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 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 |
def combine_preamble_and_source(self, preamble: str) -> str:
"""The manifest info needs to be moved to before the preamble.
Also, because rust-scipt relies on inner docs, there can't be an empty line
between the manifest and preamble.
"""
manifest, src = RustScript.extract_manife... | The manifest info needs to be moved to before the preamble.
Also, because rust-scipt relies on inner docs, there can't be an empty line
between the manifest and preamble.
| combine_preamble_and_source | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def _strip_shebang(src: str) -> Tuple[str, str]:
"""From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L312-L320"""
rgx = re.compile(r"^#![^\[].*?(\r\n|\n)")
return strip_re(rgx, src) | From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L312-L320 | _strip_shebang | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def _strip_manifest(src: str) -> Tuple[str, str]:
"""From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L405-L411"""
manifest, remainder = RustScript._strip_single_line_manifest(src)
if not manifest:
manifest, remainder = RustSc... | From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L405-L411 | _strip_manifest | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def _strip_single_line_manifest(src: str) -> Tuple[str, str]:
"""From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L618-L632"""
rgx = re.compile(r"^\s*//\s*cargo-deps\s*:(.*?)(\r\n|\n)", flags=re.IGNORECASE)
return strip_re(rgx, src) | From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L618-L632 | _strip_single_line_manifest | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def _strip_code_block_manifest(src: str) -> Tuple[str, str]:
"""From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L634-L664
We need to find the first `/*!` or `//!` that *isn't* preceded by something
that would make it apply to anything ot... | From https://github.com/fornwall/rust-script/blob/ce508bad02a11d574657d2f1debf7e73fca2bf6e/src/manifest.rs#L634-L664
We need to find the first `/*!` or `//!` that *isn't* preceded by something
that would make it apply to anything other than the create itself. Because we
can't do this accurately,... | _strip_code_block_manifest | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def strip_re(regex: Pattern, s: str) -> Tuple[str, str]:
"""Strip a substring matching a regex from a string and return the stripped part
and the remainder of the original string.
Returns an empty string and the original string if the regex is not found
"""
rgx = re.compile(regex)
match = rgx.se... | Strip a substring matching a regex from a string and return the stripped part
and the remainder of the original string.
Returns an empty string and the original string if the regex is not found
| strip_re | python | snakemake/snakemake | src/snakemake/script/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/script/__init__.py | MIT |
def get_batch(self, items: list):
"""Return the defined batch of the given items.
Items are usually input files."""
# make sure that we always consider items in the same order
if len(items) < self.batches:
raise WorkflowError(
"Batching rule {} has less input ... | Return the defined batch of the given items.
Items are usually input files. | get_batch | python | snakemake/snakemake | src/snakemake/settings/types.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/settings/types.py | MIT |
def generate(dag, path: Path, deploy=["conda", "singularity"], configfiles=None):
"""Generate unit tests from given dag at a given path."""
logger.info("Generating unit tests for each rule...")
try:
from jinja2 import Environment, PackageLoader
except ImportError:
raise WorkflowError(
... | Generate unit tests from given dag at a given path. | generate | python | snakemake/snakemake | src/snakemake/unit_tests/__init__.py | https://github.com/snakemake/snakemake/blob/master/src/snakemake/unit_tests/__init__.py | MIT |
def get_expected_files(results_dir):
"""Recursively walk through the expected-results directory to enumerate
all expected files."""
return [
os.path.relpath(f, results_dir)
for f in glob.iglob(os.path.join(results_dir, "**/**"), recursive=True)
if not os.path.isdir(f)
] | Recursively walk through the expected-results directory to enumerate
all expected files. | get_expected_files | python | snakemake/snakemake | tests/common.py | https://github.com/snakemake/snakemake/blob/master/tests/common.py | MIT |
def run(
path,
shouldfail=False,
snakefile="Snakefile",
subpath=None,
no_tmpdir=False,
check_md5=True,
check_results=None,
cores=3,
nodes=None,
set_pythonpath=True,
cleanup=True,
conda_frontend="conda",
config=dict(),
targets=set(),
container_image=os.environ.... |
Test the Snakefile in the path.
