debian/changelog

+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@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

+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936199
+Author: Andreas Tille <tille@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

 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++

-/usr/bin/ccache
\ No newline at end of file

gcc

-/usr/bin/ccache
\ No newline at end of file