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 report(
text,
path,
stylesheet=None,
defaultenc="utf8",
template=None,
metadata=None,
**files,
):
"""Create an HTML report using python docutils.
This is deprecated in favor of the --report flag.
Attention: This function needs Python docutils to be installed for the
pyt... | Create an HTML report using python docutils.
This is deprecated in favor of the --report flag.
Attention: This function needs Python docutils to be installed for the
python installation you use with Snakemake.
All keywords not listed below are interpreted as paths to files that shall
be embedded ... | report | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def R(code):
"""Execute R code.
This is deprecated in favor of the ``script`` directive.
This function executes the R code given as a string.
The function requires rpy2 to be installed.
Args:
code (str): R code to be executed
"""
try:
import rpy2.robjects as robjects
ex... | Execute R code.
This is deprecated in favor of the ``script`` directive.
This function executes the R code given as a string.
The function requires rpy2 to be installed.
Args:
code (str): R code to be executed
| R | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def format(_pattern, *args, stepout=1, _quote_all=False, quote_func=None, **kwargs):
"""Format a pattern in Snakemake style.
This means that keywords embedded in braces are replaced by any variable
values that are available in the current namespace.
"""
frame = inspect.currentframe().f_back
wh... | Format a pattern in Snakemake style.
This means that keywords embedded in braces are replaced by any variable
values that are available in the current namespace.
| format | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def read_job_properties(
jobscript, prefix="# properties", pattern=re.compile("# properties = (.*)")
):
"""Read the job properties defined in a snakemake jobscript.
This function is a helper for writing custom wrappers for the
snakemake --cluster functionality. Applying this function to a
jobscript... | Read the job properties defined in a snakemake jobscript.
This function is a helper for writing custom wrappers for the
snakemake --cluster functionality. Applying this function to a
jobscript will return a dict containing information about the job.
| read_job_properties | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def min_version(version):
"""Require minimum snakemake version, raise workflow error if not met."""
from packaging.version import parse
from snakemake.common import __version__
if parse(__version__) < parse(version):
raise WorkflowError(
"Expecting Snakemake version {} or higher (yo... | Require minimum snakemake version, raise workflow error if not met. | min_version | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def update_config(config, overwrite_config):
"""Recursively update dictionary config with overwrite_config in-place.
See
https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
for details.
Args:
config (dict): dictionary to update
overwrite_con... | Recursively update dictionary config with overwrite_config in-place.
See
https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
for details.
Args:
config (dict): dictionary to update
overwrite_config (dict): dictionary whose items will overwrite th... | update_config | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def _update_config(config, overwrite_config):
"""Necessary as recursive calls require a return value,
but `update_config()` has no return value.
"""
for key, value in overwrite_config.items():
if not isinstance(config, collections.abc.Mapping):
# the config ca... | Necessary as recursive calls require a return value,
but `update_config()` has no return value.
| _update_config | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def available_cpu_count():
"""
Return the number of available virtual or physical CPUs on this system.
The number of available CPUs can be smaller than the total number of CPUs
when the cpuset(7) mechanism is in use, as is the case on some cluster
systems.
Adapted from https://stackoverflow.com... |
Return the number of available virtual or physical CPUs on this system.
The number of available CPUs can be smaller than the total number of CPUs
when the cpuset(7) mechanism is in use, as is the case on some cluster
systems.
Adapted from https://stackoverflow.com/a/1006301/715090
| available_cpu_count | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def argvquote(arg, force=True):
"""Returns an argument quoted in such a way that CommandLineToArgvW
on Windows will return the argument string unchanged.
This is the same thing Popen does when supplied with a list of arguments.
Arguments in a command line should be separated by spaces; this
function... | Returns an argument quoted in such a way that CommandLineToArgvW
on Windows will return the argument string unchanged.
This is the same thing Popen does when supplied with a list of arguments.
Arguments in a command line should be separated by spaces; this
function does not add these spaces. This implem... | argvquote | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def cmd_exe_quote(arg):
"""Quotes an argument in a cmd.exe compliant way."""
arg = argvquote(arg)
cmd_exe_metachars = '^()%!"<>&|'
for char in cmd_exe_metachars:
arg.replace(char, "^" + char)
return arg | Quotes an argument in a cmd.exe compliant way. | cmd_exe_quote | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def find_bash_on_windows():
"""
Find the path to a usable bash on windows.
The first attempt is to look for a bash installed with a git conda package.
Alternatively, try bash installed with 'Git for Windows'.
"""
if not ON_WINDOWS:
return None
# First look for bash in git's conda pac... |
Find the path to a usable bash on windows.
The first attempt is to look for a bash installed with a git conda package.
Alternatively, try bash installed with 'Git for Windows'.
| find_bash_on_windows | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def wildcard_pattern(self):
"""Wildcard pattern over all columns of the underlying dataframe of the form
column1~{column1}/column2~{column2}/*** or of the provided custom pattern.
"""
if self.single_wildcard:
return f"{{{self.single_wildcard}}}"
else:
retu... | Wildcard pattern over all columns of the underlying dataframe of the form
column1~{column1}/column2~{column2}/*** or of the provided custom pattern.
| wildcard_pattern | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def instance_patterns(self):
"""Iterator over all instances of the parameter space (dataframe rows),
formatted as file patterns of the form column1~{value1}/column2~{value2}/...
or of the provided custom pattern.