There must be a Snakefile in the path and a subdirectory named
expected-results. If cleanup is False, we return the temporary
directory to the calling test for inspection, and the test should
clean it up.
| run | python | snakemake/snakemake | tests/common.py | https://github.com/snakemake/snakemake/blob/master/tests/common.py | MIT |
def reset_paths_between_tests():
"""Ensure that changes to sys.path are reset between tests"""
org_path = sys.path.copy()
yield
sys.path = org_path | Ensure that changes to sys.path are reset between tests | reset_paths_between_tests | python | snakemake/snakemake | tests/conftest.py | https://github.com/snakemake/snakemake/blob/master/tests/conftest.py | MIT |
def test_github_issue_14():
"""Add cleanup_scripts argument to allow the user to keep scripts"""
# Return temporary directory for inspection - we should keep scripts here
tmpdir = run(dpath("test_github_issue_14"), cleanup=False, cleanup_scripts=False)
assert os.listdir(os.path.join(tmpdir, ".snakemake"... | Add cleanup_scripts argument to allow the user to keep scripts | test_github_issue_14 | python | snakemake/snakemake | tests/tests.py | https://github.com/snakemake/snakemake/blob/master/tests/tests.py | MIT |
def test_empty_pattern_matches_everything(mocker):
"""Test that empty patterns match any filename"""
rule = mocker.Mock(
products=lambda: [Mock(constant_prefix=lambda: "", constant_suffix=lambda: "")]
)
output_index = OutputIndex([rule])
assert rule in output_index.match("")
assert rule ... | Test that empty patterns match any filename | test_empty_pattern_matches_everything | python | snakemake/snakemake | tests/test_output_index.py | https://github.com/snakemake/snakemake/blob/master/tests/test_output_index.py | MIT |
def test_empty_prefix_and_suffix(mocker):
"""Test with empty prefix and suffix"""
rule = mocker.Mock(
products=lambda: [Mock(constant_prefix=lambda: "", constant_suffix=lambda: "")]
)
output_index = OutputIndex([rule])
matches = output_index.match("anything.txt")
assert rule in matches | Test with empty prefix and suffix | test_empty_prefix_and_suffix | python | snakemake/snakemake | tests/test_output_index.py | https://github.com/snakemake/snakemake/blob/master/tests/test_output_index.py | MIT |
def test_parametrized_matches(mocker, target, expected_match):
"""Parametrized test for various matching scenarios"""
rule = mocker.Mock(
products=lambda: [
Mock(constant_prefix=lambda: "test", constant_suffix=lambda: "txt")
]
)
output_index = OutputIndex([rule])
matches ... | Parametrized test for various matching scenarios | test_parametrized_matches | python | snakemake/snakemake | tests/test_output_index.py | https://github.com/snakemake/snakemake/blob/master/tests/test_output_index.py | MIT |
def test_prefix_matching_non_consecutive():
"""Test that demonstrates why we need to keep checking even after seeing a longer prefix,
when prefixes aren't consecutive (like 'ab' vs 'abbc')."""
lookup = PrefixLookup([("a", 1), ("ab", 2), ("abbcc", 3), ("abbc", 4), ("abbd", 5)])
# Query "abbz" process:
... | Test that demonstrates why we need to keep checking even after seeing a longer prefix,
when prefixes aren't consecutive (like 'ab' vs 'abbc'). | test_prefix_matching_non_consecutive | python | snakemake/snakemake | tests/test_prefix_lookup.py | https://github.com/snakemake/snakemake/blob/master/tests/test_prefix_lookup.py | MIT |
def test_named_list_one_named_one_str(self):
"""InputFiles is a subclass of snakemake.io.NamedInput
ierate over input and store each with the integer index - i.e 0, 1, 2
then use input.items() to iterate over the named files and store them as named also
check how this works with named th... | InputFiles is a subclass of snakemake.io.NamedInput
ierate over input and store each with the integer index - i.e 0, 1, 2
then use input.items() to iterate over the named files and store them as named also
check how this works with named things being lists
| test_named_list_one_named_one_str | python | snakemake/snakemake | tests/test_script.py | https://github.com/snakemake/snakemake/blob/master/tests/test_script.py | MIT |
def test_named_list_named_is_list(self):
"""Named lists that are lists of files become a space-separated string as you
can't nest arrays in bash"""
named_list = InputFiles(["test1.in", ["test2.in", "named.in"]])
named_list._set_name("named", 1)
actual = BashEncoder.encode_namedl... | Named lists that are lists of files become a space-separated string as you
can't nest arrays in bash | test_named_list_named_is_list | python | snakemake/snakemake | tests/test_script.py | https://github.com/snakemake/snakemake/blob/master/tests/test_script.py | MIT |
def append(
self: "ContentSequence",
part_or_parts: Union[BasePart, List[BasePart]],
add_end: bool = False,
speaker: Union[str, int] | None = None,
):
"""
Append a part or list of parts to the sequence.
