Changes

 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

-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

@@ -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

@@ -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

@@ -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,

debian/changelog

+libbio-db-seqfeature-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 13:17:15 +0100
+
 libbio-db-seqfeature-perl (1.7.3-2) unstable; urgency=medium
 
   * debian/control: Breaks+Replaces the old libbio-bio-perl. (Closes: #942789)

debian/control

@@ -11,7 +11,7 @@ Build-Depends-Indep: libbio-perl-perl,
                      libdbi-perl,
                      perl,
                      libtest-most-perl
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-seqfeature-perl
 Vcs-Git: https://salsa.debian.org/med-team/libbio-db-seqfeature.git
 Homepage: https://metacpan.org/release/Bio-DB-SeqFeature

dist.ini

 name = Bio-DB-SeqFeature
-version = 1.7.3
+version = 1.7.4
 author = Lincoln Stein <lstein@cshl.org>
 author = Nathan Weeks <Nathan.Weeks@ars.usda.gov>
 copyright_holder = Cold Spring Harbor Laboratory, Nathan Weeks, Ontario Institute for Cancer Research
 license = Perl_5
 
 ;; Modules should be fixed so that these don't have to be removed.
+
 [@BioPerl]
 -remove = PodCoverageTests
 -remove = PodWeaver
 -remove = Test::EOL
 -remove = Test::NoTabs
+
+;; Skip requiring DBD::Pg
+AutoPrereqs.skips[0] = ^DBD::\S+$
+
+;; skip compilation tests, which fail if DBD::* modules aren't installed
+Test::Compile.skip[0] = Bio::DB::SeqFeature::Store::DBI::Pg
+Test::Compile.skip[1] = Bio::DB::SeqFeature::Store::DBI::SQLite

lib/Bio/DB/SeqFeature.pm

 package Bio::DB::SeqFeature;
-$Bio::DB::SeqFeature::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::VERSION = '1.7.4';
 
 =head1 NAME
 

lib/Bio/DB/SeqFeature/NormalizedFeature.pm

 package Bio::DB::SeqFeature::NormalizedFeature;
-$Bio::DB::SeqFeature::NormalizedFeature::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::NormalizedFeature::VERSION = '1.7.4';
 
 =head1 NAME
 

lib/Bio/DB/SeqFeature/NormalizedFeatureI.pm

 package Bio::DB::SeqFeature::NormalizedFeatureI;
-$Bio::DB::SeqFeature::NormalizedFeatureI::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::NormalizedFeatureI::VERSION = '1.7.4';
 
 =head1 NAME
 

lib/Bio/DB/SeqFeature/NormalizedTableFeatureI.pm

 package Bio::DB::SeqFeature::NormalizedTableFeatureI;
-$Bio::DB::SeqFeature::NormalizedTableFeatureI::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::NormalizedTableFeatureI::VERSION = '1.7.4';
 
 =head1 NAME
 

lib/Bio/DB/SeqFeature/Segment.pm

 package Bio::DB::SeqFeature::Segment;
-$Bio::DB::SeqFeature::Segment::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Segment::VERSION = '1.7.4';
 
 =head1 NAME
 

lib/Bio/DB/SeqFeature/Store.pm

 package Bio::DB::SeqFeature::Store;
-$Bio::DB::SeqFeature::Store::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Store::VERSION = '1.7.4';
 
 =head1 NAME
 
@@ -2711,7 +2711,7 @@ sub coverage_array {
 
 
 package Bio::DB::SeqFeature::Store::FeatureIterator;
-$Bio::DB::SeqFeature::Store::FeatureIterator::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Store::FeatureIterator::VERSION = '1.7.4';
 sub new {
     my $self     = shift;
     my @features = @_;

lib/Bio/DB/SeqFeature/Store/DBI/Iterator.pm

 package Bio::DB::SeqFeature::Store::DBI::Iterator;
-$Bio::DB::SeqFeature::Store::DBI::Iterator::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Store::DBI::Iterator::VERSION = '1.7.4';
 
 =head1 NAME
 

lib/Bio/DB/SeqFeature/Store/DBI/Pg.pm

-
-package Bio::DB::SeqFeature::Store::DBI::Pg;
-$Bio::DB::SeqFeature::Store::DBI::Pg::VERSION = '1.7.3';
-use DBD::Pg qw(:pg_types);
-use MIME::Base64;
-# $Id: Pg.pm 14656 2008-04-14 15:05:37Z lstein $
-
 =head1 NAME
 
 Bio::DB::SeqFeature::Store::DBI::Pg -- PostgreSQL implementation of Bio::DB::SeqFeature::Store
@@ -153,11 +146,15 @@ sections.
 
 =cut
 
+package Bio::DB::SeqFeature::Store::DBI::Pg;
+$Bio::DB::SeqFeature::Store::DBI::Pg::VERSION = '1.7.4';
 use strict;
-
 use base 'Bio::DB::SeqFeature::Store::DBI::mysql';
+use MIME::Base64;
+
 use Bio::DB::SeqFeature::Store::DBI::Iterator;
 use DBI;
+use DBD::Pg qw(:pg_types);
 use Memoize;
 use Cwd 'abs_path';
 use Bio::DB::GFF::Util::Rearrange 'rearrange';

lib/Bio/DB/SeqFeature/Store/DBI/SQLite.pm

 package Bio::DB::SeqFeature::Store::DBI::SQLite;
-$Bio::DB::SeqFeature::Store::DBI::SQLite::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Store::DBI::SQLite::VERSION = '1.7.4';
 #$Id$
 
 =head1 NAME

lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm

 package Bio::DB::SeqFeature::Store::DBI::mysql;
-$Bio::DB::SeqFeature::Store::DBI::mysql::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Store::DBI::mysql::VERSION = '1.7.4';
 =head1 NAME
 
 Bio::DB::SeqFeature::Store::DBI::mysql -- Mysql implementation of Bio::DB::SeqFeature::Store

lib/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm

 package Bio::DB::SeqFeature::Store::FeatureFileLoader;
-$Bio::DB::SeqFeature::Store::FeatureFileLoader::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Store::FeatureFileLoader::VERSION = '1.7.4';
 
 =head1 NAME
 

lib/Bio/DB/SeqFeature/Store/GFF2Loader.pm

 package Bio::DB::SeqFeature::Store::GFF2Loader;
-$Bio::DB::SeqFeature::Store::GFF2Loader::VERSION = '1.7.3';
+$Bio::DB::SeqFeature::Store::GFF2Loader::VERSION = '1.7.4';
 # $Id: GFF2Loader.pm 11755 2007-11-08 02:19:29Z cjfields $
 
 =head1 NAME