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View file @ 02f1fde0
Summary of important user-visible changes for Bio-DB-GFF
--------------------------------------------------------
1.7.4 2020-01-08 14:41:24-06:00 America/Chicago
* Explicitly remove Bio::GMOD::CMap::Utils as a requirement, this is
a non-CPAN module that is used in a loader script, so ignore.
1.7.3 2019-02-19 14:12:42-05:00 America/Detroit
* First release after split from bioperl-live.
LICENSE
View file @ 02f1fde0
This software is copyright (c) 2019 by See individual modules.
This software is copyright (c) 2020 by See individual modules.
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 See individual modules.
This software is Copyright (c) 2020 by See individual modules.
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 See individual modules.
This software is Copyright (c) 2020 by See individual modules.
This is free software, licensed under:
......
META.json
View file @ 02f1fde0
......@@ -4,7 +4,7 @@
"See individual modules"
],
"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"
],
......@@ -36,7 +36,6 @@
"Bio::Das::FeatureTypeI" : "0",
"Bio::Das::SegmentI" : "0",
"Bio::DasI" : "0",
"Bio::GMOD::CMap::Utils" : "0",
"Bio::Location::Simple" : "0",
"Bio::Location::Split" : "0",
"Bio::LocationI" : "0",
......@@ -97,10 +96,10 @@
"web" : "https://github.com/bioperl/bio-db-gff"
}
},
"version" : "1.7.3",
"version" : "1.7.4",
"x_Dist_Zilla" : {
"perl" : {
"version" : "5.022001"
"version" : "5.028001"
},
"plugins" : [
{
......@@ -208,7 +207,7 @@
"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",
......@@ -272,7 +271,7 @@
"changelog" : "Changes"
},
"Dist::Zilla::Role::Git::Repo" : {
"git_version" : "2.7.4",
"git_version" : "2.20.1",
"repo_root" : "."
}
},
......@@ -295,7 +294,7 @@
"changelog" : "Changes"
},
"Dist::Zilla::Role::Git::Repo" : {
"git_version" : "2.7.4",
"git_version" : "2.20.1",
"repo_root" : "."
},
"Dist::Zilla::Role::Git::StringFormatter" : {
......@@ -312,12 +311,12 @@
"branch" : null,
"changelog" : "Changes",
"signed" : 0,
"tag" : "Bio-DB-GFF-v1.7.3",
"tag" : "Bio-DB-GFF-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" : {
......@@ -381,12 +380,12 @@
"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
View file @ 02f1fde0
......@@ -13,7 +13,7 @@ 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
......@@ -29,7 +29,6 @@ requires:
Bio::Das::FeatureTypeI: '0'
Bio::Das::SegmentI: '0'
Bio::DasI: '0'
Bio::GMOD::CMap::Utils: '0'
Bio::Location::Simple: '0'
Bio::Location::Split: '0'
Bio::LocationI: '0'
......@@ -67,10 +66,10 @@ resources:
bugtracker: https://github.com/bioperl/bio-db-gff/issues
homepage: https://metacpan.org/release/Bio-DB-GFF
repository: git://github.com/bioperl/bio-db-gff.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
......@@ -206,7 +205,7 @@ 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'
......@@ -223,7 +222,7 @@ 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
......@@ -236,11 +235,11 @@ x_Dist_Zilla:
branch: ~
changelog: Changes
signed: 0
tag: Bio-DB-GFF-v1.7.3
tag: Bio-DB-GFF-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
......@@ -291,5 +290,5 @@ 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
View file @ 02f1fde0
......@@ -35,7 +35,6 @@ my %WriteMakefileArgs = (
"Bio::Das::FeatureTypeI" => 0,
"Bio::Das::SegmentI" => 0,
"Bio::DasI" => 0,
"Bio::GMOD::CMap::Utils" => 0,
"Bio::Location::Simple" => 0,
"Bio::Location::Split" => 0,
"Bio::LocationI" => 0,
......@@ -78,7 +77,7 @@ my %WriteMakefileArgs = (
"Module::Build" => 0,
"Test::More" => 0
},
"VERSION" => "1.7.3",
"VERSION" => "1.7.4",
"test" => {
"TESTS" => "t/*.t"
}
......@@ -95,7 +94,6 @@ my %FallbackPrereqs = (
"Bio::Das::FeatureTypeI" => 0,
"Bio::Das::SegmentI" => 0,
"Bio::DasI" => 0,
"Bio::GMOD::CMap::Utils" => 0,
"Bio::Location::Simple" => 0,
"Bio::Location::Split" => 0,
"Bio::LocationI" => 0,
......
bin/bp_bulk_load_gff
View file @ 02f1fde0
......@@ -121,7 +121,7 @@ disclaimers of warranty.