Args:
part_or_parts: A single part or list o... |
Append a part or list of parts to the sequence.
Args:
part_or_parts: A single part or list of parts to add
add_end: Whether to add the IM_END_TOKEN after these parts
speaker: Optional speaker identifier (name or ID) to add before the parts
| append | python | fishaudio/fish-speech | fish_speech/content_sequence.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/content_sequence.py | Apache-2.0 |
def encode(
self: "ContentSequence",
tokenizer: FishTokenizer,
add_shift: bool = True,
ignore_loss_tokens: list[str] = [],
) -> EncodedMessage:
"""
Encode the sequence parts into tokens for the model.
Args:
tokenizer: The tokenizer to use
... |
Encode the sequence parts into tokens for the model.
Args:
tokenizer: The tokenizer to use
add_shift: Whether to shift tokens for next-token prediction
ignore_loss_tokens: List of token strings to ignore when calculating loss
Returns:
EncodedMes... | encode | python | fishaudio/fish-speech | fish_speech/content_sequence.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/content_sequence.py | Apache-2.0 |
def visualize(
self: "ContentSequence",
tokenizer: FishTokenizer,
ignore_loss_tokens: list[str] = [],
merge_semantic_tokens: bool = False,
):
"""
Visualize the encoded sequence with color-coded tokens.
Blue/cyan tokens contribute to loss, green tokens do not.
... |
Visualize the encoded sequence with color-coded tokens.
Blue/cyan tokens contribute to loss, green tokens do not.
| visualize | python | fishaudio/fish-speech | fish_speech/content_sequence.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/content_sequence.py | Apache-2.0 |
def __init__(self) -> None:
"""
Component of the TTSInferenceEngine class.
Loads and manages the cache for the reference audio and text.
"""
self.ref_by_id: dict = {}
self.ref_by_hash: dict = {}
# Make Pylance happy (attribut/method not defined...)
self.d... |
Component of the TTSInferenceEngine class.
Loads and manages the cache for the reference audio and text.
| __init__ | python | fishaudio/fish-speech | fish_speech/inference_engine/reference_loader.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/inference_engine/reference_loader.py | Apache-2.0 |
def load_audio(self, reference_audio, sr):
"""
Load the audio data from a file or bytes.
"""
if len(reference_audio) > 255 or not Path(reference_audio).exists():
audio_data = reference_audio
reference_audio = io.BytesIO(audio_data)
waveform, original_sr =... |
Load the audio data from a file or bytes.
| load_audio | python | fishaudio/fish-speech | fish_speech/inference_engine/reference_loader.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/inference_engine/reference_loader.py | Apache-2.0 |
def inference(self, req: ServeTTSRequest) -> Generator[InferenceResult, None, None]:
"""
Main inference function:
- Loads the reference audio and text.
- Calls the LLAMA model for inference.
- Decodes the VQ tokens to audio.
"""
ref_id: str | None = req.reference... |
Main inference function:
- Loads the reference audio and text.
- Calls the LLAMA model for inference.
- Decodes the VQ tokens to audio.
| inference | python | fishaudio/fish-speech | fish_speech/inference_engine/__init__.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/inference_engine/__init__.py | Apache-2.0 |
def send_Llama_request(
self, req: ServeTTSRequest, prompt_tokens: list, prompt_texts: list
) -> queue.Queue:
"""
Send a request to the LLAMA model to generate the symbolic tokens.
