__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016-2019, Johannes Köster"
__email__ = "johannes.koester@protonmail.com"
__license__ = "MIT"
from functools import update_wrapper
import inspect
import uuid
import os
from ._version import get_versions
__version__ = get_versions()["version"]
del get_versions
MIN_PY_VERSION = (3, 5)
DYNAMIC_FILL = "__snakemake_dynamic__"
SNAKEMAKE_SEARCHPATH = os.path.dirname(os.path.dirname(__file__))
UUID_NAMESPACE = uuid.uuid5(uuid.NAMESPACE_URL, "https://snakemake.readthedocs.io")
[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]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):
callerframerecord = inspect.stack()[1]
frame = callerframerecord[0]
info = inspect.getframeinfo(frame)
logger.debug(
"{}: {info.filename}, {info.function}, {info.lineno}".format(msg, info=info)
)
[docs]def escape_backslash(path):
return path.replace("\\", "\\\\")