bio 1.5.1 → 2.0.2

data/Rakefile

@@ -68,19 +68,23 @@ GEM_SPEC_FILE = "bioruby.gemspec"
 GEM_SPEC_TEMPLATE_FILE = "bioruby.gemspec.erb"
 
 # gets gem spec string
-gem_spec_string = File.open(GEM_SPEC_TEMPLATE_FILE, "rb") do |f|
-                    ERB.new(f.read).result
-                  end
+current_gem_spec_string = File.read(GEM_SPEC_FILE) rescue nil
+
+next_gem_spec_string = File.open(GEM_SPEC_TEMPLATE_FILE, "rb") do |f|
+  ERB.new(f.read).result
+end
 
 # gets gem spec object
-spec = eval(gem_spec_string)
+current_spec = eval(current_gem_spec_string || '')
+next_spec = eval(next_gem_spec_string)
+spec = (current_spec || next_spec)
 
 # adds notice of automatically generated file
-gem_spec_string = "# This file is automatically generated from #{GEM_SPEC_TEMPLATE_FILE} and\n# should NOT be edited by hand.\n# \n" + gem_spec_string
+next_gem_spec_string = "# This file is automatically generated from #{GEM_SPEC_TEMPLATE_FILE} and\n# should NOT be edited by hand.\n# \n" + next_gem_spec_string
 
 # compares current gemspec file and newly generated gemspec string
-current_string = File.read(GEM_SPEC_FILE) rescue nil
-if current_string and current_string != gem_spec_string then
+if current_gem_spec_string &&
+   current_gem_spec_string != next_gem_spec_string then
   #Rake::Task[GEM_SPEC_FILE].invoke
   flag_update_gemspec = true
 else
@@ -101,7 +105,7 @@ file GEM_SPEC_FILE => [ GEM_SPEC_TEMPLATE_FILE, 'Rakefile',
                         'lib/bio/version.rb' ] do |t|
   puts "creates #{GEM_SPEC_FILE}"
   File.open(t.name, 'wb') do |w|
-    w.print gem_spec_string
+    w.print next_gem_spec_string
   end
 end
 
@@ -188,7 +192,7 @@ task :rechangelog do
   # The tag name in the command line should be changed
   # after releasing new version, updating ChangeLog,
   # and doing "git mv ChangeLog doc/ChangeLog-X.X.X".
-  sh "git log --stat --summary 1.4.3..HEAD > ChangeLog"
+  sh "git log --stat --summary 1.5.0..HEAD > ChangeLog"
 end
 
 # define mktmpdir
@@ -268,36 +272,6 @@ task :"see-env" do
   end
 end
 
-desc "DANGER: build tar and install (GNU tar needed)"
-task :"tar-install" => [ :package ] do
-  pwd = Dir.pwd
-  work_in_another_directory do |dirname|
-    begin
-      # remove tar file in direname
-      FileUtils.remove_entry_secure(tar_filename, true)
-      # chdir to old pwd
-      chdir_with_message(pwd)
-      # copy (or link) tar file
-      safe_ln(tar_pkg_filepath, dirname)
-      # chdir to dirname again
-      chdir_with_message(dirname)
-      # remove a directory the tar file will contain
-      FileUtils.remove_entry_secure(tar_basename, true)
-      # extract tar
-      sh("tar zxvf #{tar_filename}")
-      # chdir to the directory
-      chdir_with_message(tar_basename)
-      # run tests
-      ruby("setup.rb")
-    ensure
-      # cleanup
-      chdir_with_message(dirname)
-      FileUtils.remove_entry_secure(tar_basename, true)
-      FileUtils.remove_entry_secure(tar_filename, true)
-    end
-  end
-end
-
 desc "test installed bioruby on system"
 task :"installed-test" do
   data_path = File.join(Dir.pwd, "test/data")
@@ -314,10 +288,6 @@ task :"installed-test" do
   end
 end
 
