New upstream version 1.7.4 (e6fc3b12) · Commits · Debian Med / libbio-db-seqfeature-perl

Changes

+6 −0

Original line number	Diff line number	Diff line
		Summary of important user-visible changes for Bio-DB-SeqFeature
		---------------------------------------------------------------

		1.7.4 2020-01-08 22:03:25-06:00 America/Chicago
		* The prior release required both DBD::Pg and DBD::SQLite; we now
		skip these.
		* We now explicitly require Bio::DB::GFF::Typename; tests depend on
		it and the dynamic loading used (which caused issue #1) now doesn't make sense.

		1.7.3 2019-02-19 14:26:06-05:00 America/Detroit
		* First release after split from bioperl-live.

LICENSE

+3 −3

Original line number	Diff line number	Diff line
		This software is copyright (c) 2019 by Cold Spring Harbor Laboratory, Nathan Weeks, Ontario Institute for Cancer Research.
		This software is copyright (c) 2020 by Cold Spring Harbor Laboratory, Nathan Weeks, Ontario Institute for Cancer Research.

		This is free software; you can redistribute it and/or modify it under
		the same terms as the Perl 5 programming language system itself.
		@@ -12,7 +12,7 @@ b) the "Artistic License"

		--- The GNU General Public License, Version 1, February 1989 ---

		This software is Copyright (c) 2019 by Cold Spring Harbor Laboratory, Nathan Weeks, Ontario Institute for Cancer Research.
		This software is Copyright (c) 2020 by Cold Spring Harbor Laboratory, Nathan Weeks, Ontario Institute for Cancer Research.

		This is free software, licensed under:

		@@ -272,7 +272,7 @@ That's all there is to it!

		--- The Artistic License 1.0 ---

		This software is Copyright (c) 2019 by Cold Spring Harbor Laboratory, Nathan Weeks, Ontario Institute for Cancer Research.
		This software is Copyright (c) 2020 by Cold Spring Harbor Laboratory, Nathan Weeks, Ontario Institute for Cancer Research.

		This is free software, licensed under:

META.json

+15 −13

Original line number	Diff line number	Diff line
		@@ -5,7 +5,7 @@
		"Nathan Weeks <Nathan.Weeks@ars.usda.gov>"
		],
		"dynamic_config" : 0,
		"generated_by" : "Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150005",
		"generated_by" : "Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010",
		"license" : [
		"perl_5"
		],
		@@ -29,6 +29,7 @@
		"runtime" : {
		"requires" : {
		"Bio::DB::Fasta" : "0",
		"Bio::DB::GFF::Typename" : "0",
		"Bio::DB::GFF::Util::Rearrange" : "0",
		"Bio::Location::Simple" : "0",
		"Bio::PrimarySeq" : "0",
		@@ -39,8 +40,6 @@
		"Bio::SeqFeature::Lite" : "0",
		"Carp" : "0",
		"Cwd" : "0",
		"DBD::Pg" : "0",
		"DBD::SQLite" : "0",
		"DBI" : "0",
		"DB_File" : "0",
		"Fcntl" : "0",
		@@ -90,10 +89,10 @@
		"web" : "https://github.com/bioperl/bio-db-seqfeature"
		}
		},
		"version" : "1.7.3",
		"version" : "1.7.4",
		"x_Dist_Zilla" : {
		"perl" : {
		"version" : "5.022001"
		"version" : "5.028001"
		},
		"plugins" : [
		{
		@@ -201,7 +200,7 @@
		"class" : "Dist::Zilla::Plugin::Test::Compile",
		"config" : {
		"Dist::Zilla::Plugin::Test::Compile" : {
		"bail_out_on_fail" : "0",
		"bail_out_on_fail" : 0,
		"fail_on_warning" : "author",
		"fake_home" : 0,
		"filename" : "t/00-compile.t",
		@@ -213,7 +212,10 @@
		"script_finder" : [
		":PerlExecFiles"
		],
		"skips" : [],
		"skips" : [
		"Bio::DB::SeqFeature::Store::DBI::Pg",
		"Bio::DB::SeqFeature::Store::DBI::SQLite"
		],
		"switch" : []
		}
		},
		@@ -265,7 +267,7 @@
		"changelog" : "Changes"
		},
		"Dist::Zilla::Role::Git::Repo" : {
		"git_version" : "2.7.4",
		"git_version" : "2.20.1",
		"repo_root" : "."
		}
		},
		@@ -288,7 +290,7 @@
		"changelog" : "Changes"
		},
		"Dist::Zilla::Role::Git::Repo" : {
		"git_version" : "2.7.4",
		"git_version" : "2.20.1",
		"repo_root" : "."
		},
		"Dist::Zilla::Role::Git::StringFormatter" : {
		@@ -305,12 +307,12 @@
		"branch" : null,
		"changelog" : "Changes",
		"signed" : 0,
		"tag" : "Bio-DB-SeqFeature-v1.7.3",
		"tag" : "Bio-DB-SeqFeature-v1.7.4",
		"tag_format" : "%N-v%v",
		"tag_message" : "%N-v%v"
		},
		"Dist::Zilla::Role::Git::Repo" : {
		"git_version" : "2.7.4",
		"git_version" : "2.20.1",
		"repo_root" : "."
		},
		"Dist::Zilla::Role::Git::StringFormatter" : {
		@@ -374,12 +376,12 @@
		"zilla" : {
		"class" : "Dist::Zilla::Dist::Builder",
		"config" : {
		"is_trial" : "0"
		"is_trial" : 0
		},
		"version" : "6.012"
		}
		},
		"x_generated_by_perl" : "v5.22.1",
		"x_generated_by_perl" : "v5.28.1",
		"x_serialization_backend" : "Cpanel::JSON::XS version 4.09"
		}