"""
import pandas as pd
fmt_value = lambda value: "NA" if ... | Iterator over all instances of the parameter space (dataframe rows),
formatted as file patterns of the form column1~{value1}/column2~{value2}/...
or of the provided custom pattern.
| instance_patterns | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def instance(self, wildcards):
"""Obtain instance (dataframe row) with the given wildcard values."""
import pandas as pd
from snakemake.io import regex_from_filepattern
def convert_value_dtype(name, value):
if self.dataframe.dtypes[name] == bool and value == "False":
... | Obtain instance (dataframe row) with the given wildcard values. | instance | python | snakemake/snakemake | src/snakemake/utils.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/utils.py | MIT |
def cleanup_source_archive(self):
"""cleanup source archive form remote storage"""
if self._source_archive is not None:
obj = self.storage_registry.default_storage_provider.object(
self._source_archive.query
)
async_run(obj.managed_remove()) | cleanup source archive form remote storage | cleanup_source_archive | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def get_rule(self, name):
"""
Get rule by name.
Arguments
name -- the name of the rule
"""
if not self._rules:
raise NoRulesException()
if name not in self._rules:
raise UnknownRuleException(name)
return self._rules[name] |
Get rule by name.
Arguments
name -- the name of the rule
| get_rule | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def inputfile(self, path):
"""Mark file as being an input file of the workflow.
This also means that eventual --default-remote-provider/prefix settings
will be applied to this file. The file is returned as _IOFile object,
such that it can e.g. be transparently opened with _IOFile.open()... | Mark file as being an input file of the workflow.
This also means that eventual --default-remote-provider/prefix settings
will be applied to this file. The file is returned as _IOFile object,
such that it can e.g. be transparently opened with _IOFile.open().
| inputfile | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def generate_unit_tests(self, path: Path):
"""Generate unit tests for the workflow.
Arguments
path -- Path to the directory where the unit tests shall be generated.
"""
from snakemake import unit_tests
assert self.dag_settings is not None
self._prepare_dag(
... | Generate unit tests for the workflow.
Arguments
path -- Path to the directory where the unit tests shall be generated.
| generate_unit_tests | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def export_cwl(self, path: Path):
"""Export the workflow as CWL document.
Arguments
path -- the path to the CWL document to be created.
"""
assert self.dag_settings is not None
self._prepare_dag(
forceall=self.dag_settings.forceall,
ignore_incompl... | Export the workflow as CWL document.
Arguments
path -- the path to the CWL document to be created.
| export_cwl | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def source_path(self, rel_path):
"""Return path to source file from work dir derived from given path relative to snakefile"""
# TODO download to disk (use source cache) in case of remote file
import inspect
frame = inspect.currentframe()
assert frame is not None and frame.f_back... | Return path to source file from work dir derived from given path relative to snakefile | source_path | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def register_envvars(self, *envvars):
"""
Register environment variables that shall be passed to jobs.
If used multiple times, union is taken.
"""
invalid_envvars = [
envvar
for envvar in envvars
if re.match(r"^\w+$", envvar, flags=re.ASCII) is... |
Register environment variables that shall be passed to jobs.
If used multiple times, union is taken.
| register_envvars | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def configfile(self, fp):
"""Update the global config with data from the given file."""
from snakemake.common.configfile import load_configfile
if not self.modifier.skip_configfile:
if os.path.exists(fp):
self.configfiles.append(fp)
c = load_configfil... | Update the global config with data from the given file. | configfile | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def report(self, path):
"""Define a global report description in .rst format."""
if not self.modifier.skip_global_report_caption:
self.report_text = self.current_basedir.join(path) | Define a global report description in .rst format. | report | python | snakemake/snakemake | src/snakemake/workflow.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/workflow.py | MIT |
def wrapper(
path,
input,
output,
params,
wildcards,
threads,
resources,
log,
config,
rulename,
conda_env,
conda_base_path,
container_img,
singularity_args,
env_modules,
bench_record,
prefix,
jobid,
bench_iteration,
cleanup_scripts,
sha... |
Load a wrapper from https://github.com/snakemake/snakemake-wrappers under
the given path + wrapper.(py|R|Rmd) and execute it.
| wrapper | python | snakemake/snakemake | src/snakemake/wrapper.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/wrapper.py | MIT |
def _get_provenance_hash(self, job: Job, cache_mode: str):
"""
Recursively calculate hash for the output of the given job
and all upstream jobs in a blockchain fashion.
This is based on an idea of Sven Nahnsen.
Fails if job has more than one output file. The reason is that there... |
Recursively calculate hash for the output of the given job
and all upstream jobs in a blockchain fashion.
This is based on an idea of Sven Nahnsen.
Fails if job has more than one output file. The reason is that there
is no way to generate a per-output file hash without generati... | _get_provenance_hash | python | snakemake/snakemake | src/snakemake/caching/hash.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/caching/hash.py | MIT |
async def store(self, job: Job, cache_mode: str):
"""
Store generated job output in the cache.
"""
if not os.access(self.path, os.W_OK):
raise WorkflowError(
"Cannot access cache location {}. Please ensure that "
"it is present and writeable."... |
Store generated job output in the cache.
| store | python | snakemake/snakemake | src/snakemake/caching/local.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/caching/local.py | MIT |
async def fetch(self, job: Job, cache_mode: str):
"""
Retrieve cached output file and symlink to the place where the job expects it's output.
