[DRE-commits] [ruby-bio] branch master updated (a132329 -> 01be182)
zeha at debian.org
zeha at debian.org
Sun Nov 8 22:28:40 UTC 2015
This is an automated email from the git hooks/post-receive script.
zeha pushed a change to branch master
in repository ruby-bio.
from a132329 prepare changelog
new a94ce20 Imported Upstream version 1.5.0
new bfed3dc Remove upstream-applied patch fix_shebang_for_examples
new c315950 Refresh debian packaging with dh-make-ruby -w
new 01be182 Update changelog for 1.5.0-1 release
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.travis.yml | 72 +-
BSDL | 22 +
COPYING | 4 +-
COPYING.ja | 72 +-
ChangeLog | 3429 ++++++++++++++------
KNOWN_ISSUES.rdoc | 70 +-
README.rdoc | 40 +-
RELEASE_NOTES.rdoc | 429 +--
Rakefile | 5 +-
bin/br_biofetch.rb | 34 +-
bioruby.gemspec | 47 +-
bioruby.gemspec.erb | 30 +-
debian/changelog | 10 +
debian/compat | 2 +-
debian/control | 17 +-
debian/copyright | 5 +-
debian/patches/fix_shebang_for_examples.patch | 11 -
debian/patches/series | 1 -
debian/ruby-bio.docs | 2 +-
debian/rules | 5 +-
debian/{upstream => upstream/metadata} | 0
ChangeLog => doc/ChangeLog-1.4.3 | 310 +-
doc/KEGG_API.rd | 1843 -----------
doc/KEGG_API.rd.ja | 1834 -----------
RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc | 18 -
doc/Tutorial.rd | 6 -
doc/Tutorial.rd.html | 19 +-
doc/Tutorial.rd.ja | 2024 ++++++------
doc/Tutorial.rd.ja.html | 2044 ++++++------
extconf.rb | 2 -
gemfiles/Gemfile.travis-jruby1.8 | 3 +-
gemfiles/Gemfile.travis-jruby1.9 | 6 +-
gemfiles/Gemfile.travis-rbx | 13 +
gemfiles/Gemfile.travis-ruby1.8 | 3 +-
gemfiles/Gemfile.travis-ruby1.9 | 6 +-
gemfiles/Gemfile.travis-ruby2.2 | 9 +
lib/bio.rb | 53 +-
lib/bio/alignment.rb | 22 +-
lib/bio/appl/blast.rb | 3 +-
lib/bio/appl/blast/ddbj.rb | 131 -
lib/bio/appl/blast/format0.rb | 25 +-
lib/bio/appl/blast/remote.rb | 9 -
lib/bio/appl/blast/report.rb | 2 +-
lib/bio/appl/clustalw/report.rb | 4 +-
lib/bio/appl/genscan/report.rb | 3 +-
lib/bio/appl/iprscan/report.rb | 3 +-
lib/bio/appl/meme/mast.rb | 8 +-
lib/bio/appl/meme/mast/report.rb | 2 +-
lib/bio/appl/paml/codeml.rb | 4 +-
lib/bio/appl/paml/codeml/report.rb | 1 +
lib/bio/appl/paml/common.rb | 2 +-
lib/bio/appl/sosui/report.rb | 3 +-
lib/bio/command.rb | 64 +-
lib/bio/data/aa.rb | 44 +-
lib/bio/data/codontable.rb | 3 +-
lib/bio/db/biosql/biosql_to_biosequence.rb | 1 +
lib/bio/db/biosql/sequence.rb | 2 +-
lib/bio/db/embl/common.rb | 2 +-
lib/bio/db/embl/embl.rb | 9 +-
lib/bio/db/embl/format_embl.rb | 6 +-
lib/bio/db/embl/sptr.rb | 1453 +--------
lib/bio/db/embl/swissprot.rb | 41 +-
lib/bio/db/embl/trembl.rb | 43 +-
lib/bio/db/embl/uniprot.rb | 41 +-
lib/bio/db/embl/{sptr.rb => uniprotkb.rb} | 152 +-
lib/bio/db/fasta.rb | 17 +
lib/bio/db/fasta/defline.rb | 4 +-
lib/bio/db/fastq.rb | 2 +-
lib/bio/db/genbank/ddbj.rb | 14 +-
