Source code for snakemake.common

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016-2019, Johannes Köster"
__email__ = ""
__license__ = "MIT"

from functools import update_wrapper
import platform
import hashlib
import inspect
import uuid
import os

from ._version import get_versions

__version__ = get_versions()["version"]
del get_versions

DYNAMIC_FILL = "__snakemake_dynamic__"
SNAKEMAKE_SEARCHPATH = os.path.dirname(os.path.dirname(__file__))
UUID_NAMESPACE = uuid.uuid5(uuid.NAMESPACE_URL, "")

ON_WINDOWS = platform.system() == "Windows"

[docs]class TBDInt(int): """An integer that prints into <TBD>""" def __str__(self): return "<TBD>"
# A string that prints as TBD TBDString = "<TBD>"
[docs]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
[docs]def get_last_stable_version(): return __version__.split("+")[0]
[docs]def get_container_image(): return "snakemake/snakemake:v{}".format(get_last_stable_version())
[docs]def get_uuid(name): return uuid.uuid5(UUID_NAMESPACE, name)
[docs]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 = except ValueError as ex: logger.error("%s is not an available algorithm." % algorithm) raise ex with open(filename, "rb") as f: for chunk in iter(lambda:, b""): hasher.update(chunk) return hasher.hexdigest()
[docs]def bytesto(bytes, to, bsize=1024): """convert bytes to megabytes. bytes to mb: bytesto(bytes, 'm') bytes to gb: bytesto(bytes, 'g' etc. From """ levels = {"k": 1, "m": 2, "g": 3, "t": 4, "p": 5, "e": 6} answer = float(bytes) for _ in range(levels[to]): answer = answer / bsize return answer
[docs]class Mode: """ Enum for execution mode of Snakemake. This handles the behavior of e.g. the logger. """ default = 0 subprocess = 1 cluster = 2
[docs]class lazy_property(property): __slots__ = ["method", "cached", "__doc__"]
[docs] @staticmethod def clean(instance, method): delattr(instance, method)
def __init__(self, method): self.method = method self.cached = "_{}".format(method.__name__) super().__init__(method, doc=method.__doc__) def __get__(self, instance, owner): cached = ( getattr(instance, self.cached) if hasattr(instance, self.cached) else None ) if cached is not None: return cached value = self.method(instance) setattr(instance, self.cached, value) return value
[docs]def strip_prefix(text, prefix): if text.startswith(prefix): return text[len(prefix) :] return text
[docs]def log_location(msg): from snakemake.logging import logger callerframerecord = inspect.stack()[1] frame = callerframerecord[0] info = inspect.getframeinfo(frame) logger.debug( "{}: {info.filename}, {info.function}, {info.lineno}".format(msg, info=info) )