"""
# Prepare the request
request = dict(
device=self.decoder_model.device... |
Send a request to the LLAMA model to generate the symbolic tokens.
| send_Llama_request | python | fishaudio/fish-speech | fish_speech/inference_engine/__init__.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/inference_engine/__init__.py | Apache-2.0 |
def get_audio_segment(self, result: GenerateResponse) -> np.ndarray:
"""
Decode the VQ tokens to audio.
"""
# Don't use autocast on MPS devices
with autocast_exclude_mps(
device_type=self.decoder_model.device.type, dtype=self.precision
):
# Decode... |
Decode the VQ tokens to audio.
| get_audio_segment | python | fishaudio/fish-speech | fish_speech/inference_engine/__init__.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/inference_engine/__init__.py | Apache-2.0 |
def setup_caches(self, max_batch_size, max_seq_length):
"""
This method will only be called during inference when using KV cache.
"""
head_dim = self.config.dim // self.config.n_head
max_seq_length = find_multiple(max_seq_length, 8)
self.max_seq_length = max_seq_length
... |
This method will only be called during inference when using KV cache.
| setup_caches | python | fishaudio/fish-speech | fish_speech/models/dac/modded_dac.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/models/dac/modded_dac.py | Apache-2.0 |
def make_mask(
self,
max_length: int,
x_lens: Optional[Tensor] = None,
) -> Tensor:
"""
Make ordinary mask if window size is not specified.
"""
if self.causal:
mask = torch.tril(torch.ones(max_length, max_length))
else:
mask = t... |
Make ordinary mask if window size is not specified.
| make_mask | python | fishaudio/fish-speech | fish_speech/models/dac/modded_dac.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/models/dac/modded_dac.py | Apache-2.0 |
def pad1d(
x: torch.Tensor,
paddings: tp.Tuple[int, int],
mode: str = "zeros",
value: float = 0.0,
):
"""Tiny wrapper around F.pad, just to allow for reflect padding on small input.
If this is the case, we insert extra 0 padding to the right
before the reflection happen.
"""
length =... | Tiny wrapper around F.pad, just to allow for reflect padding on small input.
If this is the case, we insert extra 0 padding to the right
before the reflection happen.
| pad1d | python | fishaudio/fish-speech | fish_speech/models/dac/modded_dac.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/models/dac/modded_dac.py | Apache-2.0 |
def generate(
*,
model: BaseTransformer,
prompt: torch.Tensor,
max_new_tokens: int,
audio_masks: torch.Tensor,
audio_parts: torch.Tensor,
decode_one_token=decode_one_token_ar,
num_samples: int = 1,
**sampling_kwargs,
):
"""
Takes a conditioning sequence (prompt) as input and ... |
Takes a conditioning sequence (prompt) as input and continues to generate as many tokens as requested.
| generate | python | fishaudio/fish-speech | fish_speech/models/text2semantic/inference.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/models/text2semantic/inference.py | Apache-2.0 |
def precompute_freqs_cis(seq_len: int, n_elem: int, base: int = 10000) -> Tensor:
"""
Precomputes frequency tensors for complex exponentials (cis)
Args:
seq_len: Length of the sequence for which positional embeddings are needed.
n_elem: Number of elements in the frequency tensor.
ba... |
Precomputes frequency tensors for complex exponentials (cis)
Args:
seq_len: Length of the sequence for which positional embeddings are needed.
n_elem: Number of elements in the frequency tensor.
base: Base value for the frequency scaling (default: 10000).
Returns:
A tensor... | precompute_freqs_cis | python | fishaudio/fish-speech | fish_speech/models/text2semantic/llama.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/models/text2semantic/llama.py | Apache-2.0 |
def list_files(
path: Union[Path, str],
extensions: set[str] = set(),
recursive: bool = False,
sort: bool = True,
) -> list[Path]:
"""List files in a directory.
Args:
path (Path): Path to the directory.
extensions (set, optional): Extensions to filter. Defaults to None.
... | List files in a directory.
