[DRE-commits] [ruby-bio] branch master updated (7126978 -> 0756f38)
Cédric Boutillier
boutil at alioth.debian.org
Tue Aug 6 22:19:01 UTC 2013
This is an automated email from the git hooks/post-receive script.
boutil pushed a change to branch master
in repository ruby-bio.
from 7126978 use canonical URI in Vcs-* fields
adds 9e15cc5 Imported Upstream version 1.4.3.0001
new e4f32fe Merge tag 'upstream/1.4.3.0001'
new 8ec260a Build-depend on ruby-test-unit
new aca420b omit chi2 tests instead of commenting them out
new 14f47a3 do not exclude manually tests requiring network in ruby-tests.rb
new 30a819f drop disable-test-soap.patch, fix_definition_CutSymbol_in_test_cut_symbol.patch, do_not_rely_on_keys_order_for_hashes.patch
new 337cb63 Bump Standards-Version to 3.9.4 (no changes needed); update my email address
new aa5a798 drop transitional packages and remove related lintian-overrides
new 71552d0 install as doc KNOWN_ISSUES.rdoc
new 4b25bfd provide more complete copyright information
new 839f761 remove_rubygems.patch: remove requirement on rubygems from bin/bioruby
new 0756f38 prepare changelog
The 11 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 | 66 +
ChangeLog | 5496 ++++----------------
KNOWN_ISSUES.rdoc | 69 +-
README.rdoc | 112 +-
README_DEV.rdoc | 95 +-
RELEASE_NOTES.rdoc | 274 +-
Rakefile | 206 +-
bioruby.gemspec | 39 +-
bioruby.gemspec.erb | 9 +-
debian/changelog | 24 +
debian/control | 27 +-
debian/copyright | 27 +-
debian/patches/disable-test-soap.patch | 59 -
debian/patches/disable_tests_using_chi2.patch | 30 +-
.../do_not_rely_on_keys_order_for_hashes.patch | 27 -
...x_definition_CutSymbol_in_test_cut_symbol.patch | 21 -
debian/patches/remove_rubygems.patch | 21 +
debian/patches/series | 4 +-
debian/ruby-bio.docs | 1 +
debian/ruby-tests.rb | 15 +-
debian/source/lintian-overrides | 2 -
ChangeLog => doc/ChangeLog-before-1.4.2 | 9 +
RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.2.rdoc | 0
doc/Tutorial.rd | 24 +-
doc/Tutorial.rd.html | 32 +-
etc/bioinformatics/seqdatabase.ini | 209 +-
gemfiles/Gemfile.travis-jruby1.8 | 7 +
gemfiles/Gemfile.travis-jruby1.9 | 10 +
gemfiles/Gemfile.travis-ruby1.8 | 7 +
gemfiles/Gemfile.travis-ruby1.9 | 10 +
gemfiles/modify-Gemfile.rb | 28 +
gemfiles/prepare-gemspec.rb | 25 +
lib/bio/alignment.rb | 2 +-
lib/bio/appl/bl2seq/report.rb | 6 +-
lib/bio/appl/blast/ddbj.rb | 3 -
lib/bio/appl/blast/format0.rb | 64 +-
lib/bio/appl/blast/genomenet.rb | 49 +-
lib/bio/appl/blast/ncbioptions.rb | 11 +-
lib/bio/appl/blast/remote.rb | 11 +-
lib/bio/appl/blast/report.rb | 16 +-
lib/bio/appl/blast/rpsblast.rb | 5 +-
lib/bio/appl/blast/wublast.rb | 6 +-
lib/bio/command.rb | 154 +-
lib/bio/data/na.rb | 2 +-
lib/bio/db/embl/embl.rb | 74 +
lib/bio/db/embl/format_embl.rb | 4 -
lib/bio/db/fasta.rb | 102 +-
lib/bio/db/fasta/defline.rb | 2 +-
lib/bio/db/fasta/format_fasta.rb | 4 -
lib/bio/db/fasta/format_qual.rb | 5 -
lib/bio/db/fastq/format_fastq.rb | 1 -
lib/bio/db/genbank/format_genbank.rb | 4 -
