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 <[email protected]> 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 <[email protected]> +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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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