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. #