lib/bio/db/gff.rb | 54 +-
lib/bio/db/kegg/genes.rb | 6 +-
lib/bio/db/kegg/kgml.rb | 529 +-
lib/bio/db/newick.rb | 244 -
lib/bio/db/pdb.rb | 5 +-
lib/bio/db/pdb/atom.rb | 5 +-
lib/bio/db/pdb/chain.rb | 5 +-
lib/bio/db/pdb/chemicalcomponent.rb | 5 +-
lib/bio/db/pdb/model.rb | 4 +-
lib/bio/db/pdb/pdb.rb | 3 +-
lib/bio/db/pdb/residue.rb | 4 +-
lib/bio/db/pdb/utils.rb | 11 +-
lib/bio/db/phyloxml/phyloxml_parser.rb | 57 +-
lib/bio/feature.rb | 5 +-
lib/bio/io/flatfile/autodetection.rb | 2 +-
lib/bio/io/flatfile/buffer.rb | 84 +
lib/bio/sequence.rb | 10 +-
lib/bio/sequence/aa.rb | 8 +-
lib/bio/sequence/adapter.rb | 12 +-
lib/bio/sequence/common.rb | 6 +-
lib/bio/sequence/compat.rb | 9 +-
lib/bio/sequence/dblink.rb | 11 +-
lib/bio/sequence/format.rb | 6 -
lib/bio/sequence/format_raw.rb | 4 -
lib/bio/sequence/generic.rb | 7 +-
lib/bio/sequence/na.rb | 10 +-
lib/bio/sequence/quality_score.rb | 2 +
lib/bio/sequence/sequence_masker.rb | 3 +
lib/bio/shell/core.rb | 1 +
lib/bio/tree.rb | 3 +-
lib/bio/tree/output.rb | 264 +
lib/bio/util/restriction_enzyme.rb | 4 +-
lib/bio/util/restriction_enzyme/analysis.rb | 13 +-
lib/bio/util/restriction_enzyme/analysis_basic.rb | 7 +-
lib/bio/util/restriction_enzyme/cut_symbol.rb | 5 +-
lib/bio/util/restriction_enzyme/dense_int_array.rb | 3 +
lib/bio/util/restriction_enzyme/double_stranded.rb | 7 +-
.../double_stranded/aligned_strands.rb | 7 +-
.../double_stranded/cut_location_pair.rb | 7 +-
.../cut_location_pair_in_enzyme_notation.rb | 7 +-
.../double_stranded/cut_locations.rb | 7 +-
.../cut_locations_in_enzyme_notation.rb | 7 +-
lib/bio/util/restriction_enzyme/range/cut_range.rb | 7 +-
.../util/restriction_enzyme/range/cut_ranges.rb | 7 +-
.../range/horizontal_cut_range.rb | 7 +-
.../restriction_enzyme/range/sequence_range.rb | 7 +-
.../range/sequence_range/calculated_cuts.rb | 7 +-
.../range/sequence_range/fragment.rb | 7 +-
.../range/sequence_range/fragments.rb | 7 +-
.../restriction_enzyme/range/vertical_cut_range.rb | 7 +-
lib/bio/util/restriction_enzyme/single_strand.rb | 6 +-
.../cut_locations_in_enzyme_notation.rb | 7 +-
.../restriction_enzyme/single_strand_complement.rb | 7 +-
.../util/restriction_enzyme/sorted_num_array.rb | 3 +
.../util/restriction_enzyme/string_formatting.rb | 7 +-
lib/bio/version.rb | 15 +-
metadata.yml | 2079 +++++---
rdoc.zsh | 8 -
{etc/bioinformatics => sample}/seqdatabase.ini | 0
test/bioruby_test_helper.rb | 49 +-
test/data/KEGG/test.kgml | 37 +
test/data/command/echoarg2.sh | 4 +
test/functional/bio/test_command.rb | 86 +-
.../bio/appl/blast/test_remote.rb | 0
.../{functional => network}/bio/appl/test_blast.rb | 0
test/{functional => network}/bio/appl/test_pts1.rb | 0
.../bio/io/test_ddbjrest.rb | 0
.../{functional => network}/bio/io/test_ensembl.rb | 0
test/{functional => network}/bio/io/test_pubmed.rb | 0
.../bio/io/test_soapwsdl.rb | 0
test/{functional => network}/bio/io/test_togows.rb | 0
test/network/bio/test_command.rb | 35 +
