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Commits on Jul 7, 2018
  1. Add https requests in command. Fix genomenet query by allowing https …

    ramadis committed Jul 7, 2018
    …requests.
Commits on Jun 7, 2018
  1. directly refer to the given hash

    tomoakin committed Mar 31, 2018
Commits on Jun 2, 2018
  1. precalculated ambiguity codontable

    tomoakin committed Jun 2, 2018
Commits on Dec 12, 2017
  1. fixing Fasta Report parser for fasta36 -m10

    markwilkinson committed Dec 12, 2017
Commits on Sep 15, 2017
  1. Remove settings about executables

    ngoto committed Sep 15, 2017
     * Definitions and settings about executables are removed because
       all files in bin/ have been moved to separate gem packages
       (bio-shell and bio-executables).
  2. bin/br_*.rb is moved to bio-executables gem

    ngoto committed Sep 15, 2017
     * The following executable files are moved to "bio-executables" gem.
       * bin/br_biofetch.rb
       * bin/br_bioflat.rb
       * bin/br_biogetseq.rb
       * bin/br_pmfetch.rb
  3. regenerate bioruby.gemspec with rake regemspec

    ngoto committed Sep 15, 2017
Commits on Sep 13, 2017
  1. Suppress warning "assigned but unused variable"

    ngoto committed Sep 13, 2017
  2. Suppress warning: "instance variable @top_strand not initialized"

    ngoto committed Sep 13, 2017
     * Suppress warning: "instance variable @top_strand not initialized".
       To do so, force to raise NoMethodError when @top_strand is not
       initialized or is nil. This should be changed to appropriate
       exception in the future.
  3. Suppress warning "parentheses after method name is interpreted as an …

    ngoto committed Sep 13, 2017
    …argument list, not a decomposed argument" in Ruby 2.4
Commits on Nov 29, 2016
  1. Gemfile for local development.

    junaruga committed Nov 18, 2016
Commits on Nov 18, 2016
  1. Fixes ruby1.8 Travis failure that is because rdoc 4.3.0 requires Ruby…

    junaruga committed Nov 17, 2016
    … >= 1.9.3.
Commits on Aug 12, 2016
  1. Update URLs and use https for NCBI REST web services

    ngoto committed Aug 12, 2016
  2. New method Bio::Command#start_http_uri(uri) with tests

    ngoto committed Aug 12, 2016
     * lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
       that supports HTTPS. Note that this method is intended to be
       called only from BioRuby internals.
     * lib/bio/command.rb: Bio::Command#post and #post_form are changed
       to use the start_http_uri().
     * test/network/bio/test_command.rb: tests for start_http_uri().
Commits on Jun 17, 2016
  1. gemfiles/Gemfile.*: remove dependency on libxml-ruby

    ngoto committed Jun 17, 2016
     * gemfiles/Gemfile.*: remove dependency on libxml-ruby.
       Bio::PhyloXML required libxml-ruby but was already removed.
  2. regenerate bioruby.gemspec with rake regemspec

    ngoto committed Jun 17, 2016
  3. README.rdoc: about bioruby-phyloxml and bio-biosql

    ngoto committed Jun 17, 2016
  4. remove autoload of Bio::SQL

    ngoto committed Jun 17, 2016
  5. Removed Bio::SQL that have been moved to separate repository

    ngoto committed Jun 17, 2016
     * Bio::SQL is moved to https://github.com/bioruby/bioruby-biosql
       and removed from this repository.
    
     * List of deleted files:
       * deleted:    lib/bio/db/biosql/biosql_to_biosequence.rb
       * deleted:    lib/bio/db/biosql/sequence.rb
       * deleted:    lib/bio/io/biosql/ar-biosql.rb
       * deleted:    lib/bio/io/biosql/biosql.rb
       * deleted:    lib/bio/io/biosql/config/database.yml
       * deleted:    lib/bio/io/sql.rb
       * deleted:    test/unit/bio/db/biosql/tc_biosql.rb
       * deleted:    test/unit/bio/db/biosql/ts_suite_biosql.rb
Commits on Jun 8, 2016
Commits on Jun 7, 2016
  1. .travis.yml: fix to use rbx-3.29

    ngoto committed Jun 7, 2016
  2. Workaround to avoid bug in old versions of Bundler

    ngoto committed Jun 7, 2016
     * gemfiles/prepare-gemspec.rb: execute "gem update bundler" to avoid
       "NoMethodError: undefined method `spec' for nil:NilClass"
       during "bundle install". This error may be due to a bug of Bundler
       and the bug seems to be fixed in the latest version of Budler.
  3. .travis.yml: Update ruby versions and remove temporary workaround

    ngoto committed Jun 7, 2016
     * Update Ruby versions to 2.2, 2.1.10, and rbx-3.
     * Remove temporary workaround about RubyGems introduced in
       e92e09e.
  4. Test bug: fix gem version mismatch error on Travis-CI

    ngoto committed Jun 7, 2016
     * Rakefile: prefer to use spec read from existing bioruby.gemspec file
       instead of that of generated from bioruby.gemspec.erb.
       This fixes "can't activate bio (= 1.5.1.2016XXXX), already activated
       bio-1.5.1.2015NNNN" occurred on Travis-CI during gem integration tests.