debian/changelog

+bedtools (2.29.0+dfsg-2) unstable; urgency=medium
+
+  * Fix Build-Depends (s/python/python3/) and replace remaining references
+    to python by python3
+    Closes: #936199
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+  * Remove patches louder, reproducible_build.patch that are missing
+    from debian/patches/series.
+  * Set fields Upstream-Contact in debian/copyright.
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata.
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Dec 2019 12:11:59 +0100
+
 bedtools (2.29.0+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 12),
-               python,
+               python3,
                zlib1g-dev,
                libbz2-dev,
                liblzma-dev,

debian/copyright

@@ -6,6 +6,7 @@ Files-Excluded: */barski_binding_site.png
                 */g++
                 */gcc
 Upstream-Name: bedtools
+Upstream-Contact: http://groups.google.com/group/bedtools-discuss
 
 Files: *
 Copyright: © 2009,2010,2011 Aaron Quinlan

debian/patches/2to3.patch

@@ -70,3 +70,33 @@ Last-Update: Sun, 01 Sep 2019 10:31:52 +0200
  # 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())
+--- a/src/utils/BamTools/Makefile.frag
++++ b/src/utils/BamTools/Makefile.frag
+@@ -1,4 +1,4 @@
+ src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map
+ 
+ src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map
+-	python $^ > $@
++	python3 $^ > $@
+--- a/test/bigchroms/test-bigchroms.sh
++++ b/test/bigchroms/test-bigchroms.sh
+@@ -28,7 +28,7 @@ check obs abig.bed
+ rm obs
+ 
+ if [[ "$BT_NO_BIG_FILES" != "" ]]; then
+-python make-big-chrom.py
++python3 make-big-chrom.py
+ 
+ echo -e "    bigchroms.t03...big get fasta \c"
+ $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
+--- a/Makefile
++++ b/Makefile
+@@ -175,7 +175,7 @@ $(BIN_DIR)/bedtools: autoversion $(BUILT
+ 
+ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+ 	@echo "- Creating executables for old CLI."
+-	@python scripts/makeBashScripts.py
++	@python3 scripts/makeBashScripts.py
+ 	@chmod +x bin/*
+ 	@echo "done."
+ 

debian/patches/reproducible_build.patch

-Author: Chris Lamb <lamby@debian.org>
-Last-Update: Fri, 12 Aug 2016 00:22:02 +0100
-Bug-Debian: https://bugs.debian.org/834110
-Description: Enable reproducible builds
-

debian/tests/run-unit-test

 #!/bin/sh -e
 
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/bedtools-test.XXXXXX`
-  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/bedtools-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
 # Copy test suite there
-cp -a /usr/share/bedtools/test $ADTTMP
+cp -a /usr/share/bedtools/test $AUTOPKGTEST_TMP
 
 # Link to genomes files
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
 
 ln -s /usr/share/bedtools/genomes
 
 # Enter the directory and run the tests
-cd $ADTTMP/test
+cd $AUTOPKGTEST_TMP/test
 DATA=/usr/share/bedtools/data BT=/usr/bin/bedtools sh test.sh
 

debian/upstream/metadata

 Archive: GitHub
-Contact: http://groups.google.com/group/bedtools-discuss
-Name: BEDTools
 Reference:
   Author: Quinlan, Aaron R. and Hall, Ira M.
   Title: >