-desc "DANGER: build tar, install and run test"
-task :"tar-integration-test" => [ :"tar-install",
-                                  :"installed-test" ]
-
 desc "test installed bioruby gem version #{spec.version.to_s}"
 task :"gem-test" do
   data_path = File.join(Dir.pwd, "test/data")

data/appveyor.yml

@@ -0,0 +1,29 @@
+---
+version: "{build}"
+branches:
+  only:
+    - master
+clone_depth: 10
+install:
+  - SET PATH=C:\Ruby%ruby_version%\bin;%PATH%
+  - SET BUNDLE_GEMFILE=gemfiles/Gemfile.windows
+  - bundle install
+  - bundle exec rake regemspec
+  - bundle exec rake gem
+  - bundle exec gem install pkg/bio-*.gem
+  - echo gem "bio" >> gemfiles\Gemfile.windows
+build: off
+before_test:
+  - ruby --version
+  - gem --version
+  - bundle --version
+test_script:
+  - bundle exec rake gem-test
+environment:
+  matrix:
+    - ruby_version: "23"
+    - ruby_version: "23-x64"
+    - ruby_version: "24"
+    - ruby_version: "24-x64"
+    - ruby_version: "25"
+    - ruby_version: "25-x64"

data/bioruby.gemspec

@@ -3,7 +3,7 @@
 # 
 Gem::Specification.new do |s|
   s.name = 'bio'
-  s.version = "1.5.1"
+  s.version = "2.0.2"
 
