input file
recorded for the output of the given job.
"""
return set(
self.metadata(output_path).get("input_checksums", {}).get(input_path)
for output_path in job.output
) | Return all checksums of the given input file
recorded for the output of the given job.
| input_checksums | python | snakemake/snakemake | src/snakemake/persistence.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/persistence.py | MIT |
def params_changed(self, job, file=None):
"""Yields output files with changed params or bool if file given."""
files = [file] if file is not None else job.output
changes = NO_PARAMS_CHANGE
new = set(self._params(job))
for outfile in files:
fmt_version = self.record... | Yields output files with changed params or bool if file given. | params_changed | python | snakemake/snakemake | src/snakemake/persistence.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/persistence.py | MIT |
def _get_layers(cls, resources, constraints, sortby=None):
"""Calculate required consecutive job layers.
Layers are used to keep resource requirements within given
constraint. For instance, if the jobs together require 50 threads,
but only 12 are available, we will use 5 layers. If mult... | Calculate required consecutive job layers.
Layers are used to keep resource requirements within given
constraint. For instance, if the jobs together require 50 threads,
but only 12 are available, we will use 5 layers. If multiple constraints are
used, all will be considered and met. Any... | _get_layers | python | snakemake/snakemake | src/snakemake/resources.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/resources.py | MIT |
def infer_resources(name, value, resources: dict):
"""Infer resources from a given one, if possible."""
from humanfriendly import parse_size, parse_timespan, InvalidTimespan, InvalidSize
if isinstance(value, str):
value = value.strip("'\"")
if (
(name == "mem" or name == "disk")
... | Infer resources from a given one, if possible. | infer_resources | python | snakemake/snakemake | src/snakemake/resources.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/resources.py | MIT |
def apply_modifier(
self,
modifier,
rulename,
prefix_replacables={"input", "output", "log", "benchmark"},
):
"""Update this ruleinfo with the given one (used for 'use rule' overrides)."""
path_modifier = modifier.path_modifier
skips = set()
if modifie... | Update this ruleinfo with the given one (used for 'use rule' overrides). | apply_modifier | python | snakemake/snakemake | src/snakemake/ruleinfo.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ruleinfo.py | MIT |
def __init__(self, name, workflow, lineno=None, snakefile=None):
"""
Create a rule
Arguments
name -- the name of the rule
"""
self._name = name
self.workflow = workflow
self.docstring = None
self.message = None
self._input = InputFiles()
... |
Create a rule
Arguments
name -- the name of the rule
| __init__ | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def set_input(self, *input, **kwinput):
"""
Add a list of input files. Recursive lists are flattened.
Arguments
input -- the list of input files
"""
consider_ancient = self.workflow.workflow_settings.consider_ancient.get(
self.name, frozenset()
)
... |
Add a list of input files. Recursive lists are flattened.
Arguments
input -- the list of input files
| set_input | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def set_output(self, *output, **kwoutput):
"""
Add a list of output files. Recursive lists are flattened.
After creating the output files, they are checked for duplicates.
Arguments
output -- the list of output files
"""
for item in output:
# Named m... |
Add a list of output files. Recursive lists are flattened.
After creating the output files, they are checked for duplicates.
Arguments
output -- the list of output files
| set_output | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def check_output_duplicates(self):
"""Check ``Namedlist`` for duplicate entries and raise a ``WorkflowError``
on problems. Does not raise if the entry is empty.
"""
seen = dict()
idx = None
for name, value in self.output._allitems():
if name is None:
... | Check ``Namedlist`` for duplicate entries and raise a ``WorkflowError``
on problems. Does not raise if the entry is empty.
| check_output_duplicates | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def _set_inoutput_item(self, item, output=False, name=None, mark_ancient=False):
"""
Set an item to be input or output.
Arguments
item -- the item
inoutput -- a Namedlist of either input or output items
name -- an optional name for the item
"""
i... |
Set an item to be input or output.
Arguments
item -- the item
inoutput -- a Namedlist of either input or output items
name -- an optional name for the item
| _set_inoutput_item | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def handle_incomplete_checkpoint(exception):
"""If checkpoint is incomplete, target it such that it is completed
before this rule gets executed."""
if exception.targetfile in input:
return TBDString()
else:
raise WorkflowError(
... | If checkpoint is incomplete, target it such that it is completed
before this rule gets executed. | handle_incomplete_checkpoint | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def is_producer(self, requested_output):
"""
Returns True if this rule is a producer of the requested output.
"""
try:
for o in self.products():
if o.match(requested_output):
return True
return False
except sre_constants... |
Returns True if this rule is a producer of the requested output.
| is_producer | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def get_wildcards(self, requested_output, wildcards_dict=None):
"""
Return wildcard dictionary by
1. trying to format the output with the given wildcards and comparing with the requested output
2. matching regular expression output files to the requested concrete ones.
Arguments... |
Return wildcard dictionary by
1. trying to format the output with the given wildcards and comparing with the requested output
2. matching regular expression output files to the requested concrete ones.
Arguments
requested_output -- a concrete filepath
| get_wildcards | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def compare(self, rule1, rule2):
"""
Return whether rule2 has a higher priority than rule1.
