コード例 #1
0
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 ""
コード例 #2
0
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 ""
コード例 #3
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ファイル: formatters.py プロジェクト: trnkatomas/Pweave
    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
コード例 #4
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ファイル: conf.py プロジェクト: mlettau/linearmodels
# 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.
コード例 #5
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ファイル: conf.py プロジェクト: codacy-badger/linearmodels
# 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.
#