debian/changelog

+bowtie (1.2.3+dfsg-3) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
+  * `make simple-test` in addition to our own tests
+  * Remove obsolete fields Contact from debian/upstream/metadata.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 07 Jan 2020 12:11:17 +0100
+
 bowtie (1.2.3+dfsg-2) unstable; urgency=medium
 
   * Use python3 in (Build-)Depends in d/control

debian/control

@@ -12,7 +12,9 @@ Build-Depends: debhelper-compat (= 12),
                libtbb-dev,
                python3,
                seqan-dev,
-               zlib1g-dev
+               zlib1g-dev,
+               libclone-perl,
+               libtest-deep-perl
 Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/bowtie
 Vcs-Git: https://salsa.debian.org/med-team/bowtie.git
@@ -20,6 +22,7 @@ Homepage: http://bowtie-bio.sourceforge.net/
 
 Package: bowtie
 Architecture: alpha any-amd64 arm64 mips64el ppc64 ppc64el s390x sparc64
+Multi-Arch: foreign
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          python3

debian/patches/series

@@ -16,3 +16,4 @@ enable_arm64.patch
 reproducible.patch
 gcc-64bit.patch
 build-as-Cpp03.patch
+simple-test

debian/patches/simple-test

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Sys::Info isn't packaged for Debian, so work around it
+--- bowtie.orig/scripts/test/simple_tests.pl
++++ bowtie/scripts/test/simple_tests.pl
+@@ -14,8 +14,6 @@
+ use DNA;
+ use Clone qw(clone);
+ use Test::Deep;
+-use Sys::Info;
+-use Sys::Info::Constants qw( :device_cpu );
+ 
+ my $bowtie = "";
+ my $bowtie_build = "";
+@@ -1130,9 +1128,7 @@
+ 	while(<FA>) { print $_; }
+ 	close(FA);
+ 	if($do_build) {
+-		my $info = Sys::Info->new;
+-		my $cpu = $info->device('CPU');
+-		my $nthreads = int(rand($cpu->count || 1)) + 1;
++		my $nthreads = 2;
+ 		my $build_args = "";
+ 		$build_args .= " -C " if $color;
+ 		my $cmd = "$bowtie_build $idx_type --threads $nthreads --quiet --sanity $build_args $fa .simple_tests.tmp";
+@@ -1285,7 +1281,7 @@
+ my $tmpfafn = ".simple_tests.pl.fa";
+ my $last_ref = undef;
+ foreach my $large_idx (undef,1) {
+-	foreach my $debug_mode (1,undef) {
++	foreach my $debug_mode (undef) {
+ 		for (my $ci = 0; $ci < scalar(@cases); $ci++) {
+ 			my $c = $cases[$ci];
+ 			last unless defined($c);
+--- bowtie.orig/Makefile
++++ bowtie/Makefile
+@@ -438,12 +438,11 @@
+ 	done
+ 
+ .PHONY: simple-test
+-simple-test: allall perl-deps
+-	eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
++simple-test: all
+ 	./scripts/test/simple_tests.pl --bowtie=./bowtie --bowtie-build=./bowtie-build
+ 
+ .PHONY: random-test
+-random-test: all perl-deps
++random-test: all
+ 	eval `perl -I $(CURDIR)/.perllib.tmp/lib/perl5 -Mlocal::lib=$(CURDIR)/.perllib.tmp` ; \
+ 	./scripts/test/random_bowtie_tests.sh
+ 

debian/rules

@@ -44,10 +44,9 @@ override_dh_auto_clean:
 	dh_auto_clean
 
 override_dh_auto_test:
-	# print DEB_BUILD_OPTIONS
-	$(info $$DEB_BUILD_OPTIONS is [${DEB_BUILD_OPTIONS}])
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	make simple-test
 	ln -s debian/tests
-	sh debian/tests/run-unit-test test_at_build_time
+	unset LD_PRELOAD && sh debian/tests/run-unit-test test_at_build_time
 	rm -f tests examples[0-9].out
 endif

debian/tests/run-unit-test

@@ -5,13 +5,13 @@ if [ "$1" = "test_at_build_time" ] ; then
     export PATH=.:$PATH
 else
     pkg=bowtie
-    if [ "$ADTTMP" = "" ] ; then
-      ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+    if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+      AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
     fi
-    mkdir -p $ADTTMP/tests
-    cp -a debian/tests/example* $ADTTMP/tests
-    cd $ADTTMP
-    cp -a /usr/share/doc/bowtie/examples/indexes $ADTTMP
+    mkdir -p $AUTOPKGTEST_TMP/tests
+    cp -a debian/tests/example* $AUTOPKGTEST_TMP/tests
+    cd $AUTOPKGTEST_TMP
+    cp -a /usr/share/doc/bowtie/examples/indexes $AUTOPKGTEST_TMP
 fi
 
 check_result () {

debian/upstream/metadata

-Contact: Ben Langmead <blangmea@jhsph.edu>
 Reference:
- author: >
-  Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg
- title: >
-  Ultrafast and memory-efficient alignment of short DNA sequences to
-  the human genome
+  author: "Ben Langmead and Cole Trapnell and Mihai Pop and Steven L Salzberg\n"
+  title: "Ultrafast and memory-efficient alignment of short DNA sequences to the human\
+    \ genome\n"
   journal: Genome Biology
   volume: 10
   pages: R25