META.yml

+13 −12

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ build_requires:
		configure_requires:
		ExtUtils::MakeMaker: '0'
		dynamic_config: 0
		generated_by: 'Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150005'
		generated_by: 'Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010'
		license: perl
		meta-spec:
		url: http://module-build.sourceforge.net/META-spec-v1.4.html
		@@ -22,6 +22,7 @@ meta-spec:
		name: Bio-DB-SeqFeature
		requires:
		Bio::DB::Fasta: '0'
		Bio::DB::GFF::Typename: '0'
		Bio::DB::GFF::Util::Rearrange: '0'
		Bio::Location::Simple: '0'
		Bio::PrimarySeq: '0'
		@@ -32,8 +33,6 @@ requires:
		Bio::SeqFeature::Lite: '0'
		Carp: '0'
		Cwd: '0'
		DBD::Pg: '0'
		DBD::SQLite: '0'
		DBI: '0'
		DB_File: '0'
		Fcntl: '0'
		@@ -60,10 +59,10 @@ resources:
		bugtracker: https://github.com/bioperl/bio-db-seqfeature/issues
		homepage: https://metacpan.org/release/Bio-DB-SeqFeature
		repository: git://github.com/bioperl/bio-db-seqfeature.git
		version: 1.7.3
		version: 1.7.4
		x_Dist_Zilla:
		perl:
		version: '5.022001'
		version: '5.028001'
		plugins:
		-
		class: Dist::Zilla::Plugin::GatherDir
		@@ -159,7 +158,9 @@ x_Dist_Zilla:
		phase: test
		script_finder:
		- ':PerlExecFiles'
		skips: []
		skips:
		- Bio::DB::SeqFeature::Store::DBI::Pg
		- Bio::DB::SeqFeature::Store::DBI::SQLite
		switch: []
		name: '@BioPerl/Test::Compile'
		version: '2.058'
		@@ -199,7 +200,7 @@ x_Dist_Zilla:
		allow_dirty_match: []
		changelog: Changes
		Dist::Zilla::Role::Git::Repo:
		git_version: 2.7.4
		git_version: 2.20.1
		repo_root: .
		name: '@BioPerl/Git::Check'
		version: '2.045'
		@@ -216,7 +217,7 @@ x_Dist_Zilla:
		allow_dirty_match: []
		changelog: Changes
		Dist::Zilla::Role::Git::Repo:
		git_version: 2.7.4
		git_version: 2.20.1
		repo_root: .
		Dist::Zilla::Role::Git::StringFormatter:
		time_zone: local
		@@ -229,11 +230,11 @@ x_Dist_Zilla:
		branch: ~
		changelog: Changes
		signed: 0
		tag: Bio-DB-SeqFeature-v1.7.3
		tag: Bio-DB-SeqFeature-v1.7.4
		tag_format: '%N-v%v'
		tag_message: '%N-v%v'
		Dist::Zilla::Role::Git::Repo:
		git_version: 2.7.4
		git_version: 2.20.1
		repo_root: .
		Dist::Zilla::Role::Git::StringFormatter:
		time_zone: local
		@@ -284,5 +285,5 @@ x_Dist_Zilla:
		config:
		is_trial: '0'
		version: '6.012'
		x_generated_by_perl: v5.22.1
		x_serialization_backend: 'YAML::Tiny version 1.69'
		x_generated_by_perl: v5.28.1
		x_serialization_backend: 'YAML::Tiny version 1.73'

Makefile.PL

+3 −5

Original line number	Diff line number	Diff line
		@@ -23,6 +23,7 @@ my %WriteMakefileArgs = (
		"NAME" => "Bio::DB::SeqFeature",
		"PREREQ_PM" => {
		"Bio::DB::Fasta" => 0,
		"Bio::DB::GFF::Typename" => 0,
		"Bio::DB::GFF::Util::Rearrange" => 0,
		"Bio::Location::Simple" => 0,
		"Bio::PrimarySeq" => 0,
		@@ -33,8 +34,6 @@ my %WriteMakefileArgs = (
		"Bio::SeqFeature::Lite" => 0,
		"Carp" => 0,
		"Cwd" => 0,
		"DBD::Pg" => 0,
		"DBD::SQLite" => 0,
		"DBI" => 0,
		"DB_File" => 0,
		"Fcntl" => 0,
		@@ -66,7 +65,7 @@ my %WriteMakefileArgs = (
		"Test::More" => 0,
		"lib" => 0
		},
		"VERSION" => "1.7.3",
		"VERSION" => "1.7.4",
		"test" => {
		"TESTS" => "t/*.t"
		}
		@@ -75,6 +74,7 @@ my %WriteMakefileArgs = (

		my %FallbackPrereqs = (
		"Bio::DB::Fasta" => 0,
		"Bio::DB::GFF::Typename" => 0,
		"Bio::DB::GFF::Util::Rearrange" => 0,
		"Bio::Location::Simple" => 0,
		"Bio::PrimarySeq" => 0,
		@@ -86,8 +86,6 @@ my %FallbackPrereqs = (
		"Bio::SeqFeature::Lite" => 0,
		"Carp" => 0,
		"Cwd" => 0,
		"DBD::Pg" => 0,
		"DBD::SQLite" => 0,
		"DBI" => 0,
		"DB_File" => 0,
		"Fcntl" => 0,