[med-svn] [Git][med-team/bedtools][master] 5 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Sun Sep 1 10:28:59 BST 2019
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 <tille at debian.org> 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 <tille at debian.org>
+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
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