[med-svn] [Git][med-team/python-pybedtools][master] Fixed incompatibility with latest bedtools package

[Steffen Möller]

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 <moeller at debian.org>  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
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