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Branch: master
Commits on Jun 14, 2019
  1. version changed to 1.0.0

    ngoto committed Jun 14, 2019
Commits on Jun 13, 2019
  1. Bug fix: printf format syntax error about single percent character

    ngoto committed Sep 20, 2018
     * Bio::Shell#seqstat: Fix format specifier syntax error.
       Recent version of Ruby raised error: 'ArgumentError:
       incomplete format specifier;use %% (double %) instead'.
Commits on Sep 15, 2017
  1. fix url

    ngoto committed Sep 15, 2017
  2. Add fles for packaging independent bio-shell gem

    ngoto committed Sep 15, 2017
    Some files are based on "bundle gem" command.
    Some files are coming from BioRuby gem.
Commits on Sep 14, 2017
  1. deleted lib/bio/shell/plugin/soap.rb

    ngoto committed Jun 29, 2015
     * deleted lib/bio/shell/plugin/soap.rb because Bio::SOAPWSDL and
       all SOAP client classes in BioRuby are removed.
  2. delete obsolete $Id:$ line

    ngoto committed Mar 23, 2015
  3. delete obsolete $Id:$ line

    ngoto committed Mar 23, 2015
  4. delete obsolete $Id:$ line

    ngoto committed Mar 23, 2015
  5. delete obsolete $Id:$ line

    ngoto committed Mar 23, 2015
  6. delete obsolete $Id:$ line

    ngoto committed Mar 23, 2015
  7. delete obsolete $Id:$ line

    ngoto committed Mar 20, 2015
  8. Bug fix: Ruby 1.9 support: did not yield the last part of the string

    ngoto committed Mar 20, 2015
     * lib/bio/shell/plugin/seq.rb: Bug fix: Ruby 1.9 support:
       String#step and #skip (extended by bioruby-shell) did not yield
       the last part of the string due to a change from Ruby 1.8 to 1.9.
     * Suppress warning message "shadowing outer local variable - i"
  9. Bug fix: bin/bioruby failed to save object

    ngoto committed Aug 21, 2012
     * Bug fix: bin/bioruby: Failed to save object with error message
       "can't convert Symbol into String" on Ruby 1.9.
  10. BIORUBY_TEST_LIB is always added on the top of $LOAD_PATH

    ngoto committed Jun 25, 2012
     * When BIORUBY_TEST_LIB is specified, the specified directory name
       is always added on the top of $LOAD_PATH even if it is already
       included in the middle of $LOAD_PATH.
  11. New env BIORUBY_TEST_GEM and BIORUBY_TEST_LIB behavior changed

    ngoto committed Jun 25, 2012
     * New environment variable BIORUBY_TEST_GEM for testing installed
       bio-X.X.X gem. Version number can be specified.
       Example with version number:
        % env BIORUBY_TEST_GEM=1.4.2.5000 ruby test/runner.rb
       Example without version number:
        % env BIORUBY_TEST_GEM="" ruby test/runner.rb
     * When BIORUBY_TEST_LIB is empty, it no longer add an empty string to
       $LOAD_PATH. Moreover, when BIORUBY_TEST_GEM is set, the variable is
       ignored.
  12. New methods Bio::NCBI::REST::EFetch.nucleotide and protein

    ngoto committed Aug 26, 2011
     * New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
       to get data from "nucleotide" and "protein" database respectively.
       Because NCBI changed not to accept "gb" format for the database
       "sequence", the two new methods are added for convenience.
     * In BioRuby Shell, efetch method uses the above new methods.
  13. The "libpath magic" in tests are replaced by the load of helper routine.

    ngoto committed Nov 12, 2009
     * In all unit tests, the "libpath magic" are replaced by the load
       of helper routine.
     * Changed to use a constant BioRubyTestDataPath for generating test
       data file path.
     * Some "require" lines are modified.
     * "File.open(...).read" in some tests are replaced by "File.read(...)".
     * Header comment lines of some tests with wrong filename and/or
       class/module name information are fixed.
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