Commit 1c8eef09 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 1.7.6

parent 46c91e7d

Changes

+17 −0
Original line number Diff line number Diff line 
Summary of important user-visible changes for BioPerl

-----------------------------------------------------



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



    * The program bp_classify_hits_kingdom has been removed and is

      now part of the examples documentation instead.



    * GD is now listed as a suggestion instead of a requirement.  The

      bp_chaos_plot program will now work with the GD module.



    * New method Bio::Tree::Statistics::transfer_bootstrap_expectation

      to compute Transfer Bootstrap Expectation (TBE) for internal

      nodes based on the methods outlined in Lemoine et al, Nature,

      2018.



    * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next

      sequence in the stream faster but not perfect.





1.7.5     2019-02-11 14:57:45+00:00 Europe/London



    * The following modules have been removed from the BioPerl

MANIFEST

+1 −1
Original line number Diff line number Diff line
@@ -12,7 +12,6 @@ bin/bp_aacomp 
bin/bp_bioflat_index

bin/bp_biogetseq

bin/bp_chaos_plot

bin/bp_classify_hits_kingdom

bin/bp_dbsplit

bin/bp_extract_feature_seq

bin/bp_fastam9_to_table
@@ -56,6 +55,7 @@ examples/align/FastAlign.pl 
examples/align/align_on_codons.pl

examples/align/aligntutorial.pl

examples/align/simplealign.pl

examples/classify_hits_kingdom

examples/contributed/nmrpdb_parse.pl

examples/contributed/prosite2perl.pl

examples/contributed/rebase2list.pl

META.json

+18 −7
Original line number Diff line number Diff line
@@ -30,13 +30,11 @@ 
            "AnyDBM_File" : "0",

            "Carp" : "0",

            "Cwd" : "0",

            "DBI" : "0",

            "DB_File" : "0",

            "Data::Dumper" : "0",

            "Data::Stag" : "0",

            "Digest::MD5" : "0",

            "Dumpvalue" : "0",

            "Env" : "0",

            "Error" : "0",

            "Exporter" : "0",

            "Fcntl" : "0",
@@ -47,7 +45,6 @@ 
            "File::Spec::Functions" : "0",

            "File::Temp" : "0",

            "FileHandle" : "0",

            "GD" : "0",

            "Getopt::Long" : "0",

            "Graph::Directed" : "0",

            "HTTP::Request::Common" : "0",
@@ -108,17 +105,20 @@ 
            "Bio::DB::EMBL" : "0",

            "Bio::DB::GenBank" : "0",

            "Bio::DB::GenPept" : "0",

            "Bio::DB::SwissProt" : "0"

            "Bio::DB::SwissProt" : "0",

            "GD" : "0"

         }

      },

      "test" : {

         "requires" : {

            "File::Spec" : "0",

            "FindBin" : "0",

            "IO::Handle" : "0",

            "IPC::Open3" : "0",

            "Test::Memory::Cycle" : "0",

            "Test::More" : "0",

            "Test::Weaken" : "0",

            "lib" : "0",

            "perl" : "5.006"

         }

      }
@@ -136,7 +136,7 @@ 
         "web" : "https://github.com/bioperl/bioperl-live"

      }

   },

   "version" : "1.7.5",

   "version" : "1.7.6",

   "x_Dist_Zilla" : {

      "perl" : {

         "version" : "5.028001"
@@ -346,7 +346,7 @@ 
                  "branch" : null,

                  "changelog" : "Changes",

                  "signed" : 0,

                  "tag" : "BioPerl-v1.7.5",

                  "tag" : "BioPerl-v1.7.6",

                  "tag_format" : "%N-v%v",

                  "tag_message" : "%N-v%v"

               },
@@ -382,6 +382,17 @@ 
            "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",
@@ -589,6 +600,6 @@ 
      }

   },

   "x_generated_by_perl" : "v5.28.1",

   "x_serialization_backend" : "Cpanel::JSON::XS version 4.08"

   "x_serialization_backend" : "Cpanel::JSON::XS version 4.09"

}

META.yml

+12 −5
Original line number Diff line number Diff line
@@ -4,11 +4,13 @@ author: 
  - 'See individual modules'

build_requires:

  File::Spec: '0'

  FindBin: '0'

  IO::Handle: '0'

  IPC::Open3: '0'

  Test::Memory::Cycle: '0'