test/runner.rb | 22 +-
test/unit/bio/appl/blast/test_report.rb | 119 +
test/unit/bio/appl/blast/test_rpsblast.rb | 1 +
test/unit/bio/data/test_na.rb | 2 +-
test/unit/bio/db/embl/test_embl.rb | 9 +-
test/unit/bio/db/embl/test_embl_rel89.rb | 9 +-
test/unit/bio/db/fasta/test_defline.rb | 2 +-
test/unit/bio/db/genbank/test_genpept.rb | 2 +-
test/unit/bio/db/kegg/test_drug.rb | 2 +-
test/unit/bio/db/kegg/test_genome.rb | 2 +-
test/unit/bio/db/kegg/test_glycan.rb | 2 +-
test/unit/bio/db/kegg/test_kgml.rb | 1022 ++++
test/unit/bio/db/sanger_chromatogram/test_abif.rb | 3 +-
test/unit/bio/db/sanger_chromatogram/test_scf.rb | 6 +-
test/unit/bio/db/test_newick.rb | 2 +
test/unit/bio/db/test_phyloxml.rb | 56 +-
test/unit/bio/db/test_phyloxml_writer.rb | 24 +-
test/unit/bio/db/test_soft.rb | 2 +-
test/unit/bio/io/flatfile/test_autodetection.rb | 6 +
test/unit/bio/io/flatfile/test_buffer.rb | 141 +
test/unit/bio/sequence/test_common.rb | 40 +-
test/unit/bio/sequence/test_na.rb | 2 +-
test/unit/bio/test_command.rb | 13 +-
test/unit/bio/test_sequence.rb | 4 +-
test/unit/bio/test_tree.rb | 22 +-
test/unit/bio/util/test_restriction_enzyme.rb | 2 +-
150 files changed, 6434 insertions(+), 6445 deletions(-)
create mode 100644 .travis.yml
delete mode 100644 debian/patches/disable-test-soap.patch
delete mode 100644 debian/patches/do_not_rely_on_keys_order_for_hashes.patch
delete mode 100644 debian/patches/fix_definition_CutSymbol_in_test_cut_symbol.patch
create mode 100644 debian/patches/remove_rubygems.patch
delete mode 100644 debian/source/lintian-overrides
copy ChangeLog => doc/ChangeLog-before-1.4.2 (99%)
copy RELEASE_NOTES.rdoc => doc/RELEASE_NOTES-1.4.2.rdoc (100%)
create mode 100644 gemfiles/Gemfile.travis-jruby1.8
create mode 100644 gemfiles/Gemfile.travis-jruby1.9
create mode 100644 gemfiles/Gemfile.travis-ruby1.8
create mode 100644 gemfiles/Gemfile.travis-ruby1.9
create mode 100644 gemfiles/modify-Gemfile.rb
create mode 100644 gemfiles/prepare-gemspec.rb
create mode 100644 lib/bio/tree/output.rb
delete mode 100644 rdoc.zsh
copy {etc/bioinformatics => sample}/seqdatabase.ini (100%)
create mode 100644 test/data/KEGG/test.kgml
mode change 100644 => 100755 test/data/command/echoarg2.bat
create mode 100755 test/data/command/echoarg2.sh
rename test/{functional => network}/bio/appl/blast/test_remote.rb (100%)
rename test/{functional => network}/bio/appl/test_blast.rb (100%)
rename test/{functional => network}/bio/appl/test_pts1.rb (100%)
rename test/{functional => network}/bio/io/test_ddbjrest.rb (100%)
rename test/{functional => network}/bio/io/test_ensembl.rb (100%)
rename test/{functional => network}/bio/io/test_pubmed.rb (100%)
rename test/{functional => network}/bio/io/test_soapwsdl.rb (100%)
rename test/{functional => network}/bio/io/test_togows.rb (100%)
create mode 100644 test/network/bio/test_command.rb
create mode 100644 test/unit/bio/db/kegg/test_kgml.rb
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