   s.author = "BioRuby project"
   s.email = "staff@bioruby.org"
@@ -21,6 +21,7 @@ Gem::Specification.new do |s|
     "COPYING.ja",
     "ChangeLog",
     "GPL",
+    "Gemfile",
     "KNOWN_ISSUES.rdoc",
     "LEGAL",
     "LGPL",
@@ -28,14 +29,11 @@ Gem::Specification.new do |s|
     "README_DEV.rdoc",
     "RELEASE_NOTES.rdoc",
     "Rakefile",
-    "bin/bioruby",
-    "bin/br_biofetch.rb",
-    "bin/br_bioflat.rb",
-    "bin/br_biogetseq.rb",
-    "bin/br_pmfetch.rb",
+    "appveyor.yml",
     "bioruby.gemspec",
     "bioruby.gemspec.erb",
     "doc/ChangeLog-1.4.3",
+    "doc/ChangeLog-1.5.0",
     "doc/ChangeLog-before-1.3.1",
     "doc/ChangeLog-before-1.4.2",
     "doc/Changes-0.7.rd",
@@ -44,6 +42,7 @@ Gem::Specification.new do |s|
     "doc/RELEASE_NOTES-1.4.1.rdoc",
     "doc/RELEASE_NOTES-1.4.2.rdoc",
     "doc/RELEASE_NOTES-1.4.3.rdoc",
+    "doc/RELEASE_NOTES-1.5.0.rdoc",
     "doc/Tutorial.rd",
     "doc/Tutorial.rd.html",
     "doc/Tutorial.rd.ja",
@@ -55,7 +54,7 @@ Gem::Specification.new do |s|
     "gemfiles/Gemfile.travis-rbx",
     "gemfiles/Gemfile.travis-ruby1.8",
     "gemfiles/Gemfile.travis-ruby1.9",
-    "gemfiles/Gemfile.travis-ruby2.2",
+    "gemfiles/Gemfile.windows",
     "gemfiles/modify-Gemfile.rb",
     "gemfiles/prepare-gemspec.rb",
     "lib/bio.rb",
@@ -71,7 +70,6 @@ Gem::Specification.new do |s|
     "lib/bio/appl/blast/rexml.rb",
     "lib/bio/appl/blast/rpsblast.rb",
     "lib/bio/appl/blast/wublast.rb",
-    "lib/bio/appl/blast/xmlparser.rb",
     "lib/bio/appl/blat/report.rb",
     "lib/bio/appl/clustalw.rb",
     "lib/bio/appl/clustalw/report.rb",
@@ -120,8 +118,6 @@ Gem::Specification.new do |s|
     "lib/bio/data/na.rb",
     "lib/bio/db.rb",
     "lib/bio/db/aaindex.rb",
-    "lib/bio/db/biosql/biosql_to_biosequence.rb",
-    "lib/bio/db/biosql/sequence.rb",
     "lib/bio/db/embl/common.rb",
     "lib/bio/db/embl/embl.rb",
     "lib/bio/db/embl/embl_to_biosequence.rb",
@@ -180,10 +176,6 @@ Gem::Specification.new do |s|
     "lib/bio/db/pdb/pdb.rb",
     "lib/bio/db/pdb/residue.rb",
     "lib/bio/db/pdb/utils.rb",
-    "lib/bio/db/phyloxml/phyloxml.xsd",
-    "lib/bio/db/phyloxml/phyloxml_elements.rb",
-    "lib/bio/db/phyloxml/phyloxml_parser.rb",
-    "lib/bio/db/phyloxml/phyloxml_writer.rb",
     "lib/bio/db/prosite.rb",
     "lib/bio/db/rebase.rb",
     "lib/bio/db/sanger_chromatogram/abif.rb",
@@ -193,9 +185,6 @@ Gem::Specification.new do |s|
     "lib/bio/db/soft.rb",
     "lib/bio/db/transfac.rb",
     "lib/bio/feature.rb",
-    "lib/bio/io/biosql/ar-biosql.rb",
-    "lib/bio/io/biosql/biosql.rb",
-    "lib/bio/io/biosql/config/database.yml",
     "lib/bio/io/das.rb",
     "lib/bio/io/fastacmd.rb",
     "lib/bio/io/fetch.rb",
@@ -210,7 +199,6 @@ Gem::Specification.new do |s|
     "lib/bio/io/ncbirest.rb",
     "lib/bio/io/pubmed.rb",
     "lib/bio/io/registry.rb",
-    "lib/bio/io/sql.rb",
     "lib/bio/io/togows.rb",
     "lib/bio/location.rb",
     "lib/bio/map.rb",
@@ -228,44 +216,6 @@ Gem::Specification.new do |s|
     "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",
-    "lib/bio/shell/object.rb",
-    "lib/bio/shell/plugin/blast.rb",
-    "lib/bio/shell/plugin/codon.rb",
-    "lib/bio/shell/plugin/das.rb",
-    "lib/bio/shell/plugin/emboss.rb",
-    "lib/bio/shell/plugin/entry.rb",
-    "lib/bio/shell/plugin/flatfile.rb",
-    "lib/bio/shell/plugin/midi.rb",
-    "lib/bio/shell/plugin/ncbirest.rb",
-    "lib/bio/shell/plugin/obda.rb",
-    "lib/bio/shell/plugin/psort.rb",
-    "lib/bio/shell/plugin/seq.rb",
-    "lib/bio/shell/plugin/togows.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml",