"""
if rule1.name != rule2.name:
# try the last clause first,
# i.e. clauses added later overwrite those before.
for clause in reversed(self.order):
... |
Return whether rule2 has a higher priority than rule1.
| compare | python | snakemake/snakemake | src/snakemake/rules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/rules.py | MIT |
def remaining_jobs(self):
"""Return jobs to be scheduled including not yet ready ones."""
return [
job
for job in self.workflow.dag.needrun_jobs()
if job not in self.running
and not self.workflow.dag.finished(job)
and job not in self.failed
... | Return jobs to be scheduled including not yet ready ones. | remaining_jobs | python | snakemake/snakemake | src/snakemake/scheduler.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/scheduler.py | MIT |
def schedule(self):
"""Schedule jobs that are ready, maximizing cpu usage."""
try:
while True:
if self.workflow.dag.queue_input_jobs:
self.update_queue_input_jobs()
# work around so that the wait does not prevent keyboard interrupts
... | Schedule jobs that are ready, maximizing cpu usage. | schedule | python | snakemake/snakemake | src/snakemake/scheduler.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/scheduler.py | MIT |
def _proceed(self, job):
"""Do stuff after job is finished."""
with self._lock:
self._tofinish.append(job)
if self.dryrun:
if len(self.running) - len(self._tofinish) - len(self._toerror) <= 0:
# During dryrun, only release when all running job... | Do stuff after job is finished. | _proceed | python | snakemake/snakemake | src/snakemake/scheduler.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/scheduler.py | MIT |
def _handle_error(self, job, postprocess_job: bool = True):
"""Clear jobs and stop the workflow.
If Snakemake is configured to restart jobs then the job might have
"restart_times" left and we just decrement and let the scheduler
try to run the job again.
"""
# must be ca... | Clear jobs and stop the workflow.
If Snakemake is configured to restart jobs then the job might have
"restart_times" left and we just decrement and let the scheduler
try to run the job again.
| _handle_error | python | snakemake/snakemake | src/snakemake/scheduler.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/scheduler.py | MIT |
def job_selector_ilp(self, jobs):
"""
Job scheduling by optimization of resource usage by solving ILP using pulp
"""
import pulp
from pulp import lpSum
if len(jobs) == 1:
return self.job_selector_greedy(jobs)
with self._lock:
if not self.... |
Job scheduling by optimization of resource usage by solving ILP using pulp
| job_selector_ilp | python | snakemake/snakemake | src/snakemake/scheduler.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/scheduler.py | MIT |
def job_selector_greedy(self, jobs):
"""
Using the greedy heuristic from
"A Greedy Algorithm for the General Multidimensional Knapsack
Problem", Akcay, Li, Xu, Annals of Operations Research, 2012
Args:
jobs (list): list of jobs
"""
logger.debug("Se... |
Using the greedy heuristic from
"A Greedy Algorithm for the General Multidimensional Knapsack
Problem", Akcay, Li, Xu, Annals of Operations Research, 2012
Args:
jobs (list): list of jobs
| job_selector_greedy | python | snakemake/snakemake | src/snakemake/scheduler.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/scheduler.py | MIT |
def general_args(
self,
executor_common_settings: CommonSettings,
) -> str:
"""Return a string to add to self.exec_job that includes additional
arguments from the command line. This is currently used in the
ClusterExecutor and CPUExecutor, as both were using the same
... | Return a string to add to self.exec_job that includes additional
arguments from the command line. This is currently used in the
ClusterExecutor and CPUExecutor, as both were using the same
code. Both have base class of the RealExecutor.
| general_args | python | snakemake/snakemake | src/snakemake/spawn_jobs.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/spawn_jobs.py | MIT |
def validate(data, schema, set_default=True):
"""Validate data with JSON schema at given path.
Args:
data (object): data to validate. Can be a config dict or a pandas data frame.
schema (str): Path to JSON schema used for validation. The schema can also be
in YAML format. If validat... | Validate data with JSON schema at given path.
Args:
data (object): data to validate. Can be a config dict or a pandas data frame.
schema (str): Path to JSON schema used for validation. The schema can also be
in YAML format. If validating a pandas data frame, the schema has to
... | validate | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def simplify_path(path):
"""Return a simplified version of the given path."""
relpath = os.path.relpath(path)
if relpath.startswith("../../"):
return path
else:
return relpath | Return a simplified version of the given path. | simplify_path | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def linecount(filename):
"""Return the number of lines of the given file.
Args:
filename (str): the path to the file
"""
with open(filename) as f:
return sum(1 for l in f) | Return the number of lines of the given file.
Args:
filename (str): the path to the file
| linecount | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def makedirs(dirnames):
"""Recursively create the given directory or directories without
reporting errors if they are present.
"""
if isinstance(dirnames, str):
dirnames = [dirnames]
for dirname in dirnames:
os.makedirs(dirname, exist_ok=True) | Recursively create the given directory or directories without
reporting errors if they are present.
| makedirs | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
Subsets and Splits
Django Code with Docstrings
Filters Python code examples from Django repository that contain Django-related code, helping identify relevant code snippets for understanding Django framework usage patterns.
SQL Console for Shuu12121/python-treesitter-filtered-datasetsV2
Retrieves specific code examples from the Flask repository but doesn't provide meaningful analysis or patterns beyond basic data retrieval.
HTTPX Repo Code and Docstrings
Retrieves specific code examples from the httpx repository, which is useful for understanding how particular libraries are used but doesn't provide broader analytical insights about the dataset.
Requests Repo Docstrings & Code
Retrieves code examples with their docstrings and file paths from the requests repository, providing basic filtering but limited analytical value beyond finding specific code samples.
Quart Repo Docstrings & Code
Retrieves code examples with their docstrings from the Quart repository, providing basic code samples but offering limited analytical value for understanding broader patterns or relationships in the dataset.