  Test::More: '0'

  Test::Weaken: '0'

  lib: '0'

  perl: '5.006'

configure_requires:

  ExtUtils::MakeMaker: '0'
@@ -23,13 +25,11 @@ requires: 
  AnyDBM_File: '0'

  Carp: '0'

  Cwd: '0'

  DBI: '0'

  DB_File: '0'

  Data::Dumper: '0'

  Data::Stag: '0'

  Digest::MD5: '0'

  Dumpvalue: '0'

  Env: '0'

  Error: '0'

  Exporter: '0'

  Fcntl: '0'
@@ -40,7 +40,6 @@ requires: 
  File::Spec::Functions: '0'

  File::Temp: '0'

  FileHandle: '0'

  GD: '0'

  Getopt::Long: '0'

  Graph::Directed: '0'

  HTTP::Request::Common: '0'
@@ -99,7 +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: 1.7.5

version: 1.7.6

x_Dist_Zilla:

  perl:

    version: '5.028001'
@@ -264,7 +263,7 @@ x_Dist_Zilla: 
          branch: ~

          changelog: Changes

          signed: 0

          tag: BioPerl-v1.7.5

          tag: BioPerl-v1.7.6

          tag_format: '%N-v%v'

          tag_message: '%N-v%v'

        Dist::Zilla::Role::Git::Repo:
@@ -289,6 +288,14 @@ 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

Makefile.PL

+6 −9
Original line number Diff line number Diff line
@@ -18,7 +18,6 @@ my %WriteMakefileArgs = ( 
    "bin/bp_bioflat_index",

    "bin/bp_biogetseq",

    "bin/bp_chaos_plot",

    "bin/bp_classify_hits_kingdom",

    "bin/bp_dbsplit",

    "bin/bp_extract_feature_seq",

    "bin/bp_fastam9_to_table",
@@ -64,13 +63,11 @@ my %WriteMakefileArgs = ( 
    "AnyDBM_File" => 0,

    "Carp" => 0,

    "Cwd" => 0,

    "DBI" => 0,

    "DB_File" => 0,

    "Data::Dumper" => 0,

    "Data::Stag" => 0,

    "Digest::MD5" => 0,

    "Dumpvalue" => 0,

    "Env" => 0,

    "Error" => 0,

    "Exporter" => 0,

    "Fcntl" => 0,
@@ -81,7 +78,6 @@ my %WriteMakefileArgs = ( 
    "File::Spec::Functions" => 0,

    "File::Temp" => 0,

    "FileHandle" => 0,

    "GD" => 0,

    "Getopt::Long" => 0,

    "Graph::Directed" => 0,

    "HTTP::Request::Common" => 0,
@@ -139,13 +135,15 @@ my %WriteMakefileArgs = ( 
  },

  "TEST_REQUIRES" => {

    "File::Spec" => 0,

    "FindBin" => 0,

    "IO::Handle" => 0,

    "IPC::Open3" => 0,

    "Test::Memory::Cycle" => 0,

    "Test::More" => 0,

    "Test::Weaken" => 0

    "Test::Weaken" => 0,

    "lib" => 0

  },

  "VERSION" => "1.7.5",

  "VERSION" => "1.7.6",

  "test" => {

    "TESTS" => "t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t"

  }
@@ -156,13 +154,11 @@ my %FallbackPrereqs = ( 
  "AnyDBM_File" => 0,

  "Carp" => 0,

  "Cwd" => 0,

  "DBI" => 0,

  "DB_File" => 0,

  "Data::Dumper" => 0,

  "Data::Stag" => 0,

  "Digest::MD5" => 0,

  "Dumpvalue" => 0,

  "Env" => 0,

  "Error" => 0,

  "Exporter" => 0,

  "Fcntl" => 0,
@@ -173,7 +169,7 @@ my %FallbackPrereqs = ( 
  "File::Spec::Functions" => 0,

  "File::Temp" => 0,

  "FileHandle" => 0,

  "GD" => 0,

  "FindBin" => 0,

  "Getopt::Long" => 0,

  "Graph::Directed" => 0,

  "HTTP::Request::Common" => 0,
@@ -225,6 +221,7 @@ my %FallbackPrereqs = ( 
  "base" => 0,

  "constant" => 0,

  "integer" => 0,

  "lib" => 0,

  "overload" => 0,

  "parent" => 0,

  "strict" => 0,