-    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif",
-    "lib/bio/shell/script.rb",
-    "lib/bio/shell/setup.rb",
-    "lib/bio/shell/web.rb",
     "lib/bio/tree.rb",
     "lib/bio/tree/output.rb",
     "lib/bio/util/color_scheme.rb",
@@ -308,6 +258,7 @@ Gem::Specification.new do |s|
     "sample/any2fasta.rb",
     "sample/benchmark_clustalw_report.rb",
     "sample/biofetch.rb",
+    "sample/color_scheme_aa.rb",
     "sample/color_scheme_na.rb",
     "sample/demo_aaindex.rb",
     "sample/demo_aminoacid.rb",
@@ -346,6 +297,9 @@ Gem::Specification.new do |s|
     "sample/fasta2tab.rb",
     "sample/fastagrep.rb",
     "sample/fastasort.rb",
+    "sample/fastq2html.cwl",
+    "sample/fastq2html.rb",
+    "sample/fastq2html.testdata.yaml",
     "sample/fsplit.rb",
     "sample/gb2fasta.rb",
     "sample/gb2tab.rb",
@@ -357,17 +311,20 @@ Gem::Specification.new do |s|
     "sample/genome2tab.rb",
     "sample/goslim.rb",
     "sample/gt2fasta.rb",
+    "sample/na2aa.cwl",
     "sample/na2aa.rb",
+    "sample/na2aa.testdata.yaml",
     "sample/pmfetch.rb",
     "sample/pmsearch.rb",
+    "sample/rev_comp.cwl",
+    "sample/rev_comp.rb",
+    "sample/rev_comp.testdata.yaml",
     "sample/seqdatabase.ini",
     "sample/ssearch2tab.rb",
     "sample/tdiary.rb",
-    "sample/test_phyloxml_big.rb",
     "sample/test_restriction_enzyme_long.rb",
     "sample/tfastx2tab.rb",
     "sample/vs-genes.rb",
-    "setup.rb",
     "test/bioruby_test_helper.rb",
     "test/data/HMMER/hmmpfam.out",
     "test/data/HMMER/hmmsearch.out",
@@ -485,11 +442,6 @@ Gem::Specification.new do |s|
     "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",
-    "test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
-    "test/data/phyloxml/phyloxml_examples.xml",
     "test/data/pir/CRAB_ANAPL.pir",
     "test/data/prosite/prosite.dat",
     "test/data/refseq/nm_126355.entret",
@@ -508,6 +460,7 @@ Gem::Specification.new do |s|
     "test/network/bio/appl/blast/test_remote.rb",
     "test/network/bio/appl/test_blast.rb",
     "test/network/bio/appl/test_pts1.rb",
+    "test/network/bio/db/kegg/test_genes_hsa7422.rb",
     "test/network/bio/io/test_pubmed.rb",
     "test/network/bio/io/test_togows.rb",
     "test/network/bio/test_command.rb",
@@ -539,8 +492,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/data/test_aa.rb",
     "test/unit/bio/data/test_codontable.rb",
     "test/unit/bio/data/test_na.rb",
-    "test/unit/bio/db/biosql/tc_biosql.rb",
-    "test/unit/bio/db/biosql/ts_suite_biosql.rb",
     "test/unit/bio/db/embl/test_common.rb",
     "test/unit/bio/db/embl/test_embl.rb",
     "test/unit/bio/db/embl/test_embl_rel89.rb",
@@ -579,8 +530,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/db/test_nbrf.rb",
     "test/unit/bio/db/test_newick.rb",
     "test/unit/bio/db/test_nexus.rb",
-    "test/unit/bio/db/test_phyloxml.rb",
-    "test/unit/bio/db/test_phyloxml_writer.rb",
     "test/unit/bio/db/test_prosite.rb",
     "test/unit/bio/db/test_qual.rb",
     "test/unit/bio/db/test_rebase.rb",
@@ -598,7 +547,6 @@ Gem::Specification.new do |s|
     "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",
@@ -608,7 +556,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/test_pathway.rb",
     "test/unit/bio/test_reference.rb",
     "test/unit/bio/test_sequence.rb",
-    "test/unit/bio/test_shell.rb",
     "test/unit/bio/test_tree.rb",
     "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb",
     "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb",
@@ -633,7 +580,6 @@ Gem::Specification.new do |s|
     "test/unit/bio/util/test_sirna.rb"
   ]
 
