New upstream version 1.7.5 (46c91e7d) · Commits · Debian Med / bioperl

Changes

+26 −0

Original line number	Diff line number	Diff line
		Summary of important user-visible changes for BioPerl
		-----------------------------------------------------

		1.7.5 2019-02-11 14:57:45+00:00 Europe/London

		* The following modules have been removed from the BioPerl
		distribution to be part of a separate distribution with
		independent development:

		Bio::Symbol::*

		* The Bio::Seq::SeqWithQuality module, which was deprecated since
		2001, was finally removed.

		* The deprecated() method has been deprecated. It is recommended
		to use Carp::carp to warn.

		* The following methods have been deprecated for a long while and
		have now been removed:

		Bio::Align::AlignI->no_residues
		Bio::Align::AlignI->no_sequences
		Bio::LocatableSeq->no_gap
		Bio::LocatableSeq->no_sequences
		Bio::SeqFeature::Generic->slurp_gff_file
		Bio::SimpleAlign->no_residues
		Bio::SimpleAlign->no_sequences


		1.7.4 2019-02-05 16:23:53+00:00 Europe/London

		* Fix Bio::Root::Test, and the testuite, to properly check for

MANIFEST

+0 −38

Original line number	Diff line number	Diff line
		@@ -386,7 +386,6 @@ lib/Bio/Seq/RichSeqI.pm
		lib/Bio/Seq/SeqBuilder.pm
		lib/Bio/Seq/SeqFactory.pm
		lib/Bio/Seq/SeqFastaSpeedFactory.pm
		lib/Bio/Seq/SeqWithQuality.pm
		lib/Bio/Seq/SequenceTrace.pm
		lib/Bio/Seq/SimulatedRead.pm
		lib/Bio/Seq/TraceI.pm
		@@ -469,13 +468,6 @@ lib/Bio/SeqUtils.pm
		lib/Bio/SimpleAlign.pm
		lib/Bio/SimpleAnalysisI.pm
		lib/Bio/Species.pm
		lib/Bio/Symbol/Alphabet.pm
		lib/Bio/Symbol/AlphabetI.pm
		lib/Bio/Symbol/DNAAlphabet.pm
		lib/Bio/Symbol/ProteinAlphabet.pm
		lib/Bio/Symbol/README.Symbol
		lib/Bio/Symbol/Symbol.pm
		lib/Bio/Symbol/SymbolI.pm
		lib/Bio/Taxon.pm
		lib/Bio/Tools/Alignment/Consed.pm
		lib/Bio/Tools/Alignment/Trim.pm
		@@ -531,7 +523,6 @@ lib/Bio/Tools/Run/AnalysisFactory.pm
		lib/Bio/Tools/Run/GenericParameters.pm
		lib/Bio/Tools/Run/ParametersI.pm
		lib/Bio/Tools/Run/Phylo/PhyloBase.pm
		lib/Bio/Tools/Run/README
		lib/Bio/Tools/Run/WrapperBase.pm
		lib/Bio/Tools/Run/WrapperBase/CommandExts.pm
		lib/Bio/Tools/Seg.pm
		@@ -578,32 +569,6 @@ lib/Bio/TreeIO/tabtree.pm
		lib/Bio/UpdateableSeqI.pm
		lib/Bio/WebAgent.pm
		lib/BioPerl.pm
		maintenance/README
		maintenance/authors.pl
		maintenance/check_NAME.pl
		maintenance/check_URLs.pl
		maintenance/cvs2cl_by_file.pl
		maintenance/dependencies.pl
		maintenance/deprecated.pl
		maintenance/find_mod_deps.pl
		maintenance/module_usage.pl
		maintenance/modules.pl
		maintenance/ncbi_blast_switches.pl
		maintenance/perltidy.conf
		maintenance/pod.pl
		maintenance/symlink_script.pl
		maintenance/version.pl
		models/README
		models/biblio.dia
		models/bio_liveseq_variation.dia
		models/bio_map.dia
		models/bio_restriction.dia
		models/bioperl.dia
		models/coordinatemapper.dia
		models/map_proposal.txt
		models/maps_and_markers.dia
		models/popgen.dia
		models/population_proposal.txt
		t/00-compile.t
		t/Align/AlignStats.t
		t/Align/AlignUtil.t
		@@ -631,7 +596,6 @@ t/AlignIO/prodom.t
		t/AlignIO/psi.t
		t/AlignIO/selex.t
		t/AlignIO/xmfa.t
		t/Alphabet.t
		t/Annotation/Annotation.t
		t/Annotation/AnnotationAdaptor.t
		t/LocalDB/Fasta.t
		@@ -707,7 +671,6 @@ t/Seq/PrimedSeq.t
		t/Seq/Quality.t
		t/Seq/Seq.t
		t/Seq/SimulatedRead.t
		t/Seq/WithQuality.t
		t/SeqFeature/Amplicon.t
		t/SeqFeature/Clone.t
		t/SeqFeature/Collection.t
		@@ -769,7 +732,6 @@ t/SeqTools/SeqStats.t
		t/SeqTools/SeqUtils.t
		t/SeqTools/SeqWords.t
		t/Species.t
		t/Symbol.t
		t/Tools/Alignment/Consed.t
		t/Tools/AmpliconSearch.t
		t/Tools/EMBOSS/Palindrome.t

