bioruby.gemspec in bio-1.4.3.0001 vs bioruby.gemspec in bio-1.5.0
- old
+ new
@@ -1,22 +1,24 @@
# This file is automatically generated from bioruby.gemspec.erb and
# should NOT be edited by hand.
#
Gem::Specification.new do |s|
s.name = 'bio'
- s.version = "1.4.3.0001"
+ s.version = "1.5.0"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
s.homepage = "http://bioruby.org/"
- s.rubyforge_project = "bioruby"
+ s.license = "Ruby"
+
s.summary = "Bioinformatics library"
s.description = "BioRuby is a library for bioinformatics (biology + information science)."
s.platform = Gem::Platform::RUBY
s.files = [
".travis.yml",
+ "BSDL",
"COPYING",
"COPYING.ja",
"ChangeLog",
"GPL",
"KNOWN_ISSUES.rdoc",
@@ -31,37 +33,37 @@
"bin/br_bioflat.rb",
"bin/br_biogetseq.rb",
"bin/br_pmfetch.rb",
"bioruby.gemspec",
"bioruby.gemspec.erb",
+ "doc/ChangeLog-1.4.3",
"doc/ChangeLog-before-1.3.1",
"doc/ChangeLog-before-1.4.2",
"doc/Changes-0.7.rd",
"doc/Changes-1.3.rdoc",
- "doc/KEGG_API.rd",
- "doc/KEGG_API.rd.ja",
"doc/RELEASE_NOTES-1.4.0.rdoc",
"doc/RELEASE_NOTES-1.4.1.rdoc",
"doc/RELEASE_NOTES-1.4.2.rdoc",
+ "doc/RELEASE_NOTES-1.4.3.rdoc",
"doc/Tutorial.rd",
"doc/Tutorial.rd.html",
"doc/Tutorial.rd.ja",
"doc/Tutorial.rd.ja.html",
"doc/bioruby.css",
"etc/bioinformatics/seqdatabase.ini",
- "extconf.rb",
"gemfiles/Gemfile.travis-jruby1.8",
"gemfiles/Gemfile.travis-jruby1.9",
+ "gemfiles/Gemfile.travis-rbx",
"gemfiles/Gemfile.travis-ruby1.8",
"gemfiles/Gemfile.travis-ruby1.9",
+ "gemfiles/Gemfile.travis-ruby2.2",
"gemfiles/modify-Gemfile.rb",
"gemfiles/prepare-gemspec.rb",
"lib/bio.rb",
"lib/bio/alignment.rb",
"lib/bio/appl/bl2seq/report.rb",
"lib/bio/appl/blast.rb",
- "lib/bio/appl/blast/ddbj.rb",
"lib/bio/appl/blast/format0.rb",
"lib/bio/appl/blast/format8.rb",
"lib/bio/appl/blast/genomenet.rb",
"lib/bio/appl/blast/ncbioptions.rb",
"lib/bio/appl/blast/remote.rb",
@@ -126,10 +128,11 @@
"lib/bio/db/embl/format_embl.rb",
"lib/bio/db/embl/sptr.rb",
"lib/bio/db/embl/swissprot.rb",
"lib/bio/db/embl/trembl.rb",
"lib/bio/db/embl/uniprot.rb",
+ "lib/bio/db/embl/uniprotkb.rb",
"lib/bio/db/fantom.rb",
"lib/bio/db/fasta.rb",
"lib/bio/db/fasta/defline.rb",
"lib/bio/db/fasta/fasta_to_biosequence.rb",
"lib/bio/db/fasta/format_fasta.rb",
@@ -161,11 +164,10 @@
"lib/bio/db/kegg/kgml.rb",
"lib/bio/db/kegg/module.rb",
"lib/bio/db/kegg/orthology.rb",
"lib/bio/db/kegg/pathway.rb",
"lib/bio/db/kegg/reaction.rb",
- "lib/bio/db/kegg/taxonomy.rb",
"lib/bio/db/lasergene.rb",
"lib/bio/db/litdb.rb",
"lib/bio/db/medline.rb",
"lib/bio/db/nbrf.rb",
"lib/bio/db/newick.rb",
@@ -193,32 +195,23 @@
"lib/bio/feature.rb",
"lib/bio/io/biosql/ar-biosql.rb",
"lib/bio/io/biosql/biosql.rb",
"lib/bio/io/biosql/config/database.yml",