"""
for outputfile, cachefile in self.get_outputfiles_and_cachefiles(
job, cache_mode
):
if not cachefile.exists()... |
Retrieve cached output file and symlink to the place where the job expects it's output.
| fetch | python | snakemake/snakemake | src/snakemake/caching/local.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/caching/local.py | MIT |
async def exists(self, job: Job, cache_mode: str):
"""
Return True if job is already cached
"""
for outputfile, cachefile in self.get_outputfiles_and_cachefiles(
job, cache_mode
):
if not cachefile.exists():
return False
logger... |
Return True if job is already cached
| exists | python | snakemake/snakemake | src/snakemake/caching/local.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/caching/local.py | MIT |
def _load_configfile(configpath_or_obj, filetype="Config"):
"Tries to load a configfile first as JSON, then as YAML, into a dict."
import yaml
if isinstance(configpath_or_obj, str) or isinstance(configpath_or_obj, Path):
obj = open(configpath_or_obj, encoding="utf-8")
else:
obj = config... | Tries to load a configfile first as JSON, then as YAML, into a dict. | _load_configfile | python | snakemake/snakemake | src/snakemake/common/configfile.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/configfile.py | MIT |
def load_configfile(configpath):
"Loads a JSON or YAML configfile as a dict, then checks that it's a dict."
config = _load_configfile(configpath)
if not isinstance(config, dict):
raise WorkflowError(
"Config file must be given as JSON or YAML with keys at top level."
)
return... | Loads a JSON or YAML configfile as a dict, then checks that it's a dict. | load_configfile | python | snakemake/snakemake | src/snakemake/common/configfile.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/configfile.py | MIT |
def get_git_root(path):
"""
Args:
path: (str) Path a to a directory/file that is located inside the repo
Returns:
path to the root folder for git repo
"""
import git
try:
git_repo = git.Repo(path, search_parent_directories=True)
return git_repo.git.rev_parse("--s... |
Args:
path: (str) Path a to a directory/file that is located inside the repo
Returns:
path to the root folder for git repo
| get_git_root | python | snakemake/snakemake | src/snakemake/common/git.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/git.py | MIT |
def get_git_root_parent_directory(path, input_path):
"""
This function will recursively go through parent directories until a git
repository is found or until no parent directories are left, in which case
an error will be raised. This is needed when providing a path to a
file/folder that is located ... |
This function will recursively go through parent directories until a git
repository is found or until no parent directories are left, in which case
an error will be raised. This is needed when providing a path to a
file/folder that is located on a branch/tag not currently checked out.
Args:
... | get_git_root_parent_directory | python | snakemake/snakemake | src/snakemake/common/git.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/git.py | MIT |
def git_content(git_file):
"""
This function will extract a file from a git repository, one located on
the filesystem.
The expected format is git+file:///path/to/your/repo/path_to_file@version
Args:
env_file (str): consist of path to repo, @, version, and file information
... |
This function will extract a file from a git repository, one located on
the filesystem.
The expected format is git+file:///path/to/your/repo/path_to_file@version
Args:
env_file (str): consist of path to repo, @, version, and file information
Ex: git+file:///home/smeds/snake... | git_content | python | snakemake/snakemake | src/snakemake/common/git.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/git.py | MIT |
def match_iter(self, query: str) -> Generator[V, None, None]:
"""Yields all entries which are prefixes of the given key.
E.g. if "abc" is the key then "abc", "ab", "a", and "" are considered
valid prefixes.
Yields entries as (key, value) tuples as supplied to __init__()
"""
... | Yields all entries which are prefixes of the given key.
E.g. if "abc" is the key then "abc", "ab", "a", and "" are considered
valid prefixes.
Yields entries as (key, value) tuples as supplied to __init__()
| match_iter | python | snakemake/snakemake | src/snakemake/common/prefix_lookup.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/prefix_lookup.py | MIT |
def _common_prefix(self, s1: str, s2: str) -> str:
"""Utility function that gives the common prefix of two strings.
Except, if the strings are identical, returns the string minus one letter.
Behaviour is undefined if either string is empty.
"""
for i, (l1, l2) in enumerate(zip(s... | Utility function that gives the common prefix of two strings.
Except, if the strings are identical, returns the string minus one letter.
Behaviour is undefined if either string is empty.
| _common_prefix | python | snakemake/snakemake | src/snakemake/common/prefix_lookup.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/prefix_lookup.py | MIT |
def async_run(coroutine):
"""Attaches to running event loop or creates a new one to execute a
coroutine.
.. seealso::
https://github.com/snakemake/snakemake/issues/1105
https://stackoverflow.com/a/65696398
"""
try:
return asyncio.run(coroutine)
except RuntimeError as e:... | Attaches to running event loop or creates a new one to execute a
coroutine.
.. seealso::
https://github.com/snakemake/snakemake/issues/1105
https://stackoverflow.com/a/65696398
| async_run | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def num_if_possible(s):
"""Convert string to number if possible, otherwise return string."""
try:
return int(s)
except ValueError:
try:
return float(s)
except ValueError:
return s | Convert string to number if possible, otherwise return string. | num_if_possible | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def get_file_hash(filename, algorithm="sha256"):
"""find the SHA256 hash string of a file. We use this so that the
user can choose to cache working directories in storage.