Args:
path (Path): Path to the directory.
extensions (set, optional): Extensions to filter. Defaults to None.
recursive (bool, optional): Whether to search recursively. Defaults to False.
sort (bool, optional): Whether to sort the files. Defaults to True.
... | list_files | python | fishaudio/fish-speech | fish_speech/utils/file.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/file.py | Apache-2.0 |
def __init__(
self,
name: str = __name__,
rank_zero_only: bool = True,
extra: Optional[Mapping[str, object]] = None,
) -> None:
"""Initializes a multi-GPU-friendly python command line logger that logs on all processes
with their rank prefixed in the log message.
... | Initializes a multi-GPU-friendly python command line logger that logs on all processes
with their rank prefixed in the log message.
:param name: The name of the logger. Default is ``__name__``.
:param rank_zero_only: Whether to force all logs to only occur on the rank zero process. Default is `... | __init__ | python | fishaudio/fish-speech | fish_speech/utils/logger.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/logger.py | Apache-2.0 |
def log(
self, level: int, msg: str, rank: Optional[int] = None, *args, **kwargs
) -> None:
"""Delegate a log call to the underlying logger, after prefixing its message with the rank
of the process it's being logged from. If `'rank'` is provided, then the log will only
occur on that ... | Delegate a log call to the underlying logger, after prefixing its message with the rank
of the process it's being logged from. If `'rank'` is provided, then the log will only
occur on that rank/process.
:param level: The level to log at. Look at `logging.__init__.py` for more information.
... | log | python | fishaudio/fish-speech | fish_speech/utils/logger.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/logger.py | Apache-2.0 |
def log_hyperparameters(object_dict: dict) -> None:
"""Controls which config parts are saved by lightning loggers.
Additionally saves:
- Number of model parameters
"""
hparams = {}
cfg = object_dict["cfg"]
model = object_dict["model"]
trainer = object_dict["trainer"]
if not train... | Controls which config parts are saved by lightning loggers.
Additionally saves:
- Number of model parameters
| log_hyperparameters | python | fishaudio/fish-speech | fish_speech/utils/logging_utils.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/logging_utils.py | Apache-2.0 |
def print_config_tree(
cfg: DictConfig,
print_order: Sequence[str] = (
"data",
"model",
"callbacks",
"logger",
"trainer",
"paths",
"extras",
),
resolve: bool = False,
save_to_file: bool = False,
) -> None:
"""Prints content of DictConfig us... | Prints content of DictConfig using Rich library and its tree structure.
Args:
cfg (DictConfig): Configuration composed by Hydra.
print_order (Sequence[str], optional): Determines in what order config components are printed.
resolve (bool, optional): Whether to resolve reference fields of Di... | print_config_tree | python | fishaudio/fish-speech | fish_speech/utils/rich_utils.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/rich_utils.py | Apache-2.0 |
def enforce_tags(cfg: DictConfig, save_to_file: bool = False) -> None:
"""Prompts user to input tags from command line if no tags are provided in config.""" # noqa: E501
if not cfg.get("tags"):
if "id" in HydraConfig().cfg.hydra.job:
raise ValueError("Specify tags before launching a multir... | Prompts user to input tags from command line if no tags are provided in config. | enforce_tags | python | fishaudio/fish-speech | fish_speech/utils/rich_utils.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/rich_utils.py | Apache-2.0 |
def extras(cfg: DictConfig) -> None:
"""Applies optional utilities before the task is started.
Utilities:
- Ignoring python warnings
- Setting tags from command line
- Rich config printing
"""
# return if no `extras` config
if not cfg.get("extras"):
log.warning("Extras config n... | Applies optional utilities before the task is started.
Utilities:
- Ignoring python warnings
- Setting tags from command line
- Rich config printing
| extras | python | fishaudio/fish-speech | fish_speech/utils/utils.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/utils.py | Apache-2.0 |
def task_wrapper(task_func: Callable) -> Callable:
"""Optional decorator that controls the failure behavior when executing the task function.
This wrapper can be used to:
- make sure loggers are closed even if the task function raises an exception (prevents multirun failure)
- save the exception to a `... | Optional decorator that controls the failure behavior when executing the task function.