"lib/bio/io/das.rb",
- "lib/bio/io/dbget.rb",
- "lib/bio/io/ddbjrest.rb",
- "lib/bio/io/ddbjxml.rb",
- "lib/bio/io/ebisoap.rb",
- "lib/bio/io/ensembl.rb",
"lib/bio/io/fastacmd.rb",
"lib/bio/io/fetch.rb",
"lib/bio/io/flatfile.rb",
"lib/bio/io/flatfile/autodetection.rb",
"lib/bio/io/flatfile/bdb.rb",
"lib/bio/io/flatfile/buffer.rb",
"lib/bio/io/flatfile/index.rb",
"lib/bio/io/flatfile/indexer.rb",
"lib/bio/io/flatfile/splitter.rb",
- "lib/bio/io/higet.rb",
"lib/bio/io/hinv.rb",
- "lib/bio/io/keggapi.rb",
"lib/bio/io/ncbirest.rb",
- "lib/bio/io/ncbisoap.rb",
"lib/bio/io/pubmed.rb",
"lib/bio/io/registry.rb",
- "lib/bio/io/soapwsdl.rb",
"lib/bio/io/sql.rb",
"lib/bio/io/togows.rb",
"lib/bio/location.rb",
"lib/bio/map.rb",
"lib/bio/pathway.rb",
@@ -245,17 +238,15 @@
"lib/bio/shell/plugin/codon.rb",
"lib/bio/shell/plugin/das.rb",
"lib/bio/shell/plugin/emboss.rb",
"lib/bio/shell/plugin/entry.rb",
"lib/bio/shell/plugin/flatfile.rb",
- "lib/bio/shell/plugin/keggapi.rb",
"lib/bio/shell/plugin/midi.rb",
"lib/bio/shell/plugin/ncbirest.rb",
"lib/bio/shell/plugin/obda.rb",
"lib/bio/shell/plugin/psort.rb",
"lib/bio/shell/plugin/seq.rb",
- "lib/bio/shell/plugin/soap.rb",
"lib/bio/shell/plugin/togows.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
"lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml",
@@ -313,20 +304,19 @@
"lib/bio/util/restriction_enzyme/sorted_num_array.rb",
"lib/bio/util/restriction_enzyme/string_formatting.rb",
"lib/bio/util/sirna.rb",
"lib/bio/version.rb",
"sample/any2fasta.rb",
+ "sample/benchmark_clustalw_report.rb",
"sample/biofetch.rb",
"sample/color_scheme_na.rb",
- "sample/dbget",
"sample/demo_aaindex.rb",
"sample/demo_aminoacid.rb",
"sample/demo_bl2seq_report.rb",
"sample/demo_blast_report.rb",
"sample/demo_codontable.rb",
"sample/demo_das.rb",
- "sample/demo_ddbjxml.rb",
"sample/demo_fasta_remote.rb",
"sample/demo_fastaformat.rb",
"sample/demo_genbank.rb",
"sample/demo_genscan_report.rb",
"sample/demo_gff1.rb",
@@ -336,12 +326,10 @@
"sample/demo_kegg_drug.rb",
"sample/demo_kegg_genome.rb",
"sample/demo_kegg_glycan.rb",
"sample/demo_kegg_orthology.rb",
"sample/demo_kegg_reaction.rb",
- "sample/demo_kegg_taxonomy.rb",
- "sample/demo_keggapi.rb",
"sample/demo_litdb.rb",
"sample/demo_locations.rb",
"sample/demo_ncbi_rest.rb",
"sample/demo_nucleicacid.rb",
"sample/demo_pathway.rb",
@@ -370,11 +358,10 @@
"sample/goslim.rb",
"sample/gt2fasta.rb",
"sample/na2aa.rb",
"sample/pmfetch.rb",
"sample/pmsearch.rb",
- "sample/psortplot_html.rb",
"sample/seqdatabase.ini",
"sample/ssearch2tab.rb",
"sample/tdiary.rb",
"sample/test_phyloxml_big.rb",
"sample/test_restriction_enzyme_long.rb",
@@ -412,10 +399,11 @@
"test/data/blast/b0002.faa",