"""
from snakemake.logging import logger
# The algorithm must be available
try:
hasher = hashlib.new(algorithm)
... | find the SHA256 hash string of a file. We use this so that the
user can choose to cache working directories in storage.
| get_file_hash | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def bytesto(bytes, to, bsize=1024):
"""convert bytes to megabytes.
bytes to mb: bytesto(bytes, 'm')
bytes to gb: bytesto(bytes, 'g' etc.
From https://gist.github.com/shawnbutts/3906915
"""
levels = {"k": 1, "m": 2, "g": 3, "t": 4, "p": 5, "e": 6}
answer = float(bytes)
for _ in range(leve... | convert bytes to megabytes.
bytes to mb: bytesto(bytes, 'm')
bytes to gb: bytesto(bytes, 'g' etc.
From https://gist.github.com/shawnbutts/3906915
| bytesto | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def group_into_chunks(n, iterable):
"""Group iterable into chunks of size at most n.
See https://stackoverflow.com/a/8998040.
"""
it = iter(iterable)
while True:
chunk = tuple(itertools.islice(it, n))
if not chunk:
return
yield chunk | Group iterable into chunks of size at most n.
See https://stackoverflow.com/a/8998040.
| group_into_chunks | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def unique_justseen(iterable, key=None):
"""
List unique elements, preserving order. Remember only the element just seen.
From https://docs.python.org/3/library/itertools.html#itertools-recipes
"""
# unique_justseen('AAAABBBCCDAABBB') --> A B C D A B
# unique_justseen('ABBcCAD', str.lower) --> ... |
List unique elements, preserving order. Remember only the element just seen.
From https://docs.python.org/3/library/itertools.html#itertools-recipes
| unique_justseen | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def set_env(**environ):
"""
Temporarily set the process environment variables.
>>> with set_env(PLUGINS_DIR='test/plugins'):
... "PLUGINS_DIR" in os.environ
True
>>> "PLUGINS_DIR" in os.environ
False
:type environ: Dict[str, unicode]
:param environ: Environment variables to set
... |
Temporarily set the process environment variables.
>>> with set_env(PLUGINS_DIR='test/plugins'):
... "PLUGINS_DIR" in os.environ
True
>>> "PLUGINS_DIR" in os.environ
False
:type environ: Dict[str, unicode]
:param environ: Environment variables to set
| set_env | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def copy_permission_safe(src: str, dst: str):
"""Copy a file to a given destination.
If destination exists, it is removed first in order to avoid permission issues when
the destination permissions are tried to be applied to an already existing
destination.
"""
if os.path.exists(dst):
os... | Copy a file to a given destination.
If destination exists, it is removed first in order to avoid permission issues when
the destination permissions are tried to be applied to an already existing
destination.
| copy_permission_safe | python | snakemake/snakemake | src/snakemake/common/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/common/__init__.py | MIT |
def address(self):
"""Path to directory of the conda environment.
First tries full hash, if it does not exist, (8-prefix) is used
as default.
"""
if self.name:
return self.name
elif self.dir:
return self.dir
else:
env_dir = se... | Path to directory of the conda environment.
First tries full hash, if it does not exist, (8-prefix) is used
as default.
| address | python | snakemake/snakemake | src/snakemake/deployment/conda.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/deployment/conda.py | MIT |
def archive_file(self):
"""Path to archive of the conda environment, which may or may not exist."""
if self._archive_file is None:
self._archive_file = os.path.join(self._env_archive_dir, self.content_hash)
return self._archive_file | Path to archive of the conda environment, which may or may not exist. | archive_file | python | snakemake/snakemake | src/snakemake/deployment/conda.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/deployment/conda.py | MIT |
def create_archive(self):
"""Create self-contained archive of environment."""
from snakemake.shell import shell
# importing requests locally because it interferes with instantiating conda environments
import requests
self.check_is_file_based()
env_archive = self.archiv... | Create self-contained archive of environment. | create_archive | python | snakemake/snakemake | src/snakemake/deployment/conda.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/deployment/conda.py | MIT |
def execute_deployment_script(self, env_file, deploy_file):
"""Execute post-deployment script if present"""
from snakemake.shell import shell
if ON_WINDOWS:
raise WorkflowError(
"Post deploy script {} provided for conda env {} but unsupported on windows.".format(
... | Execute post-deployment script if present | execute_deployment_script | python | snakemake/snakemake | src/snakemake/deployment/conda.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/deployment/conda.py | MIT |
def shellcmd_win(self, env_address, cmd):
"""Prepend the windows activate bat script."""
# get path to activate script
activate = os.path.join(self.bin_path(), "activate.bat").replace("\\", "/")
env_address = env_address.replace("\\", "/")
return f'"{activate}" "{env_address}"&&... | Prepend the windows activate bat script. | shellcmd_win | python | snakemake/snakemake | src/snakemake/deployment/conda.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/deployment/conda.py | MIT |
def shellcmd(self, cmd):
"""Return shell command with given modules loaded."""
return "module purge && module load {to_load}; {cmd}".format(
to_load=" ".join(self.names), cmd=cmd
) | Return shell command with given modules loaded. | shellcmd | python | snakemake/snakemake | src/snakemake/deployment/env_modules.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/deployment/env_modules.py | MIT |
def shellcmd(
img_path,
cmd,
args="",
quiet=False,
envvars=None,
shell_executable=None,
container_workdir=None,
is_python_script=False,
):
"""Execute shell command inside singularity container given optional args
and environment variables to be passed."""
