Feature/cpan release 113 (#724)

* Prepare for CPAN release

- Adds file for Bio::Ensembl - this makes it easier to release to CPAN
- Adds dist.ini for Dist::Zilla
- Update cpanfile
- Add a blank line to packages, to enable Dist::Zilla to insert a
  package version

* Remove version from example code

- It's not necessary to set this explcitly. 113 is used if no version is
  given

Author: EbiArnie

Changes

@@ -0,0 +1,11 @@
+Revision history for Bio::EnsEMBL, the EnsEMBL Core Perl API
+
+{{$NEXT}}
+
+113.0.0   2024-10-17 (TRIAL RELEASE)
+
+ - Release for Ensembl 113
+
+112.0.0   2024-09-03
+
+ - Release for Ensembl 112

cpanfile

@@ -1,11 +1,13 @@
 requires 'DBI';
 requires 'DBD::mysql', '< 5.0'; # newer versions do not support MySQL 5
+requires 'DBD::SQLite';
 requires 'HTTP::Tiny';
 requires 'IO::Compress::Gzip';
 requires 'URI::Escape';
 requires 'Config::IniFiles';
 requires 'Gzip::Faster';
 requires 'List::MoreUtils';
+requires 'JSON';
 
 test_requires 'Test::Warnings';
 test_requires 'Test::Differences';
@@ -15,6 +17,8 @@ test_requires 'Test::Deep';
 test_requires 'Test::More';
 test_requires 'Devel::Peek';
 test_requires 'Devel::Cycle';
+test_requires 'Devel::Cover';
+test_requires 'Devel::Cover::Report::Coveralls';
 test_requires 'Error';
 test_requires 'PadWalker';
 test_requires 'Test::Builder::Module';

dist.ini

@@ -0,0 +1,62 @@
+name    = Bio-EnsEMBL
+; Major: the EnsEMBL release
+; Minor: for patches to an EnsEMBL release
+; Patch: for changes related to CPAN packaging
+version = 113.0.0
+author  = Arne Becker <[email protected]>
+license = Apache_2_0
+copyright_holder = EMBL-EBI
+abstract = Bio::EnsEMBL - Ensembl Core API
+main_module = lib/Bio/EnsEMBL.pm
+
+[GatherFile]
+filename = Changes
+filename = CONTRIBUTING.md
+
+[GatherDir / libs]
+root = modules
+prefix = lib
+
+[PruneFiles]
+match     = ^lib/t/
+
+[PruneCruft]
+
+[PkgVersion]
+
+[AutoPrereqs]
+skip = ^Bio::EnsEMBL::XS$
+skip = ^Bio::EnsEMBL::Utils::User_defined_load$
+skip = ^SeqStoreConverter::BasicConverter$
+skip = ^Bio::EnsEMBL::Production::DBSQL::DBAdaptor$
+skip = ^Bio::EnsEMBL::MetaData::DBSQL::MetaDataDBAdaptor$
+skip = ^Bio::EnsEMBL::Taxonomy::DBSQL::TaxonomyDBAdaptor$
+
+[NextRelease]
+format = %-9v %{yyyy-MM-dd}d%{ (TRIAL RELEASE)}T
+
+[Test::ChangesHasContent]
+
+[MinimumPerlFast]
+
+[ManifestSkip]
+
+[GitHub::Meta]
+
+[MetaYAML]
+
+[MetaJSON]
+
+[License]
+
+[ReadmeAnyFromPod]
+
+[MakeMaker]
+
+[Manifest]
+
+[TestRelease]
+
+[ConfirmRelease]
+
+[UploadToCPAN]

modules/Bio/EnsEMBL.pm

@@ -0,0 +1,73 @@
+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+Bio::EnsEMBL - API to connect to and work with EnsEMBL genomic databases
+
+=head1 SYNOPSIS
+
+    use Bio::EnsEMBL::Registry;
+
+    Bio::EnsEMBL::Registry->load_registry_from_db(
+        -host => 'ensembldb.ensembl.org',
+        -user => 'anonymous',
+        -species => 'homo sapiens',
+        -group => 'core'
+    );
+    my $slice_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
+        'homo sapiens', 'Core', 'Slice'
+    );
+    my $slice = $slice_adaptor->fetch_by_gene_stable_id('ENSG00000101266');
+    say $slice->display_id();
+
+=head1 DESCRIPTION
+
+L<Bio::EnsEMBL> is the namespace for the EnsEMBL Core API.
+The Core API provides access to the EnsEMBL genomic databases.
+
+Most people will want to use L<Bio::EnsEMBL::Registry> as an entry point.
+
+=head1 SEE ALSO
+
+L<https://www.ensembl.org/info/docs/api/index.html>
+
+=head1 SUPPORT
+
+Please email comments or questions to the public EnsEMBL developers list at
+L<http://lists.ensembl.org/mailman/listinfo/dev>.
+
+Questions may also be sent to the EnsEMBL help desk at
+L<http://www.ensembl.org/Help/Contact>.
+
+=head1 COPYRIGHT AND LICENCE
+
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0
+
+=cut
+
+use strict;
+use warnings;
+package Bio::EnsEMBL;
+# ABSTRACT: API to connect to and work with EnsEMBL genomic databases
+
+1;

modules/Bio/EnsEMBL/Analysis/Programs.pm

@@ -29,6 +29,7 @@ limitations under the License.
 =cut
 
 package Bio::EnsEMBL::Analysis::Programs;
+
 use strict;
 use vars qw( %Program_Paths );
 use Carp;

modules/Bio/EnsEMBL/CircularSlice.pm

@@ -66,6 +66,7 @@ retrieve sequence or features from an area of interest.
 =cut
 
 package Bio::EnsEMBL::CircularSlice;
+
 use vars qw(@ISA);
 use strict;
 

modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm

@@ -80,6 +80,7 @@ common mapping to an intermediate coordinate system.
 =cut
 
 package Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor;
+
 use vars qw(@ISA);
 use strict;
 

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -95,6 +95,7 @@ case the convention is to go list_XXXX, such as
 =cut
 
 package Bio::EnsEMBL::DBSQL::BaseAdaptor;
+
 require Exporter;
 use vars qw(@ISA @EXPORT);
 use strict;

modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm

@@ -48,6 +48,7 @@ DnaAlignFeatureAdaptor and ProteinAlignFeatureAdaptor.
 =cut
 
 package Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor;
+
 use vars qw(@ISA @EXPORT);
 use strict;
 

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -49,6 +49,7 @@ common to all feature adaptors.
 =cut
 
 package Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+
 use vars qw(@ISA @EXPORT);
 use strict;