Andreas Tille pushed to branch master at Debian Med / bedtools
Commits: 5369d5af by Andreas Tille at 2019-09-01T08:49:28Z Use 2to3 to port to Python3 - - - - - ac2d6f64 by Andreas Tille at 2019-09-01T09:10:26Z Remove unsafe links for gcc and g++ - - - - - 54d75c6d by Andreas Tille at 2019-09-01T09:10:38Z New upstream version 2.28.0+dfsg1 - - - - - e9648312 by Andreas Tille at 2019-09-01T09:11:49Z Update upstream source from tag '2.28.0+dfsg1' Update to upstream version '2.28.0+dfsg1' with Debian dir 46f31e170f5605cd3f01423b28ce023030406d63 - - - - - 28247b1d by Andreas Tille at 2019-09-01T09:26:40Z Upload to unstable - - - - - 7 changed files: - debian/changelog - debian/copyright - + debian/patches/2to3.patch - debian/patches/series - debian/watch - − g++ - − gcc Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +bedtools (2.28.0+dfsg1-1) unstable; urgency=medium + + * Use 2to3 to port to Python3 + Closes: #936199 + * Remove unsafe links for gcc and g++ + + -- Andreas Tille <[email protected]> Sun, 01 Sep 2019 11:14:59 +0200 + bedtools (2.28.0+dfsg-3) unstable; urgency=medium * Team upload. ===================================== debian/copyright ===================================== @@ -3,6 +3,8 @@ Source: https://github.com/arq5x/bedtools2/archive/v2.25.0.tar.gz Comment: File barski_binding_site.png is from Jothi et al, 2008, doi:10.1093/nar/gkn488, licensed under no-DFSG CC-BY-NC 2.0 Files-Excluded: */barski_binding_site.png + */g++ + */gcc Upstream-Name: bedtools Files: * ===================================== debian/patches/2to3.patch ===================================== @@ -0,0 +1,72 @@ +Description: Use 2to3 to port to Python3 +Bug-Debian: https://bugs.debian.org/936199 +Author: Andreas Tille <[email protected]> +Last-Update: Sun, 01 Sep 2019 10:31:52 +0200 + +--- a/docs/conf.py ++++ b/docs/conf.py +@@ -43,8 +43,8 @@ source_suffix = '.rst' + master_doc = 'index' + + # General information about the project. +-project = u'bedtools' +-copyright = u'2009 - 2017, Aaron R. Quinlan and Neil Kindlon' ++project = 'bedtools' ++copyright = '2009 - 2017, Aaron R. Quinlan and Neil Kindlon' + + # The version info for the project you're documenting, acts as replacement for + # |version| and |release|, also used in various other places throughout the +@@ -186,8 +186,8 @@ htmlhelp_basename = 'bedtools-docs' + # Grouping the document tree into LaTeX files. List of tuples + # (source start file, target name, title, author, documentclass [howto/manual]). + latex_documents = [ +- ('index', 'bedtools.tex', u'Bedtools Documentation', +- u'Quinlan lab @ Univ. of Utah', 'manual'), ++ ('index', 'bedtools.tex', 'Bedtools Documentation', ++ 'Quinlan lab @ Univ. of Utah', 'manual'), + ] + + # The name of an image file (relative to this directory) to place at the top of +@@ -219,7 +219,7 @@ latex_documents = [ + # One entry per manual page. List of tuples + # (source start file, name, description, authors, manual section). + man_pages = [ +- ('index', 'bedtools', u'Bedtools Documentation', [u'UU'], 1) ++ ('index', 'bedtools', 'Bedtools Documentation', ['UU'], 1) + ] + + # Example configuration for intersphinx: refer to the Python standard library. +--- a/test/fisher/README.md ++++ b/test/fisher/README.md +@@ -2,7 +2,7 @@ Fisher Testing + ============== + + Fisher is now based on the count of interval overlaps, subject to `-f`. +-We can compare the output of fisher on simulated data by running `python sim.py` ++We can compare the output of fisher on simulated data by running `python3 sim.py` + which will show the output from `bedtools fisher` and then running `bash shuf.sh` + which will repeatedly run + +--- a/test/fisher/cmp.sh ++++ b/test/fisher/cmp.sh +@@ -3,7 +3,7 @@ set -eo pipefail + echo "fisher,shuffled" + + for i in $(seq 1000); do +- fisher=$(python ./sim.py | tail -1 | cut -f 2) ++ fisher=$(python3 ./sim.py | tail -1 | cut -f 2) + shuffle=$(bash shuf.sh) + echo "$fisher,$shuffle" + done +--- a/test/fisher/sim.py ++++ b/test/fisher/sim.py +@@ -25,7 +25,7 @@ with open('taa.bed', 'w') as fh: + fh.write("chr1\t%i\t%i\n" % (s, e)) + fh.flush() + +-print >> open('tgg.genome', 'w'), ("chr1\t%i" % genome_size) ++print(("chr1\t%i" % genome_size), file=open('tgg.genome', 'w')) + + # NOTE: add -m here to make merged output +-print check_output("../../bin/bedtools fisher -a taa.bed -b tbb.bed -g tgg.genome", shell=True).strip() ++print(check_output("../../bin/bedtools fisher -a taa.bed -b tbb.bed -g tgg.genome", shell=True).strip()) ===================================== debian/patches/series ===================================== @@ -6,3 +6,4 @@ reproducible_build.patch #louder # not Debian-specific, upstream has worked on that, too flag_no_overwrite +2to3.patch ===================================== debian/watch ===================================== @@ -1,4 +1,4 @@ version=4 -opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ +opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \ https://github.com/arq5x/bedtools2/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) ===================================== g++ deleted ===================================== @@ -1 +0,0 @@ -/usr/bin/ccache \ No newline at end of file ===================================== gcc deleted ===================================== @@ -1 +0,0 @@ -/usr/bin/ccache \ No newline at end of file View it on GitLab: https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84 -- View it on GitLab: https://salsa.debian.org/med-team/bedtools/compare/2bd5eb3bc8fd6b5f9dcc597a8cee63e59f374f8b...28247b1d415b256d668a438ddfa34c12d0068b84 You're receiving this email because of your account on salsa.debian.org.
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