if envvars:
... | Execute shell command inside singularity container given optional args
and environment variables to be passed. | shellcmd | python | snakemake/snakemake | src/snakemake/deployment/singularity.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/deployment/singularity.py | MIT |
def save_files(bucket_name, source_path, destination_path):
"""given a directory path, save all files recursively to storage"""
storage_client = storage.Client()
bucket = storage_client.get_bucket(bucket_name)
# destination path should be stripped of path indicators too
bucket_name = bucket_name.st... | given a directory path, save all files recursively to storage | save_files | python | snakemake/snakemake | src/snakemake/executors/google_lifesciences_helper.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/executors/google_lifesciences_helper.py | MIT |
def get_source_files(source_path):
"""Given a directory, return a listing of files to upload"""
filenames = []
if not os.path.exists(source_path):
print("%s does not exist!" % source_path)
sys.exit(0)
for x in os.walk(source_path):
for name in glob(os.path.join(x[0], "*")):
... | Given a directory, return a listing of files to upload | get_source_files | python | snakemake/snakemake | src/snakemake/executors/google_lifesciences_helper.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/executors/google_lifesciences_helper.py | MIT |
def add_ending_slash(filename):
"""Since we want to replace based on having an ending slash, ensure it's there"""
if not filename.endswith("/"):
filename = "%s/" % filename
return filename | Since we want to replace based on having an ending slash, ensure it's there | add_ending_slash | python | snakemake/snakemake | src/snakemake/executors/google_lifesciences_helper.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/executors/google_lifesciences_helper.py | MIT |
def run_group_job(self, job: GroupJobExecutorInterface):
"""Run a pipe or service group job.
This lets all items run simultaneously."""
# we only have to consider pipe or service groups because in local running mode,
# these are the only groups that will occur
service_futures =... | Run a pipe or service group job.
This lets all items run simultaneously. | run_group_job | python | snakemake/snakemake | src/snakemake/executors/local.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/executors/local.py | MIT |
def cached_or_run(self, job: SingleJobExecutorInterface, run_func, *args):
"""
Either retrieve result from cache, or run job with given function.
"""
cache_mode = self.workflow.get_cache_mode(job.rule)
try:
if cache_mode:
async_run(self.workflow.output... |
Either retrieve result from cache, or run job with given function.
| cached_or_run | python | snakemake/snakemake | src/snakemake/executors/local.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/executors/local.py | MIT |
def run_wrapper(
job_rule,
input,
output,
params,
wildcards,
threads,
resources,
log,
benchmark,
benchmark_repeats,
benchmark_extended,
conda_env,
container_img,
singularity_args,
env_modules,
use_singularity,
linemaps,
debug,
cleanup_scripts,
... |
Wrapper around the run method that handles exceptions and benchmarking.
Arguments
job_rule -- the ``job.rule`` member
input -- a list of input files
output -- a list of output files
wildcards -- so far processed wildcards
threads -- usable threads
log -- a list of... | run_wrapper | python | snakemake/snakemake | src/snakemake/executors/local.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/executors/local.py | MIT |
def change_working_directory(directory=None):
"""Change working directory in execution context if provided."""
if directory:
try:
saved_directory = os.getcwd()
logger.info(f"Changing to shadow directory: {directory}")
os.chdir(directory)
yield
fina... | Change working directory in execution context if provided. | change_working_directory | python | snakemake/snakemake | src/snakemake/executors/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/executors/__init__.py | MIT |
def _simple_copy(self):
"""Identical copy except dictionary keys are downcast to str."""
simplified = type(self)(self.max_wait_time)
# Copy non-dictionary attributes the same.
for name in ["remaining_wait_time", "active"]:
old_attr = getattr(self, name)
setattr(s... | Identical copy except dictionary keys are downcast to str. | _simple_copy | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
async def inventory(self):
"""Starting from the given file, try to cache as much existence and
modification date information of this and other files as possible.
"""
assert self.rule is not None
cache: IOCache = self.rule.workflow.iocache
if cache.active:
task... | Starting from the given file, try to cache as much existence and
modification date information of this and other files as possible.
| inventory | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def get_inventory_parent(self):
"""If eligible for inventory, get the parent of a given path.
This code does not work on local Windows paths,
but inventory is disabled on Windows.
"""
if self.is_storage:
return self.storage_object.get_inventory_parent()
else:... | If eligible for inventory, get the parent of a given path.
This code does not work on local Windows paths,
but inventory is disabled on Windows.
| get_inventory_parent | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def open(self, mode="r", buffering=-1, encoding=None, errors=None, newline=None):
"""Open this file.
This can (and should) be used in a `with`-statement.
If the file is a remote storage file, retrieve it first if necessary.
"""
if not os.path.exists(self):
raise Inpu... | Open this file.
This can (and should) be used in a `with`-statement.
If the file is a remote storage file, retrieve it first if necessary.
| open | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
async def protected(self):
"""Returns True if the file is protected. Always False for symlinks."""
# symlinks are never regarded as protected
return (
await self.exists_local()
and not os.access(self.file, os.W_OK)
and not os.path.islink(self.file)
) | Returns True if the file is protected. Always False for symlinks. | protected | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
async def mtime_uncached(self, skip_storage: bool = False):
"""Obtain mtime.
Usually, this will be one stat call only. For symlinks and directories
it will be two, for symlinked directories it will be three,
for storage files it will additionally query the storage
location.
... | Obtain mtime.