lib/bio/db/genbank/refseq.rb | 14 +-
lib/bio/db/gff.rb | 7 +-
lib/bio/db/go.rb | 11 +-
lib/bio/db/kegg/module.rb | 9 +-
lib/bio/db/kegg/pathway.rb | 9 +-
lib/bio/db/kegg/reaction.rb | 2 +-
lib/bio/db/kegg/taxonomy.rb | 280 --
lib/bio/db/nexus.rb | 5 +-
lib/bio/db/pdb/pdb.rb | 4 +-
lib/bio/db/phyloxml/phyloxml_elements.rb | 141 +-
lib/bio/db/phyloxml/phyloxml_parser.rb | 4 +-
lib/bio/db/phyloxml/phyloxml_writer.rb | 3 +-
lib/bio/db/sanger_chromatogram/chromatogram.rb | 3 +-
lib/bio/db/transfac.rb | 2 +-
lib/bio/io/das.rb | 81 +-
lib/bio/io/dbget.rb | 194 --
lib/bio/io/ddbjrest.rb | 344 --
lib/bio/io/ddbjxml.rb | 458 ---
lib/bio/io/ebisoap.rb | 158 -
lib/bio/io/ensembl.rb | 229 --
lib/bio/io/fastacmd.rb | 16 -
lib/bio/io/fetch.rb | 166 +-
lib/bio/io/flatfile/buffer.rb | 9 +-
lib/bio/io/higet.rb | 73 -
lib/bio/io/hinv.rb | 5 +-
lib/bio/io/keggapi.rb | 363 ---
lib/bio/io/ncbirest.rb | 49 +-
lib/bio/io/ncbisoap.rb | 156 -
lib/bio/io/pubmed.rb | 157 +-
lib/bio/io/soapwsdl.rb | 119 -
lib/bio/io/togows.rb | 43 +-
lib/bio/map.rb | 2 +-
lib/bio/pathway.rb | 2 +-
lib/bio/sequence/compat.rb | 2 +-
lib/bio/sequence/na.rb | 75 +-
lib/bio/shell.rb | 2 -
lib/bio/shell/core.rb | 11 +-
lib/bio/shell/interface.rb | 7 +-
lib/bio/shell/irb.rb | 3 +-
lib/bio/shell/plugin/entry.rb | 5 +-
lib/bio/shell/plugin/keggapi.rb | 181 --
lib/bio/shell/plugin/seq.rb | 13 +-
lib/bio/shell/plugin/soap.rb | 87 -
lib/bio/shell/setup.rb | 3 +-
lib/bio/tree.rb | 4 +-
lib/bio/util/contingency_table.rb | 2 -
.../restriction_enzyme/range/sequence_range.rb | 4 +-
lib/bio/util/sirna.rb | 92 +-
lib/bio/version.rb | 17 +-
metadata.yml | 2086 ++++--------
sample/benchmark_clustalw_report.rb | 47 +
sample/biofetch.rb | 399 ++-
sample/dbget | 37 -
sample/demo_ddbjxml.rb | 212 --
sample/demo_kegg_taxonomy.rb | 92 -
sample/demo_keggapi.rb | 502 ---
sample/psortplot_html.rb | 214 --
setup.rb | 13 +-
.../clustalw/{example1.aln => example1-seqnos.aln} | 68 +-
test/network/bio/appl/blast/test_remote.rb | 16 +-
test/network/bio/appl/test_blast.rb | 12 -
test/network/bio/io/test_ddbjrest.rb | 47 -
test/network/bio/io/test_ensembl.rb | 230 --
test/network/bio/io/test_pubmed.rb | 49 +
test/network/bio/io/test_soapwsdl.rb | 53 -
test/network/bio/io/test_togows.rb | 1 -
test/network/bio/test_command.rb | 67 +-
test/unit/bio/appl/bl2seq/test_report.rb | 1 -
test/unit/bio/appl/blast/test_report.rb | 158 +-
test/unit/bio/appl/clustalw/test_report.rb | 118 +-
test/unit/bio/appl/sim4/test_report.rb | 63 +-
test/unit/bio/appl/test_blast.rb | 4 +-
test/unit/bio/db/embl/test_embl.rb | 1 -
test/unit/bio/db/embl/test_embl_rel89.rb | 1 -
.../db/embl/{test_sptr.rb => test_uniprotkb.rb} | 226 +-
...prot_new_part.rb => test_uniprotkb_new_part.rb} | 22 +-
test/unit/bio/db/genbank/test_genbank.rb | 14 +-
test/unit/bio/db/pdb/test_pdb.rb | 22 +-
