def _clean_freebayes_fmt_cl():
"""For FreeBayes pre 1.1.0, need to remove problematic DPR FORMAT annotation.
This can be removed after bcbio 1.0.1 release which will default to
FreeBayes 1.1.0
"""
version = subprocess.check_output(["freebayes", "--version"])
version = LooseVersion(version.split("version:")[-1].strip().replace("v", ""))
return "bcftools annotate -x FMT/DPR |" if version < LooseVersion("1.1.0") else ""
def _clean_freebayes_fmt_cl():
"""For FreeBayes pre 1.1.0, need to remove problematic DPR FORMAT annotation.
This can be removed after bcbio 1.0.1 release which will default to
FreeBayes 1.1.0
"""
version = subprocess.check_output(["freebayes", "--version"])
version = LooseVersion(version.split("version:")[-1].strip().replace("v", ""))
return "bcftools annotate -x FMT/DPR |" if version < LooseVersion("1.1.0") else ""
def __init__(self, source=None):
PwebFormatter.__init__(self, source)
pandoc_ver = False
try:
pandoc = Popen(["pandoc", "--version"], stdin=PIPE, stdout=PIPE)
pandoc_ver = pandoc.communicate()[0].decode('utf-8').split("\n")[0]
pandoc_ver = LooseVersion(pandoc_ver.split(" ")[1])
except:
pandoc_ver = LooseVersion("0.0.1")
print("Error in trying to detect pandoc version")
if pandoc_ver < LooseVersion("1.16.0"):
self.new_pandoc = False
print("Your pandoc version is below 1.16, not setting figure size and id")
else:
self.new_pandoc = True
# General information about the project.
project = 'linearmodels'
copyright = '2017, Kevin Sheppard'
author = 'Kevin Sheppard'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
# The short X.Y version.
version = LooseVersion(linearmodels.__version__)
if '+' in version.version:
version = linearmodels.__version__
version = version.replace('.dirty', '')
version = version.split('+')
commits, tag = version[1].split('.')
version = version[0]
tag = ' (+' + commits + ', ' + tag + ')'
version = version + tag
else:
version = linearmodels.__version__
# The full version, including alpha/beta/rc tags.
release = linearmodels.__version__
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
# General information about the project.
project = "linearmodels"
copyright = "2017, Kevin Sheppard"
author = "Kevin Sheppard"
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
# The short X.Y version.
version = LooseVersion(linearmodels.__version__)
if "+" in version.version:
version = linearmodels.__version__
version = version.replace(".dirty", "")
version = version.split("+")
commits, tag = version[1].split(".")
version = version[0]
short_tag = " (+{0})".format(commits)
tag = " (+" + commits + ", " + tag + ")"
short_version = version + short_tag
version = version + tag
else:
short_version = version = linearmodels.__version__
# The full version, including alpha/beta/rc tags.
release = linearmodels.__version__
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