Usually, this will be one stat call only. For symlinks and directories
it will be two, for symlinked directories it will be three,
for storage files it will additionally query the storage
location.
| mtime_uncached | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
async def check_broken_symlink(self):
"""Raise WorkflowError if file is a broken symlink."""
if not await self.exists_local():
try:
if os.lstat(self.file):
raise WorkflowError(
f"File {self.file} seems to be a broken symlink."
... | Raise WorkflowError if file is a broken symlink. | check_broken_symlink | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
async def is_newer(self, time):
"""Returns true of the file (which is an input file) is newer than time, or if it is
a symlink that points to a file newer than time."""
if self.is_ancient:
return False
return (await self.mtime()).local_or_storage(follow_symlinks=True) > time | Returns true of the file (which is an input file) is newer than time, or if it is
a symlink that points to a file newer than time. | is_newer | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def touch(self, times=None):
"""times must be 2-tuple: (atime, mtime)"""
try:
if self.is_directory:
file = os.path.join(self.file, ".snakemake_timestamp")
# Create the flag file if it doesn't exist
if not os.path.exists(file):
... | times must be 2-tuple: (atime, mtime) | touch | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
async def wait_for_files(
files,
latency_wait=3,
wait_for_local=False,
ignore_pipe_or_service=False,
consider_local: Set[_IOFile] = _CONSIDER_LOCAL_DEFAULT,
):
"""Wait for given files to be present in the filesystem."""
from snakemake.io.fmt import fmt_iofile
files = list(files)
a... | Wait for given files to be present in the filesystem. | wait_for_files | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def directory(value):
"""
A flag to specify that output is a directory, rather than a file or named pipe.
"""
if is_flagged(value, "pipe"):
raise SyntaxError("Pipe and directory flags are mutually exclusive.")
if is_flagged(value, "storage_object"):
raise SyntaxError("Storage and dir... |
A flag to specify that output is a directory, rather than a file or named pipe.
| directory | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def temp(value, group_jobs=False):
"""
A flag for an input or output file that shall be removed after usage.
When set to true, the extra flag "group_jobs" causes the file to also be flagged as "nodelocal":
A flag for an intermediate file that only lives on the compute node executing the group jobs and ... |
A flag for an input or output file that shall be removed after usage.
When set to true, the extra flag "group_jobs" causes the file to also be flagged as "nodelocal":
A flag for an intermediate file that only lives on the compute node executing the group jobs and not accessible from the main snakemake job... | temp | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def protected(value):
"""A flag for a file that shall be write-protected after creation."""
if is_flagged(value, "temp"):
raise SyntaxError("Protected and temporary flags are mutually exclusive.")
if is_flagged(value, "storage_object"):
raise SyntaxError("Storage and protected flags are mutu... | A flag for a file that shall be write-protected after creation. | protected | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def report(
value,
caption=None,
category=None,
subcategory=None,
labels=None,
patterns=[],
htmlindex=None,
):
"""Flag output file or directory as to be included into reports.
In the case of a directory, files to include can be specified via a glob pattern (default: *).
Argumen... | Flag output file or directory as to be included into reports.
In the case of a directory, files to include can be specified via a glob pattern (default: *).
Arguments
value -- File or directory.
caption -- Path to a .rst file with a textual description of the result.
category -- Name of the (optio... | report | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def local(value):
"""Mark a file as a local file. This disables the application of a default storage
provider.
"""
if is_flagged(value, "storage_object"):
raise SyntaxError("Storage and local flags are mutually exclusive.")
return flag(value, "local") | Mark a file as a local file. This disables the application of a default storage
provider.
| local | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def expand(*args, **wildcard_values):
"""
Expand wildcards in given filepatterns.
Arguments
*args -- first arg: filepatterns as list or one single filepattern,
second arg (optional): a function to combine wildcard values
(itertools.product per default)
**wildcard_values -- the wildc... |
Expand wildcards in given filepatterns.
Arguments
*args -- first arg: filepatterns as list or one single filepattern,
second arg (optional): a function to combine wildcard values
(itertools.product per default)
**wildcard_values -- the wildcards as keyword arguments
with their ... | expand | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def multiext(prefix, *extensions, **named_extensions):
"""Expand a given prefix with multiple extensions (e.g. .txt, .csv, _peaks.bed, ...)."""
if any(
(r"/" in ext or r"\\" in ext)
for ext in chain(extensions, named_extensions.values())
):
raise WorkflowError(
r"Extensio... | Expand a given prefix with multiple extensions (e.g. .txt, .csv, _peaks.bed, ...). | multiext | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def glob_wildcards(pattern, files=None, followlinks=False):
"""
Glob the values of the wildcards by matching the given pattern to the filesystem.
Returns a named tuple with a list of values for each wildcard.
"""
if is_flagged(pattern, "storage_object"):
if files is not None:
rai... |
Glob the values of the wildcards by matching the given pattern to the filesystem.
Returns a named tuple with a list of values for each wildcard.
| glob_wildcards | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def update_wildcard_constraints(
pattern,
wildcard_constraints: Dict[str, str],
global_wildcard_constraints: Dict[str, str],
):
"""Update wildcard constraints
Args:
pattern (str): pattern on which to update constraints
wildcard_constraints (dict): dictionary of wildcard:constraint key-v... | Update wildcard constraints
Args:
pattern (str): pattern on which to update constraints
wildcard_constraints (dict): dictionary of wildcard:constraint key-value pairs
global_wildcard_constraints (dict): dictionary of wildcard:constraint key-value pairs
| update_wildcard_constraints | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def strip_wildcard_constraints(pattern):
"""Return a string that does not contain any wildcard constraints."""
if is_callable(pattern):
# do not apply on e.g. input functions
return pattern
def strip_constraint(match):
return "{{{}}}".format(match.group("name"))
return WILDCARD... | Return a string that does not contain any wildcard constraints. | strip_wildcard_constraints | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def __call__(self, *args, **kwargs):
"""
Generic function that throws an `AttributeError`.
