New upstream version 1.7.7 (04847468) · Commits · Debian Med / bioperl

Changes

+16 −0

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		Summary of important user-visible changes for BioPerl
		-----------------------------------------------------

		1.7.7 2019-12-07 13:41:36-06:00 America/Chicago

		* The program bp_chaos_plot has been removed.

		* GD is now no longer a dependency, suggestion or requirement.

		* #321 - GenBank format fix for un-quoted features, text wrapping

		* Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(),
		and a 'private' _sleep() function that mirror those from
		Bio::DB::WebDBSeqI, primarily for compliance with potential website
		restrictions for the number and frequency of queries (e.g. NCBI eUtils).

		* Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation
		in last release.

		1.7.6 2019-08-28 12:37:01+01:00 Europe/London

		* The program bp_classify_hits_kingdom has been removed and is

+13 −0

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		@@ -26,6 +26,19 @@ The bioperl-live repository structure is organized as follows:

		## `Bio::` namespace summary

		The BioPerl project is split over multiple Perl module distributions.
		The BioPerl distribution is the BioPerl core distribution, including a
		selection of modules and namespaces but not all. For example, the
		entire Bio::Biblio is not included in the BioPerl distribution.
		Similarly, while many Bio::SearchIO modules in the BioPerl
		distribution, there also Bio::SearchIO modules in other distributions
		such as Bio-SearchIO-blastxml.

		This section describes most of the Bio:: namespaces developed by the
		BioPerl project, including those which are not part of the BioPerl
		distribution. For example, the Bio::Biblio and Bio::Assembly are
		documented here but are not part of the BioPerl distribution.

		* `Bio::Seq` is for Sequences (protein and DNA).
		* `Bio::PrimarySeq` is a plain sequence (sequence data +
		identifiers)

+0 −1

+4 −16

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		@@ -105,8 +105,7 @@
		"Bio::DB::EMBL" : "0",
		"Bio::DB::GenBank" : "0",
		"Bio::DB::GenPept" : "0",
		"Bio::DB::SwissProt" : "0",
		"GD" : "0"
		"Bio::DB::SwissProt" : "0"
		}
		},
		"test" : {
		@@ -136,7 +135,7 @@
		"web" : "https://github.com/bioperl/bioperl-live"
		}
		},
		"version" : "1.7.6",
		"version" : "1.7.7",
		"x_Dist_Zilla" : {
		"perl" : {
		"version" : "5.028001"
		@@ -346,7 +345,7 @@
		"branch" : null,
		"changelog" : "Changes",
		"signed" : 0,
		"tag" : "BioPerl-v1.7.6",
		"tag" : "BioPerl-v1.7.7",
		"tag_format" : "%N-v%v",
		"tag_message" : "%N-v%v"
		},
		@@ -382,17 +381,6 @@
		"name" : "bin_bp_fetch_RuntimeSuggests",
		"version" : "6.012"
		},
		{
		"class" : "Dist::Zilla::Plugin::Prereqs",
		"config" : {
		"Dist::Zilla::Plugin::Prereqs" : {
		"phase" : "runtime",
		"type" : "suggests"
		}
		},
		"name" : "bin_bp_chaos_plot_RuntimeSuggests",
		"version" : "6.012"
		},
		{
		"class" : "Dist::Zilla::Plugin::FileFinder::ByName",
		"name" : "PodWeaver-Ready",
		@@ -502,7 +490,7 @@
		{
		"class" : "Pod::Weaver::Section::Legal::Complicated",
		"name" : "@BioPerl/Legal",
		"version" : "1.22"
		"version" : "1.23"
		},
		{
		"class" : "Pod::Weaver::Section::Contributors",

+3 −11

Original line number	Diff line number	Diff line
		@@ -98,7 +98,7 @@ resources:
		bugtracker: https://github.com/bioperl/bioperl-live/issues
		homepage: https://metacpan.org/release/BioPerl
		repository: git://github.com/bioperl/bioperl-live.git
		version: 1.7.6
		version: 1.7.7
		x_Dist_Zilla:
		perl:
		version: '5.028001'
		@@ -263,7 +263,7 @@ x_Dist_Zilla:
		branch: ~
		changelog: Changes
		signed: 0
		tag: BioPerl-v1.7.6
		tag: BioPerl-v1.7.7
		tag_format: '%N-v%v'
		tag_message: '%N-v%v'
		Dist::Zilla::Role::Git::Repo:
		@@ -288,14 +288,6 @@ x_Dist_Zilla:
		type: suggests
		name: bin_bp_fetch_RuntimeSuggests
		version: '6.012'
		-
		class: Dist::Zilla::Plugin::Prereqs
		config:
		Dist::Zilla::Plugin::Prereqs:
		phase: runtime
		type: suggests
		name: bin_bp_chaos_plot_RuntimeSuggests
		version: '6.012'
		-
		class: Dist::Zilla::Plugin::FileFinder::ByName
		name: PodWeaver-Ready
		@@ -384,7 +376,7 @@ x_Dist_Zilla:
		-
		class: Pod::Weaver::Section::Legal::Complicated
		name: '@BioPerl/Legal'
		version: '1.22'
		version: '1.23'
		-
		class: Pod::Weaver::Section::Contributors
		name: '@BioPerl/Contributors'