bioruby.gemspec in bio-1.5.2 vs bioruby.gemspec in bio-1.6.0.pre.20181210
- old
+ new
@@ -1,11 +1,11 @@
# 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 = "1.5.2"
+ s.version = "1.6.0.pre.20181211"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
s.homepage = "http://bioruby.org/"
s.license = "Ruby"
@@ -19,33 +19,32 @@
"BSDL",
"COPYING",
"COPYING.ja",
"ChangeLog",
"GPL",
+ "Gemfile",
"KNOWN_ISSUES.rdoc",
"LEGAL",
"LGPL",
"README.rdoc",
"README_DEV.rdoc",
"RELEASE_NOTES.rdoc",
"Rakefile",
- "bin/bioruby",
- "bin/br_biofetch.rb",
- "bin/br_bioflat.rb",
- "bin/br_biogetseq.rb",
- "bin/br_pmfetch.rb",
+ "appveyor.yml",
"bioruby.gemspec",
"bioruby.gemspec.erb",
"doc/ChangeLog-1.4.3",
+ "doc/ChangeLog-1.5.0",
"doc/ChangeLog-before-1.3.1",
"doc/ChangeLog-before-1.4.2",
"doc/Changes-0.7.rd",
"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-1.4.3.rdoc",
+ "doc/RELEASE_NOTES-1.5.0.rdoc",
"doc/Tutorial.rd",
"doc/Tutorial.rd.html",
"doc/Tutorial.rd.ja",
"doc/Tutorial.rd.ja.html",
"doc/bioruby.css",
@@ -53,11 +52,10 @@
"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",
@@ -118,12 +116,10 @@
"lib/bio/data/aa.rb",
"lib/bio/data/codontable.rb",
"lib/bio/data/na.rb",
"lib/bio/db.rb",
"lib/bio/db/aaindex.rb",
- "lib/bio/db/biosql/biosql_to_biosequence.rb",
- "lib/bio/db/biosql/sequence.rb",
"lib/bio/db/embl/common.rb",
"lib/bio/db/embl/embl.rb",
"lib/bio/db/embl/embl_to_biosequence.rb",
"lib/bio/db/embl/format_embl.rb",
"lib/bio/db/embl/sptr.rb",
@@ -178,26 +174,19 @@
"lib/bio/db/pdb/chemicalcomponent.rb",
"lib/bio/db/pdb/model.rb",
"lib/bio/db/pdb/pdb.rb",
"lib/bio/db/pdb/residue.rb",
"lib/bio/db/pdb/utils.rb",
- "lib/bio/db/phyloxml/phyloxml.xsd",
- "lib/bio/db/phyloxml/phyloxml_elements.rb",
- "lib/bio/db/phyloxml/phyloxml_parser.rb",
- "lib/bio/db/phyloxml/phyloxml_writer.rb",
"lib/bio/db/prosite.rb",
"lib/bio/db/rebase.rb",
"lib/bio/db/sanger_chromatogram/abif.rb",
"lib/bio/db/sanger_chromatogram/chromatogram.rb",
"lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb",
"lib/bio/db/sanger_chromatogram/scf.rb",
"lib/bio/db/soft.rb",
"lib/bio/db/transfac.rb",
"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/fastacmd.rb",
"lib/bio/io/fetch.rb",
"lib/bio/io/flatfile.rb",
"lib/bio/io/flatfile/autodetection.rb",
@@ -208,11 +197,10 @@
"lib/bio/io/flatfile/splitter.rb",
"lib/bio/io/hinv.rb",
"lib/bio/io/ncbirest.rb",
"lib/bio/io/pubmed.rb",
"lib/bio/io/registry.rb",
- "lib/bio/io/sql.rb",
"lib/bio/io/togows.rb",
"lib/bio/location.rb",
"lib/bio/map.rb",
"lib/bio/pathway.rb",
"lib/bio/reference.rb",
@@ -226,48 +214,10 @@
"lib/bio/sequence/format_raw.rb",
"lib/bio/sequence/generic.rb",
"lib/bio/sequence/na.rb",
"lib/bio/sequence/quality_score.rb",
"lib/bio/sequence/sequence_masker.rb",
- "lib/bio/shell.rb",
- "lib/bio/shell/core.rb",
- "lib/bio/shell/demo.rb",
- "lib/bio/shell/interface.rb",
- "lib/bio/shell/irb.rb",
- "lib/bio/shell/object.rb",
- "lib/bio/shell/plugin/blast.rb",
- "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/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/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",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml",
- "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif",