-  s.has_rdoc = true
   s.extra_rdoc_files = [ 
     "KNOWN_ISSUES.rdoc",
     "README.rdoc",
@@ -643,7 +589,8 @@ Gem::Specification.new do |s|
     "doc/RELEASE_NOTES-1.4.0.rdoc",
     "doc/RELEASE_NOTES-1.4.1.rdoc",
     "doc/RELEASE_NOTES-1.4.2.rdoc",
-    "doc/RELEASE_NOTES-1.4.3.rdoc"
+    "doc/RELEASE_NOTES-1.4.3.rdoc",
+    "doc/RELEASE_NOTES-1.5.0.rdoc"
   ]
   s.rdoc_options << '--main' << 'README.rdoc'
   s.rdoc_options << '--title' << 'BioRuby API documentation'
@@ -651,14 +598,4 @@ Gem::Specification.new do |s|
   s.rdoc_options << '--line-numbers' << '--inline-source'
 
   s.require_path = 'lib'
-
-  s.bindir = "bin"
-  s.executables = [
-    "bioruby",
-    "br_biofetch.rb",
-    "br_bioflat.rb",
-    "br_biogetseq.rb",
-    "br_pmfetch.rb"
-  ]
-  s.default_executable = "bioruby"
 end

data/bioruby.gemspec.erb

@@ -7,18 +7,18 @@ Gem::Specification.new do |s|
 
     # By default, determined from lib/bio/version.rb
     load "./lib/bio/version.rb" unless defined?(BIO_VERSION_RB_LOADED)
+    ver = Bio::BIORUBY_VERSION.dup
     case Bio::BIORUBY_EXTRA_VERSION
     when nil
-      suffix = nil
-    when /\A\.(\d+)\z/
-      suffix = $1
-    when /\A\-dev\z/
-      suffix = Time.now.strftime("%Y%m%d")
+      # does nothing
+    when /\A\.(pre)\z/
+      ver.push $1
+      ver.push Time.now.strftime("%Y%m%d")
+    when /\A\.(.+)\z/
+      ver.push $1
     else
       raise "unsupported BIORUBY_EXTRA_VERSION"
     end
-    ver = Bio::BIORUBY_VERSION.dup
-    ver.push suffix if suffix
     %><%= 
     (env_ver || ver.join('.'))
        ###### Above is executed in ERB environment ######
@@ -48,7 +48,7 @@ Gem::Specification.new do |s|
           "bioruby.gemspec", "setup.rb",
           "extconf.rb", "LEGAL",
           "COPYING", "COPYING.ja", "GPL", "LGPL"
-        ] + Dir.glob("{bin,doc,etc,gemfiles,lib,sample,test}/**/*").delete_if do |item|
+        ] + Dir.glob("{doc,etc,gemfiles,lib,sample,test}/**/*").delete_if do |item|
               case item
               when /(\A|\/)CVS(\z|\/)/, /(\A|\/)rdoc(\z|\/)/, /\~\z/
                 true
@@ -63,7 +63,6 @@ Gem::Specification.new do |s|
     %>
   ]
 
-  s.has_rdoc = true
   s.extra_rdoc_files = [ 
     <%= ###### Below is executed in ERB environment ######
         # Files whose suffix are .rdoc are selected.
@@ -90,23 +89,4 @@ Gem::Specification.new do |s|
   s.rdoc_options << '--line-numbers' << '--inline-source'
 
   s.require_path = 'lib'
-
-  s.bindir = "bin"
-  s.executables = [
-    <%= ###### Below is executed in ERB environment ######
-        # Files in bin/ directory are selected.
-        exec_files = files.find_all { |item| /\Abin\// =~ item }
-        # Non-executable files are removed from the list.
-        exec_files.delete_if { |item| !File.executable?(item) }
-        # strip "bin/"
-        exec_files.collect! { |item| item.sub(/\Abin\//, '') }
-        # Fail safe settings
-        if exec_files.empty? then
-            exec_files = [ "bioruby", "br_biofetch.rb", "br_biogetseq.rb", "br_bioflat.rb", "br_pmfetch.rb" ]
-        end
-        exec_files.sort.collect { |x| x.dump }.join(",\n    ")
-        ###### Above is executed in ERB environment ######
-    %>
-  ]
-  s.default_executable = "bioruby"
 end