Used as replacement for functions such as `index()` and `sort()`,
which may be overridden by workflows, to signal to a user that
these functions should not be used.
"""
rai... |
Generic function that throws an `AttributeError`.
Used as replacement for functions such as `index()` and `sort()`,
which may be overridden by workflows, to signal to a user that
these functions should not be used.
| __call__ | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
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 ... |
Create the object.
Arguments
toclone -- another Namedlist that shall be cloned
fromdict -- a dict that shall be converted to a
Namedlist (keys become names)
| __init__ | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def _set_name(self, name, index, end=None):
"""
Set the name of an item.
Arguments
name -- a name
index -- the item index
"""
if name not in self._allowed_overrides and hasattr(self.__class__, name):
raise AttributeError(
"invalid nam... |
Set the name of an item.
Arguments
name -- a name
index -- the item index
| _set_name | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def _get_names(self):
"""
Get the defined names as (name, index) pairs.
"""
for name, index in self._names.items():
yield name, index |
Get the defined names as (name, index) pairs.
| _get_names | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def _take_names(self, names):
"""
Take over the given names.
Arguments
names -- the given names as (name, index) pairs
"""
for name, (i, j) in names:
self._set_name(name, i, end=j) |
Take over the given names.
Arguments
names -- the given names as (name, index) pairs
| _take_names | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def __init__(self, min_repeat=20, max_repeat=100):
"""
Args:
max_repeat (int): The maximum length of the periodic substring.
min_repeat (int): The minimum length of the periodic substring.
"""
self.min_repeat = min_repeat
self.regex = re.compile(
... |
Args:
max_repeat (int): The maximum length of the periodic substring.
min_repeat (int): The minimum length of the periodic substring.
| __init__ | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def is_periodic(self, value):
"""Returns the periodic substring or None if not periodic."""
# short-circuit: need at least min_repeat characters
if len(value) < self.min_repeat:
return None
# short-circuit: need at least min_repeat same characters
last_letter = value... | Returns the periodic substring or None if not periodic. | is_periodic | python | snakemake/snakemake | src/snakemake/io/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/io/__init__.py | MIT |
def branch(
condition: Union[Callable, bool],
then: Optional[Union[str, list[str], Callable]] = None,
otherwise: Optional[Union[str, list[str], Callable]] = None,
cases: Optional[Mapping] = None,
):
"""Branch based on a condition that is provided as a function pointer (i.e. a Callable)
or a valu... | Branch based on a condition that is provided as a function pointer (i.e. a Callable)
or a value.
If then and optionally otherwise are specified, do the following:
If the condition is (or evaluates to) True, return the value
of the then parameter. Otherwise, return the value of the otherwise parameter.
... | branch | python | snakemake/snakemake | src/snakemake/ioutils/branch.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ioutils/branch.py | MIT |
def evaluate(expr: str):
"""Evaluate a python expression while replacing any wildcards given as
{wildcardname} with the wildcard value represented as a string."""
def inner(wildcards):
formatted = expr.format(**{w: repr(v) for w, v in wildcards.items()})
try:
return eval(formatt... | Evaluate a python expression while replacing any wildcards given as
{wildcardname} with the wildcard value represented as a string. | evaluate | python | snakemake/snakemake | src/snakemake/ioutils/evaluate.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ioutils/evaluate.py | MIT |
def exists(path):
"""Return True if the given file or directory exists.
This function considers any storage arguments given to Snakemake.
"""
func_context = inspect.currentframe().f_back.f_locals
func_context_global = inspect.currentframe().f_back.f_globals
workflow = func_context.get("workflo... | Return True if the given file or directory exists.
This function considers any storage arguments given to Snakemake.
| exists | python | snakemake/snakemake | src/snakemake/ioutils/exists.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ioutils/exists.py | MIT |
def flatten(list_of_lists: List) -> List:
"""Flatten an irregular list of lists recursively
https://stackoverflow.com/a/53778278
:param list_of_lists: A list of lists
:return result: A list that has been flattened from a list of lists
"""
result = list()
for i in list_of_lists:
if ... | Flatten an irregular list of lists recursively
https://stackoverflow.com/a/53778278
:param list_of_lists: A list of lists
:return result: A list that has been flattened from a list of lists
| flatten | python | snakemake/snakemake | src/snakemake/ioutils/input.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ioutils/input.py | MIT |
def lookup(
dpath: Optional[str] = None,
query: Optional[str] = None,
cols: Optional[Union[List[str], str]] = None,
is_nrows: Optional[int] = None,
within=None,
default=NODEFAULT,
**namespace,
):
"""Lookup values in a pandas dataframe, series, or python mapping (e.g. dict).
Required... | Lookup values in a pandas dataframe, series, or python mapping (e.g. dict).
Required argument ``within`` should be a pandas dataframe or series (in which
case use ``query``, and optionally ``cols`` and ``is_nrows``), or a Python
mapping like a dict (in which case use the ``dpath`` argument is used).