META.json

+2 −2

Original line number	Diff line number	Diff line
		@@ -136,7 +136,7 @@
		"web" : "https://github.com/bioperl/bioperl-live"
		}
		},
		"version" : "1.7.4",
		"version" : "1.7.5",
		"x_Dist_Zilla" : {
		"perl" : {
		"version" : "5.028001"
		@@ -346,7 +346,7 @@
		"branch" : null,
		"changelog" : "Changes",
		"signed" : 0,
		"tag" : "BioPerl-v1.7.4",
		"tag" : "BioPerl-v1.7.5",
		"tag_format" : "%N-v%v",
		"tag_message" : "%N-v%v"
		},

META.yml

+2 −2

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		@@ -99,7 +99,7 @@ resources:
		bugtracker: https://github.com/bioperl/bioperl-live/issues
		homepage: https://metacpan.org/release/BioPerl
		repository: git://github.com/bioperl/bioperl-live.git
		version: 1.7.4
		version: 1.7.5
		x_Dist_Zilla:
		perl:
		version: '5.028001'
		@@ -264,7 +264,7 @@ x_Dist_Zilla:
		branch: ~
		changelog: Changes
		signed: 0
		tag: BioPerl-v1.7.4
		tag: BioPerl-v1.7.5
		tag_format: '%N-v%v'
		tag_message: '%N-v%v'
		Dist::Zilla::Role::Git::Repo:

Makefile.PL

+1 −1

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		@@ -145,7 +145,7 @@ my %WriteMakefileArgs = (
		"Test::More" => 0,
		"Test::Weaken" => 0
		},
		"VERSION" => "1.7.4",
		"VERSION" => "1.7.5",
		"test" => {
		"TESTS" => "t/.t t/Align/.t t/AlignIO/.t t/Annotation/.t t/LocalDB/.t t/LocalDB/Index/.t t/LocalDB/Taxonomy/.t t/Matrix/.t t/Matrix/IO/.t t/Ontology/.t t/Ontology/IO/.t t/RemoteDB/.t t/Root/.t t/SearchIO/.t t/SearchIO/Writer/.t t/Seq/.t t/SeqFeature/.t t/SeqIO/.t t/SeqTools/.t t/Tools/.t t/Tools/Alignment/.t t/Tools/EMBOSS/.t t/Tools/Phylo/.t t/Tools/Phylo/Phylip/.t t/Tools/Signalp/.t t/Tools/Spidey/.t t/Tree/.t t/Tree/TreeIO/.t"
		}