This wrapper can be used to:
- make sure loggers are closed even if the task function raises an exception (prevents multirun failure)
- save the exception to a `.log` file
- mark the run as failed with a dedicated f... | task_wrapper | python | fishaudio/fish-speech | fish_speech/utils/utils.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/utils.py | Apache-2.0 |
def get_metric_value(metric_dict: dict, metric_name: str) -> float:
"""Safely retrieves value of the metric logged in LightningModule."""
if not metric_name:
log.info("Metric name is None! Skipping metric value retrieval...")
return None
if metric_name not in metric_dict:
raise Exc... | Safely retrieves value of the metric logged in LightningModule. | get_metric_value | python | fishaudio/fish-speech | fish_speech/utils/utils.py | https://github.com/fishaudio/fish-speech/blob/master/fish_speech/utils/utils.py | Apache-2.0 |
def inference_wrapper(req: ServeTTSRequest, engine: TTSInferenceEngine):
"""
Wrapper for the inference function.
Used in the API server.
"""
count = 0
for result in engine.inference(req):
match result.code:
case "header":
if isinstance(result.audio, tuple):
... |
Wrapper for the inference function.
Used in the API server.
| inference_wrapper | python | fishaudio/fish-speech | tools/server/inference.py | https://github.com/fishaudio/fish-speech/blob/master/tools/server/inference.py | Apache-2.0 |
def inference_wrapper(
text,
reference_id,
reference_audio,
reference_text,
max_new_tokens,
chunk_length,
top_p,
repetition_penalty,
temperature,
seed,
use_memory_cache,
engine,
):
"""
Wrapper for the inference function.
Used in the Gradio interface.
"""
... |
Wrapper for the inference function.
Used in the Gradio interface.
| inference_wrapper | python | fishaudio/fish-speech | tools/webui/inference.py | https://github.com/fishaudio/fish-speech/blob/master/tools/webui/inference.py | Apache-2.0 |
def get_inference_wrapper(engine) -> Callable:
"""
Get the inference function with the immutable arguments.
"""
return partial(
inference_wrapper,
engine=engine,
) |
Get the inference function with the immutable arguments.
| get_inference_wrapper | python | fishaudio/fish-speech | tools/webui/inference.py | https://github.com/fishaudio/fish-speech/blob/master/tools/webui/inference.py | Apache-2.0 |
def register_objects_from_init(directory: str):
"""
Traverse the specified directory for __init__.py files and
register objects defined in __all__.
"""
for dirpath, _, filenames in os.walk(os.path.normpath(directory)):
if '__init__.py' in filenames:
module_path = dirpath.replace(... |
Traverse the specified directory for __init__.py files and
register objects defined in __all__.
| register_objects_from_init | python | modelscope/data-juicer | service.py | https://github.com/modelscope/data-juicer/blob/master/service.py | Apache-2.0 |
def register_class(module, cls):
"""Register class and its methods as endpoints."""
def create_class_call(cls, method_name: str):
async def class_call(request: Request):
try:
# wrap init method
cls.__init__ = validate_call(
cls.__init__, ... | Register class and its methods as endpoints. | register_class | python | modelscope/data-juicer | service.py | https://github.com/modelscope/data-juicer/blob/master/service.py | Apache-2.0 |
def analyze_modality_tag(code, op_prefix):
"""
Analyze the modality tag for the given code content string. Should be one
of the "Modality Tags" in `tagging_mappings.json`. It makes the choice by
finding the usages of attributes `{modality}_key` and the prefix of the OP
name. If there are multiple mo... |
Analyze the modality tag for the given code content string. Should be one
of the "Modality Tags" in `tagging_mappings.json`. It makes the choice by
finding the usages of attributes `{modality}_key` and the prefix of the OP
name. If there are multiple modality keys are used, the 'multimodal' tag
wil... | analyze_modality_tag | python | modelscope/data-juicer | .pre-commit-hooks/build_op_doc.py | https://github.com/modelscope/data-juicer/blob/master/.pre-commit-hooks/build_op_doc.py | Apache-2.0 |
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