I... | lookup | python | snakemake/snakemake | src/snakemake/ioutils/lookup.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ioutils/lookup.py | MIT |
def rule_item_factory(name: str):
"""Allows to access input, output etc. from statements inside
a rule but outside of run/shell etc. blocks. Returns an object that
defers evaluation to the DAG phase.
"""
if name == "threads":
def inner(_wildcards, threads):
return threads
... | Allows to access input, output etc. from statements inside
a rule but outside of run/shell etc. blocks. Returns an object that
defers evaluation to the DAG phase.
| rule_item_factory | python | snakemake/snakemake | src/snakemake/ioutils/rule_items_proxy.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ioutils/rule_items_proxy.py | MIT |
def subpath(
path_or_func: Union[Callable, str, Path],
strip_suffix: Optional[str] = None,
basename: bool = False,
parent: bool = False,
ancestor: Optional[int] = None,
):
"""Return the subpath of a given path.
Args:
path_or_func: A string, pathlib.Path, or a function returning a st... | Return the subpath of a given path.
Args:
path_or_func: A string, pathlib.Path, or a function returning a string or pathlib.Path.
strip_suffix: If given, strip the suffix from the path.
basename: If True, return the basename of the path (cannot be used together with parent or ancestor).
... | subpath | python | snakemake/snakemake | src/snakemake/ioutils/subpath.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/ioutils/subpath.py | MIT |
def data_uri_from_file(file, defaultenc="utf8"):
"""Craft a base64 data URI from file with proper encoding and mimetype."""
if isinstance(file, Path):
file = str(file)
mime, encoding = mime_from_file(file)
if encoding is None:
encoding = defaultenc
with open(file, "rb") as f:
... | Craft a base64 data URI from file with proper encoding and mimetype. | data_uri_from_file | python | snakemake/snakemake | src/snakemake/report/common.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/report/common.py | MIT |
def run(self):
"""
Image.run() handles most of the
"""
result = Image.run(self)
reference = directives.uri(self.arguments[0])
self.options["uri"] = data_uri_from_file(reference)
return result |
Image.run() handles most of the
| run | python | snakemake/snakemake | src/snakemake/report/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/report/__init__.py | MIT |
def log_fmt_shell(
self, stdout: bool = True, stderr: bool = True, append: bool = False
) -> str:
"""
Return a shell redirection string to be used in `shell()` calls
This function allows scripts and wrappers to support optional `log` files
specified in the calling rule. If ... |
Return a shell redirection string to be used in `shell()` calls
This function allows scripts and wrappers to support optional `log` files
specified in the calling rule. If no `log` was specified, then an
empty string "" is returned, regardless of the values of `stdout`,
`stder... | log_fmt_shell | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def _log_shell_redirect(
log: Optional[PathLike],
stdout: bool = True,
stderr: bool = True,
append: bool = False,
) -> str:
"""
Return a shell redirection string to be used in `shell()` calls
This function allows scripts and wrappers support optional `log` files
specified in the calling... |
Return a shell redirection string to be used in `shell()` calls
This function allows scripts and wrappers support optional `log` files
specified in the calling rule. If no `log` was specified, then an
empty string "" is returned, regardless of the values of `stdout`,
`stderr`, and `append`.
... | _log_shell_redirect | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def encode_list(cls, l):
"""Encode as vector if the type is homogeneous, otherwise use a list."""
is_homogeneous = False
if len(l) == 0:
# An empty list is always homogeneous
is_homogeneous = True
else:
# Numbers of different type can be stored in the ... | Encode as vector if the type is homogeneous, otherwise use a list. | encode_list | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def __init__(
self,
namedlists: List[str] = None,
dicts: List[str] = None,
prefix: str = "snakemake",
):
"""namedlists is a list of strings indicating the snakemake object's member
variables which are encoded as Namedlist.
dicts is a list of strings indicating... | namedlists is a list of strings indicating the snakemake object's member
variables which are encoded as Namedlist.
dicts is a list of strings indicating the snakemake object's member variables
that are encoded as dictionaries.
Prefix is the prefix for the bash variable name(s) e.g., snak... | __init__ | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def encode_snakemake(self, smk: Snakemake) -> str:
"""Turn a snakemake object into a collection of bash associative arrays"""
arrays = []
main_aa = dict()
for var in vars(smk):
val = getattr(smk, var)
suffix = "params" if var == "_params_store" else var.strip("_")... | Turn a snakemake object into a collection of bash associative arrays | encode_snakemake | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def dict_to_aa(d: dict) -> str:
"""Converts a dictionary to a Bash associative array
This produces the array component of the variable.
e.g. ( [var1]=val1 [var2]=val2 )
to make it a correct bash associative array, you need to name it with
name=<output of this method>
"""
... | Converts a dictionary to a Bash associative array
This produces the array component of the variable.
e.g. ( [var1]=val1 [var2]=val2 )
to make it a correct bash associative array, you need to name it with
name=<output of this method>
| dict_to_aa | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def encode_namedlist(cls, named_list: io_.Namedlist) -> str:
"""Convert a namedlist into a Bash associative array
See the comments for dict_to_aa()
"""
nl_dict = dict()
# Add the same items keyed by name and also by index
for i, (name, val) in enumerate(named_list._allit... | Convert a namedlist into a Bash associative array
See the comments for dict_to_aa()
| encode_namedlist | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.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.