Andreas Tille pushed to branch master at Debian Med / bioperl
Commits: 6de932d8 by Andreas Tille at 2026-05-27T10:08:50+02:00 Make slow progress in testing. - - - - - 1df5eba9 by Andreas Tille at 2026-05-27T10:58:29+02:00 Giving up here and ask for help in Perl group - - - - - 2 changed files: - debian/control - debian/patches/fix-missing-test-differences-import.patch Changes: ===================================== debian/control ===================================== @@ -49,6 +49,7 @@ Build-Depends-Indep: libsvg-perl, libsvg-graph-perl, libtest-differences-perl, + libtest-exception-perl, libtest-memory-cycle-perl, libtest-pod-perl, libtest-weaken-perl, ===================================== debian/patches/fix-missing-test-differences-import.patch ===================================== @@ -1,14 +1,14 @@ Description: Fix missing Test::Differences import in SimpleAlign test - unified_diff and eq_or_diff are called in t/Align/SimpleAlign.t but - Test::Differences is never explicitly imported. These were previously - available via transitive imports but this is no longer the case. + - unified_diff and eq_or_diff from Test::Differences + - lives_ok from Test::Exception + - Replace two instances of throws_ok which are failing Author: Andreas Tille <[email protected]> Bug-Debian: https://bugs.debian.org/#1136915 Last-Update: 2026-05-26 --- a/t/Align/SimpleAlign.t +++ b/t/Align/SimpleAlign.t -@@ -2,6 +2,7 @@ +@@ -2,11 +2,13 @@ # $Id$ use strict; @@ -16,3 +16,34 @@ Last-Update: 2026-05-26 BEGIN { use Bio::Root::Test; + + test_begin( -tests => 206 ); ++ use Test::Exception qw(lives_ok); + + use_ok('Bio::SimpleAlign'); + use_ok('Bio::AlignIO'); +@@ -358,7 +360,8 @@ SKIP: { + is( $a->get_seq_by_pos(1)->seq, 'AAA', "bug 2793" ); + ok( $a->add_seq( $s21, 2 ), "bug 2793" ); + is( $a->get_seq_by_pos(2)->seq, 'CCC', "bug 2793" ); +- throws_ok { $a->add_seq( $s21, 0 ) } qr/must be >= 1/, 'Bad sequence, bad!'; ++ eval { $a->add_seq( $s21, 0 ) }; ++ like( $@, qr/must be >= 1/, 'Bad sequence, bad!' ); + } + + # test for Bio::SimpleAlign annotation method and +--- a/t/Align/AlignStats.t ++++ b/t/Align/AlignStats.t +@@ -139,9 +139,9 @@ $in = Bio::AlignIO->new(-file => test_in + $stats = Bio::Align::DNAStatistics->new(-verbose => 2); + $aln = $in->next_aln(); + my $matrix; +-throws_ok { +-$matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected'); +-} qr/No distance calculated between seq3 and seq4/, "Warn if seqs don't overlap"; ++eval { $matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected') }; ++like( $@, qr/No distance calculated between seq3 and seq4/, ++ "Warn if seqs don't overlap" ); + $stats->verbose(-1); + $matrix = $stats->distance(-align=>$aln,-method=>'Uncorrected'); + like($matrix->print_matrix, qr/-1/); View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/0f140080167a4fe893fac3fec8024307c52fec7a...1df5eba98651bf376d37dc4d88432ce1a09db84c -- View it on GitLab: https://salsa.debian.org/med-team/bioperl/-/compare/0f140080167a4fe893fac3fec8024307c52fec7a...1df5eba98651bf376d37dc4d88432ce1a09db84c You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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