=cut
package Bio::DB::GFF::Adaptor::fauxmysql;
$Bio::DB::GFF::Adaptor::fauxmysql::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::fauxmysql::VERSION = '1.7.4';
use Bio::DB::GFF::Adaptor::dbi::mysqlopt;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::mysqlopt';
......@@ -133,7 +133,7 @@ sub insert_sequence {
};
package Bio::DB::GFF::Adaptor::fauxmysqlcmap;
$Bio::DB::GFF::Adaptor::fauxmysqlcmap::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::fauxmysqlcmap::VERSION = '1.7.4';
use Bio::DB::GFF::Adaptor::dbi::mysqlcmap;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::mysqlcmap';
......@@ -145,7 +145,7 @@ sub insert_sequence {
};
package Bio::DB::GFF::Adaptor::fauxpg;
$Bio::DB::GFF::Adaptor::fauxpg::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::fauxpg::VERSION = '1.7.4';
use Bio::DB::GFF::Adaptor::dbi::pg;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::pg';
......@@ -184,7 +184,7 @@ sub insert_sequence {
}
package main;
$main::VERSION = '1.7.3';
$main::VERSION = '1.7.4';
eval "use Time::HiRes"; undef $@;
my $timer = defined &Time::HiRes::time;
......
bin/bp_fast_load_gff
View file @ 02f1fde0
......@@ -116,7 +116,7 @@ disclaimers of warranty.
=cut
package Bio::DB::GFF::Adaptor::faux;
$Bio::DB::GFF::Adaptor::faux::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::faux::VERSION = '1.7.4';
use Bio::DB::GFF::Adaptor::dbi::mysqlopt;
use vars '@ISA';
@ISA = 'Bio::DB::GFF::Adaptor::dbi::mysqlopt';
......@@ -128,7 +128,7 @@ sub insert_sequence {
}
package main;
$main::VERSION = '1.7.3';
$main::VERSION = '1.7.4';
eval "use Time::HiRes"; undef $@;
my $timer = defined &Time::HiRes::time;
......
bin/bp_genbank2gff
View file @ 02f1fde0
......@@ -69,7 +69,7 @@ disclaimers of warranty.
=cut
package Bio::DB::GFF::Adaptor::biofetch_to_stdout;
$Bio::DB::GFF::Adaptor::biofetch_to_stdout::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::biofetch_to_stdout::VERSION = '1.7.4';
use CGI 'escape';
use Bio::DB::GFF::Util::Rearrange;
use Bio::DB::GFF::Adaptor::biofetch;
......@@ -129,7 +129,7 @@ sub finish_load { }
1;
package main;
$main::VERSION = '1.7.3';
$main::VERSION = '1.7.4';
my $USAGE = <<USAGE;
Usage: $0 [options] [<gff file 1> <gff file 2>] ...
......
debian/changelog
View file @ 02f1fde0
libbio-db-gff-perl (1.7.4-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.4.1
-- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 13 Jan 2020 13:16:18 +0100
libbio-db-gff-perl (1.7.3-2) unstable; urgency=medium
* debian/control: Breaks+Replaces the old libbio-bio-perl. (Closes: #942789)
......
debian/control
View file @ 02f1fde0
......@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 12),
libtest-most-perl,
libmodule-build-perl
Build-Depends-Indep: perl
Standards-Version: 4.4.0
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-gff-perl
Vcs-Git: https://salsa.debian.org/med-team/libbio-db-gdd.git
Homepage: https://metacpan.org/release/Bio-DB-GFF
......
dist.ini
View file @ 02f1fde0
name = Bio-DB-GFF
version = 1.7.3
version = 1.7.4
author = See individual modules
copyright_holder = See individual modules
license = Perl_5
......@@ -10,3 +10,5 @@ license = Perl_5
-remove = PodWeaver
-remove = Test::EOL
-remove = Test::NoTabs
AutoPrereqs.skips[0] = ^Bio::GMOD::CMap::Utils$
lib/Bio/DB/GFF.pm
View file @ 02f1fde0
......@@ -593,7 +593,7 @@ The following is the API for Bio::DB::GFF.
