bioruby.gemspec in bio-1.4.0 vs bioruby.gemspec in bio-1.4.1
- 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 = "1.4.0"
+ s.version = "1.4.1"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
s.homepage = "http://bioruby.org/"
s.rubyforge_project = "bioruby"
@@ -35,10 +35,11 @@
"doc/ChangeLog-before-1.3.1",
"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/Tutorial.rd",
"doc/Tutorial.rd.html",
"doc/Tutorial.rd.ja",
"doc/Tutorial.rd.ja.html",
"doc/bioruby.css",
@@ -122,10 +123,11 @@
"lib/bio/db/fasta/defline.rb",
"lib/bio/db/fasta/fasta_to_biosequence.rb",
"lib/bio/db/fasta/format_fasta.rb",
"lib/bio/db/fasta/format_qual.rb",
"lib/bio/db/fasta/qual.rb",
+ "lib/bio/db/fasta/qual_to_biosequence.rb",
"lib/bio/db/fastq.rb",
"lib/bio/db/fastq/fastq_to_biosequence.rb",
"lib/bio/db/fastq/format_fastq.rb",
"lib/bio/db/genbank/common.rb",
"lib/bio/db/genbank/ddbj.rb",
@@ -145,11 +147,13 @@
"lib/bio/db/kegg/genes.rb",
"lib/bio/db/kegg/genome.rb",
"lib/bio/db/kegg/glycan.rb",
"lib/bio/db/kegg/keggtab.rb",
"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",
@@ -217,10 +221,11 @@
"lib/bio/sequence/format.rb",
"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",
@@ -368,11 +373,21 @@
"test/data/KEGG/C00025.compound",
"test/data/KEGG/D00063.drug",
"test/data/KEGG/G00024.glycan",
"test/data/KEGG/G01366.glycan",
"test/data/KEGG/K02338.orthology",
+ "test/data/KEGG/M00118.module",
"test/data/KEGG/R00006.reaction",
+ "test/data/KEGG/T00005.genome",
+ "test/data/KEGG/T00070.genome",
+ "test/data/KEGG/b0529.gene",
+ "test/data/KEGG/ec00072.pathway",
+ "test/data/KEGG/hsa00790.pathway",
+ "test/data/KEGG/ko00312.pathway",
+ "test/data/KEGG/map00030.pathway",
+ "test/data/KEGG/map00052.pathway",
+ "test/data/KEGG/rn00250.pathway",
"test/data/SOSUI/sample.report",
"test/data/TMHMM/sample.report",
"test/data/aaindex/DAYM780301",
"test/data/aaindex/PRAM900102",
"test/data/bl2seq/cd8a_cd8b_blastp.bl2seq",
@@ -381,10 +396,11 @@
"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.aln",
"test/data/command/echoarg2.bat",
"test/data/embl/AB090716.embl",
"test/data/embl/AB090716.embl.rel89",
"test/data/fasta/example1.txt",
"test/data/fasta/example2.txt",
@@ -439,17 +455,27 @@
"test/data/fastq/wrapping_as_sanger.fastq",
"test/data/fastq/wrapping_as_solexa.fastq",
"test/data/fastq/wrapping_original_sanger.fastq",
"test/data/gcg/pileup-aa.msf",
"test/data/genscan/sample.report",
+ "test/data/go/selected_component.ontology",
+ "test/data/go/selected_gene_association.sgd",
+ "test/data/go/selected_wikipedia2go",
"test/data/iprscan/merged.raw",
"test/data/iprscan/merged.txt",
+ "test/data/medline/20146148_modified.medline",
"test/data/meme/db",
"test/data/meme/mast",
"test/data/meme/mast.out",
"test/data/meme/meme.out",
"test/data/paml/codeml/control_file.txt",
+ "test/data/paml/codeml/models/aa.aln",
+ "test/data/paml/codeml/models/aa.dnd",
+ "test/data/paml/codeml/models/aa.ph",
+ "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",
@@ -477,20 +503,22 @@
"test/runner.rb",
"test/unit/bio/appl/bl2seq/test_report.rb",
"test/unit/bio/appl/blast/test_ncbioptions.rb",
"test/unit/bio/appl/blast/test_report.rb",
"test/unit/bio/appl/blast/test_rpsblast.rb",
+ "test/unit/bio/appl/clustalw/test_report.rb",
"test/unit/bio/appl/gcg/test_msf.rb",
"test/unit/bio/appl/genscan/test_report.rb",
"test/unit/bio/appl/hmmer/test_report.rb",
"test/unit/bio/appl/iprscan/test_report.rb",
"test/unit/bio/appl/mafft/test_report.rb",
"test/unit/bio/appl/meme/mast/test_report.rb",
"test/unit/bio/appl/meme/test_mast.rb",
"test/unit/bio/appl/meme/test_motif.rb",
"test/unit/bio/appl/paml/codeml/test_rates.rb",
"test/unit/bio/appl/paml/codeml/test_report.rb",
+ "test/unit/bio/appl/paml/codeml/test_report_single.rb",
"test/unit/bio/appl/paml/test_codeml.rb",
"test/unit/bio/appl/sim4/test_report.rb",
"test/unit/bio/appl/sosui/test_report.rb",
"test/unit/bio/appl/targetp/test_report.rb",
"test/unit/bio/appl/test_blast.rb",
@@ -506,25 +534,31 @@
"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/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/kegg/test_compound.rb",
"test/unit/bio/db/kegg/test_drug.rb",
"test/unit/bio/db/kegg/test_enzyme.rb",
"test/unit/bio/db/kegg/test_genes.rb",
+ "test/unit/bio/db/kegg/test_genome.rb",
"test/unit/bio/db/kegg/test_glycan.rb",
+ "test/unit/bio/db/kegg/test_module.rb",
"test/unit/bio/db/kegg/test_orthology.rb",
+ "test/unit/bio/db/kegg/test_pathway.rb",
"test/unit/bio/db/kegg/test_reaction.rb",
"test/unit/bio/db/pdb/test_pdb.rb",
"test/unit/bio/db/sanger_chromatogram/test_abif.rb",
"test/unit/bio/db/sanger_chromatogram/test_scf.rb",
"test/unit/bio/db/test_aaindex.rb",
"test/unit/bio/db/test_fasta.rb",
"test/unit/bio/db/test_fastq.rb",
"test/unit/bio/db/test_gff.rb",
+ "test/unit/bio/db/test_go.rb",
"test/unit/bio/db/test_lasergene.rb",
"test/unit/bio/db/test_medline.rb",
"test/unit/bio/db/test_newick.rb",
"test/unit/bio/db/test_nexus.rb",
"test/unit/bio/db/test_phyloxml.rb",
@@ -546,10 +580,11 @@
"test/unit/bio/sequence/test_common.rb",
"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",
@@ -586,10 +621,11 @@
"ChangeLog",
"KNOWN_ISSUES.rdoc",
"README.rdoc",
"README_DEV.rdoc",
"RELEASE_NOTES.rdoc",
- "doc/Changes-1.3.rdoc"
+ "doc/Changes-1.3.rdoc",
+ "doc/RELEASE_NOTES-1.4.0.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'