[med-svn] [Git][med-team/bowtie][master] 3 commits: try out "make simple-test"
Michael R. Crusoe
gitlab at salsa.debian.org
Tue Jan 7 12:25:53 GMT 2020
Michael R. Crusoe pushed to branch master at Debian Med / bowtie
Commits:
9c2d1ce5 by Michael R. Crusoe at 2020-01-07T12:09:44+01:00
try out "make simple-test"
- - - - -
014701be by Michael R. Crusoe at 2020-01-07T12:11:13+01:00
R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
- - - - -
ca149dd0 by Michael R. Crusoe at 2020-01-07T13:07:52+01:00
Run upstream's tests in addition to our own
Remove obsolete fields Contact from debian/upstream/metadata.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/simple-test
- debian/rules
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+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 at 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
=====================================
@@ -0,0 +1,50 @@
+Author: Michael R. Crusoe <michael.crusoe at 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
=====================================
@@ -1,23 +1,20 @@
-Contact: Ben Langmead <blangmea at 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
- journal: Genome Biology
- volume: 10
- pages: R25
- year: 2009
- DOI: 10.1186/gb-2009-10-3-r25
- URL: http://genomebiology.com/2009/10/3/R25
- eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf
+ 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
+ year: 2009
+ DOI: 10.1186/gb-2009-10-3-r25
+ URL: http://genomebiology.com/2009/10/3/R25
+ eprint: http://genomebiology.com/content/pdf/gb-2009-10-3-r25.pdf
Registry:
- - Name: SciCrunch
- Entry: SCR_005476
- - Name: OMICtools
- Entry: OMICS_00653
- - Name: bio.tools
- Entry: bowtie
- - Name: conda:bioconda
- Entry: bowtie
+- Name: SciCrunch
+ Entry: SCR_005476
+- Name: OMICtools
+ Entry: OMICS_00653
+- Name: bio.tools
+ Entry: bowtie
+- Name: conda:bioconda
+ Entry: bowtie
View it on GitLab: https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15
--
View it on GitLab: https://salsa.debian.org/med-team/bowtie/compare/fbfe4d2485a081c5ae467d7912586387ab8d2d3e...ca149dd08c93cd4537c02c84f03a098b05c83a15
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