test/unit/bio/db/test_fasta.rb | 42 +-
test/unit/bio/db/test_fastq.rb | 18 +-
test/unit/bio/db/test_gff.rb | 4 +-
test/unit/bio/db/test_phyloxml.rb | 60 +-
test/unit/bio/db/test_phyloxml_writer.rb | 4 +-
test/unit/bio/io/flatfile/test_autodetection.rb | 3 +-
test/unit/bio/io/flatfile/test_buffer.rb | 8 +-
test/unit/bio/io/flatfile/test_splitter.rb | 2 +-
test/unit/bio/io/test_ddbjxml.rb | 81 -
test/unit/bio/io/test_ensembl.rb | 111 -
test/unit/bio/io/test_soapwsdl.rb | 33 -
test/unit/bio/io/test_togows.rb | 5 +-
test/unit/bio/sequence/test_dblink.rb | 2 +-
test/unit/bio/sequence/test_na.rb | 4 +-
test/unit/bio/test_alignment.rb | 3 +-
test/unit/bio/test_command.rb | 9 +-
test/unit/bio/test_db.rb | 6 +-
test/unit/bio/test_pathway.rb | 35 +-
test/unit/bio/util/test_sirna.rb | 44 +-
166 files changed, 7496 insertions(+), 15999 deletions(-)
create mode 100644 BSDL
delete mode 100644 debian/patches/fix_shebang_for_examples.patch
rename debian/{upstream => upstream/metadata} (100%)
copy ChangeLog => doc/ChangeLog-1.4.3 (85%)
delete mode 100644 doc/KEGG_API.rd
delete mode 100644 doc/KEGG_API.rd.ja
copy RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.3.rdoc (95%)
delete mode 100644 extconf.rb
create mode 100644 gemfiles/Gemfile.travis-rbx
create mode 100644 gemfiles/Gemfile.travis-ruby2.2
delete mode 100644 lib/bio/appl/blast/ddbj.rb
copy lib/bio/db/embl/{sptr.rb => uniprotkb.rb} (92%)
delete mode 100644 lib/bio/db/kegg/taxonomy.rb
delete mode 100644 lib/bio/io/dbget.rb
delete mode 100644 lib/bio/io/ddbjrest.rb
delete mode 100644 lib/bio/io/ddbjxml.rb
delete mode 100644 lib/bio/io/ebisoap.rb
delete mode 100644 lib/bio/io/ensembl.rb
delete mode 100644 lib/bio/io/higet.rb
delete mode 100644 lib/bio/io/keggapi.rb
delete mode 100644 lib/bio/io/ncbisoap.rb
delete mode 100644 lib/bio/io/soapwsdl.rb
delete mode 100644 lib/bio/shell/plugin/keggapi.rb
delete mode 100644 lib/bio/shell/plugin/soap.rb
create mode 100644 sample/benchmark_clustalw_report.rb
delete mode 100755 sample/dbget
delete mode 100644 sample/demo_ddbjxml.rb
delete mode 100644 sample/demo_kegg_taxonomy.rb
delete mode 100644 sample/demo_keggapi.rb
delete mode 100644 sample/psortplot_html.rb
copy test/data/clustalw/{example1.aln => example1-seqnos.aln} (82%)
delete mode 100644 test/network/bio/io/test_ddbjrest.rb
delete mode 100644 test/network/bio/io/test_ensembl.rb
delete mode 100644 test/network/bio/io/test_soapwsdl.rb
rename test/unit/bio/db/embl/{test_sptr.rb => test_uniprotkb.rb} (94%)
rename test/unit/bio/db/embl/{test_uniprot_new_part.rb => test_uniprotkb_new_part.rb} (89%)
delete mode 100644 test/unit/bio/io/test_ddbjxml.rb
delete mode 100644 test/unit/bio/io/test_ensembl.rb
delete mode 100644 test/unit/bio/io/test_soapwsdl.rb
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