"test/data/blast/b0002.faa.m0",
"test/data/blast/b0002.faa.m7",
"test/data/blast/b0002.faa.m8",
"test/data/blast/blastp-multi.m7",
+ "test/data/clustalw/example1-seqnos.aln",
"test/data/clustalw/example1.aln",
"test/data/command/echoarg2.bat",
"test/data/command/echoarg2.sh",
"test/data/embl/AB090716.embl",
"test/data/embl/AB090716.embl.rel89",
@@ -518,14 +506,11 @@
"test/functional/bio/sequence/test_output_embl.rb",
"test/functional/bio/test_command.rb",
"test/network/bio/appl/blast/test_remote.rb",
"test/network/bio/appl/test_blast.rb",
"test/network/bio/appl/test_pts1.rb",
- "test/network/bio/io/test_ddbjrest.rb",
- "test/network/bio/io/test_ensembl.rb",
"test/network/bio/io/test_pubmed.rb",
- "test/network/bio/io/test_soapwsdl.rb",
"test/network/bio/io/test_togows.rb",
"test/network/bio/test_command.rb",
"test/runner.rb",
"test/unit/bio/appl/bl2seq/test_report.rb",
"test/unit/bio/appl/blast/test_ncbioptions.rb",
@@ -558,13 +543,13 @@
"test/unit/bio/db/biosql/ts_suite_biosql.rb",
"test/unit/bio/db/embl/test_common.rb",
"test/unit/bio/db/embl/test_embl.rb",
"test/unit/bio/db/embl/test_embl_rel89.rb",
"test/unit/bio/db/embl/test_embl_to_bioseq.rb",
- "test/unit/bio/db/embl/test_sptr.rb",
"test/unit/bio/db/embl/test_uniprot.rb",
- "test/unit/bio/db/embl/test_uniprot_new_part.rb",
+ "test/unit/bio/db/embl/test_uniprotkb.rb",
+ "test/unit/bio/db/embl/test_uniprotkb_new_part.rb",
"test/unit/bio/db/fasta/test_defline.rb",
"test/unit/bio/db/fasta/test_defline_misc.rb",
"test/unit/bio/db/fasta/test_format_qual.rb",
"test/unit/bio/db/genbank/test_common.rb",
"test/unit/bio/db/genbank/test_genbank.rb",
@@ -601,15 +586,12 @@
"test/unit/bio/db/test_rebase.rb",
"test/unit/bio/db/test_soft.rb",
"test/unit/bio/io/flatfile/test_autodetection.rb",
"test/unit/bio/io/flatfile/test_buffer.rb",
"test/unit/bio/io/flatfile/test_splitter.rb",
- "test/unit/bio/io/test_ddbjxml.rb",
- "test/unit/bio/io/test_ensembl.rb",
"test/unit/bio/io/test_fastacmd.rb",
"test/unit/bio/io/test_flatfile.rb",
- "test/unit/bio/io/test_soapwsdl.rb",
"test/unit/bio/io/test_togows.rb",
"test/unit/bio/sequence/test_aa.rb",
"test/unit/bio/sequence/test_common.rb",
"test/unit/bio/sequence/test_compat.rb",
"test/unit/bio/sequence/test_dblink.rb",
@@ -658,10 +640,11 @@
"README_DEV.rdoc",
"RELEASE_NOTES.rdoc",
"doc/Changes-1.3.rdoc",
"doc/RELEASE_NOTES-1.4.0.rdoc",
"doc/RELEASE_NOTES-1.4.1.rdoc",
- "doc/RELEASE_NOTES-1.4.2.rdoc"
+ "doc/RELEASE_NOTES-1.4.2.rdoc",
+ "doc/RELEASE_NOTES-1.4.3.rdoc"
]
s.rdoc_options << '--main' << 'README.rdoc'
s.rdoc_options << '--title' << 'BioRuby API documentation'
s.rdoc_options << '--exclude' << '\.yaml\z'
s.rdoc_options << '--line-numbers' << '--inline-source'