- "lib/bio/shell/script.rb",
- "lib/bio/shell/setup.rb",
- "lib/bio/shell/web.rb",
"lib/bio/tree.rb",
"lib/bio/tree/output.rb",
"lib/bio/util/color_scheme.rb",
"lib/bio/util/color_scheme/buried.rb",
"lib/bio/util/color_scheme/helix.rb",
@@ -361,11 +311,10 @@
"sample/pmfetch.rb",
"sample/pmsearch.rb",
"sample/seqdatabase.ini",
"sample/ssearch2tab.rb",
"sample/tdiary.rb",
- "sample/test_phyloxml_big.rb",
"sample/test_restriction_enzyme_long.rb",
"sample/tfastx2tab.rb",
"sample/vs-genes.rb",
"setup.rb",
"test/bioruby_test_helper.rb",
@@ -483,15 +432,10 @@
"test/data/paml/codeml/models/alignment.phy",
"test/data/paml/codeml/models/results0-3.txt",
"test/data/paml/codeml/models/results7-8.txt",
"test/data/paml/codeml/output.txt",
"test/data/paml/codeml/rates",
- "test/data/phyloxml/apaf.xml",
- "test/data/phyloxml/bcl_2.xml",
- "test/data/phyloxml/made_up.xml",
- "test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
- "test/data/phyloxml/phyloxml_examples.xml",
"test/data/pir/CRAB_ANAPL.pir",
"test/data/prosite/prosite.dat",
"test/data/refseq/nm_126355.entret",
"test/data/rpsblast/misc.rpsblast",
"test/data/sanger_chromatogram/test_chromatogram_abif.ab1",
@@ -537,12 +481,10 @@
"test/unit/bio/appl/test_pts1.rb",
"test/unit/bio/appl/tmhmm/test_report.rb",
"test/unit/bio/data/test_aa.rb",
"test/unit/bio/data/test_codontable.rb",
"test/unit/bio/data/test_na.rb",
- "test/unit/bio/db/biosql/tc_biosql.rb",
- "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_uniprot.rb",
@@ -577,12 +519,10 @@
"test/unit/bio/db/test_litdb.rb",
"test/unit/bio/db/test_medline.rb",
"test/unit/bio/db/test_nbrf.rb",
"test/unit/bio/db/test_newick.rb",
"test/unit/bio/db/test_nexus.rb",
- "test/unit/bio/db/test_phyloxml.rb",
- "test/unit/bio/db/test_phyloxml_writer.rb",
"test/unit/bio/db/test_prosite.rb",
"test/unit/bio/db/test_qual.rb",
"test/unit/bio/db/test_rebase.rb",
"test/unit/bio/db/test_soft.rb",
"test/unit/bio/io/flatfile/test_autodetection.rb",
@@ -596,21 +536,19 @@
"test/unit/bio/sequence/test_compat.rb",
"test/unit/bio/sequence/test_dblink.rb",
"test/unit/bio/sequence/test_na.rb",
"test/unit/bio/sequence/test_quality_score.rb",
"test/unit/bio/sequence/test_sequence_masker.rb",
- "test/unit/bio/shell/plugin/test_seq.rb",
"test/unit/bio/test_alignment.rb",
"test/unit/bio/test_command.rb",
"test/unit/bio/test_db.rb",
"test/unit/bio/test_feature.rb",
"test/unit/bio/test_location.rb",
"test/unit/bio/test_map.rb",
"test/unit/bio/test_pathway.rb",
"test/unit/bio/test_reference.rb",
"test/unit/bio/test_sequence.rb",
- "test/unit/bio/test_shell.rb",
"test/unit/bio/test_tree.rb",
"test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb",
"test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb",
"test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb",
"test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb",
@@ -641,24 +579,15 @@
"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-1.4.3.rdoc"
+ "doc/RELEASE_NOTES-1.4.3.rdoc",
+ "doc/RELEASE_NOTES-1.5.0.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'
s.require_path = 'lib'
-
- s.bindir = "bin"
- s.executables = [
- "bioruby",
- "br_biofetch.rb",
- "br_bioflat.rb",
- "br_biogetseq.rb",
- "br_pmfetch.rb"
- ]
- s.default_executable = "bioruby"
end