=cut
package Bio::DB::GFF;
$Bio::DB::GFF::VERSION = '1.7.3';
$Bio::DB::GFF::VERSION = '1.7.4';
use strict;
use IO::File;
......@@ -3824,7 +3824,7 @@ END
package Bio::DB::GFF::ID_Iterator;
$Bio::DB::GFF::ID_Iterator::VERSION = '1.7.3';
$Bio::DB::GFF::ID_Iterator::VERSION = '1.7.4';
use strict;
use base qw(Bio::Root::Root);
......@@ -3849,7 +3849,7 @@ sub next_seq {
}
package Bio::DB::GFF::FeatureIterator;
$Bio::DB::GFF::FeatureIterator::VERSION = '1.7.3';
$Bio::DB::GFF::FeatureIterator::VERSION = '1.7.4';
sub new {
my $self = shift;
my @features = @_;
......
lib/Bio/DB/GFF/Adaptor/berkeleydb.pm
View file @ 02f1fde0
package Bio::DB::GFF::Adaptor::berkeleydb;
$Bio::DB::GFF::Adaptor::berkeleydb::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::berkeleydb::VERSION = '1.7.4';
=head1 NAME
......@@ -1003,7 +1003,7 @@ sub get_features_iterator {
#--------------------------------------------------------------------------#
package FeatureStore;
$FeatureStore::VERSION = '1.7.3';
$FeatureStore::VERSION = '1.7.4';
# This is a very specialized package that stores serialized features onto a file-based
# array. The array is indexed by the physical offset to the beginning of each serialized
# feature.
......
lib/Bio/DB/GFF/Adaptor/berkeleydb/iterator.pm
View file @ 02f1fde0
......@@ -34,7 +34,7 @@ it under the same terms as Perl itself.
=cut
package Bio::DB::GFF::Adaptor::berkeleydb::iterator;
$Bio::DB::GFF::Adaptor::berkeleydb::iterator::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::berkeleydb::iterator::VERSION = '1.7.4';
use strict;
use DB_File qw(R_FIRST R_NEXT);
......
lib/Bio/DB/GFF/Adaptor/biofetch.pm
View file @ 02f1fde0
package Bio::DB::GFF::Adaptor::biofetch;
$Bio::DB::GFF::Adaptor::biofetch::VERSION = '1.7.3';
#$Id$
$Bio::DB::GFF::Adaptor::biofetch::VERSION = '1.7.4';
=head1 NAME
Bio::DB::GFF::Adaptor::biofetch -- Cache BioFetch objects in a Bio::DB::GFF database
......
lib/Bio/DB/GFF/Adaptor/biofetch_oracle.pm
View file @ 02f1fde0
package Bio::DB::GFF::Adaptor::biofetch_oracle;
$Bio::DB::GFF::Adaptor::biofetch_oracle::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::biofetch_oracle::VERSION = '1.7.4';
#$Id$
=head1 NAME
......
lib/Bio/DB/GFF/Adaptor/dbi.pm
View file @ 02f1fde0
......@@ -16,7 +16,7 @@ QUERIES TO IMPLEMENT for the list of methods that must be implemented.
=cut
package Bio::DB::GFF::Adaptor::dbi;
$Bio::DB::GFF::Adaptor::dbi::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::dbi::VERSION = '1.7.4';
# base class for dbi-based implementations
use strict;
......
lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
View file @ 02f1fde0
package Bio::DB::GFF::Adaptor::dbi::caching_handle;
$Bio::DB::GFF::Adaptor::dbi::caching_handle::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::dbi::caching_handle::VERSION = '1.7.4';
use strict;
use DBI;
use vars '$AUTOLOAD';
......@@ -200,7 +200,7 @@ sub dbi_quote {
}
package Bio::DB::GFF::Adaptor::dbi::faux_dbh;
$Bio::DB::GFF::Adaptor::dbi::faux_dbh::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::dbi::faux_dbh::VERSION = '1.7.4';
use vars '$AUTOLOAD';
sub new {
......
lib/Bio/DB/GFF/Adaptor/dbi/iterator.pm
View file @ 02f1fde0
......@@ -34,7 +34,7 @@ it under the same terms as Perl itself.
=cut
package Bio::DB::GFF::Adaptor::dbi::iterator;
$Bio::DB::GFF::Adaptor::dbi::iterator::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::dbi::iterator::VERSION = '1.7.4';
use strict;
use Bio::Root::Version;
......
lib/Bio/DB/GFF/Adaptor/dbi/mysql.pm
View file @ 02f1fde0
package Bio::DB::GFF::Adaptor::dbi::mysql;
$Bio::DB::GFF::Adaptor::dbi::mysql::VERSION = '1.7.3';
$Bio::DB::GFF::Adaptor::dbi::mysql::VERSION = '1.7.4';
=head1 NAME
Bio::DB::GFF::Adaptor::dbi::mysql -- Database adaptor for a specific mysql schema
......