Steffen Möller pushed to branch master at Debian Med / python-pybedtools
Commits: fbfeb1f3 by Steffen Moeller at 2019-08-02T14:20:06Z Fixed incompatibility with latest bedtools package - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/parseDebianVersions.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +python-pybedtools (0.8.0-2) unstable; urgency=medium + + * Improved parsing of version of bedtool binary + * Standards-Version: 4.3.0 + + -- Steffen Moeller <[email protected]> Fri, 02 Aug 2019 16:15:52 +0200 + python-pybedtools (0.8.0-1) unstable; urgency=medium * New upstream version. ===================================== debian/control ===================================== @@ -21,7 +21,7 @@ Build-Depends: debhelper (>= 10), python3-sphinx, r-base-core, zlib1g-dev -Standards-Version: 4.3.0 +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/python-pybedtools Vcs-Git: https://salsa.debian.org/med-team/python-pybedtools.git Homepage: https://daler.github.io/pybedtools/ ===================================== debian/patches/parseDebianVersions.patch ===================================== @@ -0,0 +1,45 @@ +Index: python-pybedtools/pybedtools/helpers.py +=================================================================== +--- python-pybedtools.orig/pybedtools/helpers.py ++++ python-pybedtools/pybedtools/helpers.py +@@ -11,6 +11,7 @@ import struct + import atexit + import six + import pysam ++import re + from six.moves import urllib + from . import cbedtools + from . import settings +@@ -60,7 +61,7 @@ def set_R_path(path=""): + paths._set_R_path(path) + + +-def _check_for_bedtools(program_to_check='intersectBed', force_check=False): ++def _check_for_bedtools(program_to_check='intersectBed', force_check=False, verbose=False): + """ + Checks installation as well as version (based on whether or not "bedtools + intersect" works, or just "intersectBed") +@@ -76,15 +77,18 @@ def _check_for_bedtools(program_to_check + [ + os.path.join( + settings._bedtools_path, 'bedtools'), +- '--version']) ++ '--version']).decode('utf-8').rstrip() ++ ++ if verbose: ++ print("I: Found bedtools version '%s'" % v) + + settings._bedtools_installed = True + +- # e.g., +- # ++ # To allow more complicated versions as found in Linux distributions, e.g.: + # bedtools v2.26.0 +- # +- vv = v.decode().split('v')[1] ++ # bedtools debian/2.28.0+dfsg-2-dirty ++ m = re.search('^bedtools [^0-9]*([0-9][0-9.]*)', v) ++ vv = m.group(1) + + settings.bedtools_version = [int(i) for i in vv.split(".")] + ===================================== debian/patches/series ===================================== @@ -6,3 +6,4 @@ spelling #c8dff864dbc942bb7adb3e719b0702f7e3989d36.patch define_filenotfounderror_python2.patch remove_badges_from_documentation.patch +parseDebianVersions.patch View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/commit/fbfeb1f3107ab2051cf1046a858a63386a6a5f8b -- View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/commit/fbfeb1f3107ab2051cf1046a858a63386a6a5f8b You're receiving this email because of your account on salsa.debian.org.
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