Permalink
Browse files

Version bump to 0.5.7

  • Loading branch information...
1 parent 080a890 commit 12935ab8c627725097e5aad5f196b644a38ff7f5 @dimus dimus committed Aug 12, 2009
Showing with 165 additions and 103 deletions.
  1. +5 −0 .document
  2. +5 −0 .gitignore
  3. +20 −21 LICENSE
  4. +14 −34 README.rdoc
  5. +43 −25 Rakefile
  6. +1 −0 VERSION
  7. +0 −4 VERSION.yml
  8. +77 −19 biodiversity.gemspec
  9. 0 spec/biodiversity_spec.rb
  10. 0 spec/spec_helper.rb
View
5 .document
@@ -0,0 +1,5 @@
+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE
View
5 .gitignore
@@ -1,3 +1,8 @@
+*.sw?
+.DS_Store
+coverage
+rdoc
+pkg
*.swp
*.swo
biodiversity*.gem
View
41 LICENSE
@@ -1,21 +1,20 @@
-Copyright (c) 2007 Tusk-It Contributors See:
- http://code.google.com/p/tuskit/wiki/ProjectContributors
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+Copyright (c) 2009 Dmitry Mozzherin
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
View
48 README.rdoc
@@ -1,38 +1,18 @@
-= Biodiversity
+= biodiversity
-Parses species scientific name and breaks it into elements.
+Description goes here.
-== Installation
+== Note on Patches/Pull Requests
+
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+ future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+ (if you want to have your own version, that is fine but
+ bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
-To install gem you need RubyGems >= 1.2.0
-
- $ gem sources -a http://gems.github.com (you only have to do this once)
- $ sudo gem install dimus-biodiversity
-
-== Example usage
-
-You can parse file with species names from command line. File should contain one scientific name per line
-
- nnparser file_with_names
-
-You can use it as a library
-
- require 'biodiversity'
-
- parser = ScientificNameParser.new
-
- # to parse a scientific name
- parser.parse("Plantago major")
-
- # to clean name up
- parser.parse(" Plantago major ").value
-
- # to get only cleaned up latin part of the name
- parser.parse("Pseudocercospora dendrobii (H.C. Burnett) U. Braun & Crous 2003").canonical
-
- # to get detailed information about elements of the name
- parser.parse("Pseudocercospora dendrobii (H.C. Burnett 1883) U. Braun & Crous 2003").details
-
- # to resolve lsid and get back RDF file
- LsidResolver.resolve("urn:lsid:ubio.org:classificationbank:2232671")
+== Copyright
+Copyright (c) 2009 Dmitry Mozzherin. See LICENSE for details.
View
68 Rakefile
@@ -1,41 +1,59 @@
-dir = File.dirname(__FILE__)
require 'rubygems'
require 'rake'
-$LOAD_PATH.unshift(File.join(dir, 'vendor', 'rspec', 'lib'))
+
+begin
+ require 'jeweler'
+ Jeweler::Tasks.new do |gem|
+ gem.name = "biodiversity"
+ gem.summary = %Q{TODO: one-line summary of your gem}
+ gem.description = %Q{TODO: longer description of your gem}
+ gem.email = "dmozzherin@gmail.com"
+ gem.homepage = "http://github.com/dimus/biodiversity"
+ gem.authors = ["Dmitry Mozzherin"]
+ gem.has_rdoc = false
+ gem.bindir = 'bin'
+ gem.executables = ['nnparse']
+ gem.add_dependency('treetop')
+ gem.add_dependency('json') if RUBY_VERSION.split(".")[0..1].join('').to_i < 19
+ gem.add_development_dependency "rspec"
+ # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+ end
+rescue LoadError
+ puts "Jeweler (or a dependency) not available. Install it with: sudo gem install jeweler"
+end
+
require 'spec/rake/spectask'
+Spec::Rake::SpecTask.new(:spec) do |spec|
+ spec.libs << 'lib' << 'spec'
+ spec.spec_files = FileList['spec/**/*_spec.rb']
+end
-#Gem::manage_gems
-require 'rake/gempackagetask'
+Spec::Rake::SpecTask.new(:rcov) do |spec|
+ #spec.libs << 'lib' << 'spec'
+ spec.pattern = 'spec/**/*_spec.rb'
+ #spec.rcov = true
+end
task :default => :spec
-#begin
-# require 'jeweler'
-# Jeweler::Tasks.new do |gemspec|
-# gemspec.name = "biodiversity"
-# gemspec.summary = "scientific species name parser\n\nExecutable is nnparse"
-# gemspec.email = "dmozzherin {et} eol {dt} org"
-# gemspec.homepage = "http://github.com/dimus/biodiversity"
-# gemspec.description = "Biodiversity library provides a parser tool for scientific species names"
-# gemspec.authors = ["Dmitry Mozzherin", "Anna Shipunova"]
+#require 'rake/rdoctask'
+#Rake::RDocTask.new do |rdoc|
+# if File.exist?('VERSION')
+# version = File.read('VERSION')
+# else
+# version = ""
# end
-#rescue LoadError
-# puts "Jeweler not available. Install it with: sudo gem install technicalpickles-jeweler -s http://gems.github.com"
+#
+# rdoc.rdoc_dir = 'rdoc'
+# rdoc.title = "biodiversity #{version}"
+# rdoc.rdoc_files.include('README*')
+# #rdoc.rdoc_files.include('lib/**/*.rb')
#end
-
-
task :tt do
+ dir = File.dirname(__FILE__)
system("tt #{dir}/lib/biodiversity/parser/scientific_name_clean.treetop")
system("tt #{dir}/lib/biodiversity/parser/scientific_name_dirty.treetop")
system("tt #{dir}/lib/biodiversity/parser/scientific_name_canonical.treetop")
end
-task :files do
- puts FileList["LICENSE", "README.rdoc", "Rakefile", "{spec,lib,bin,doc,examples}/**/*"].to_a.join(' ')
-end
-
-Spec::Rake::SpecTask.new do |t|
- t.pattern = 'spec/**/*spec.rb'
-end
-
View
1 VERSION
@@ -0,0 +1 @@
+0.5.7
View
4 VERSION.yml
@@ -1,4 +0,0 @@
----
-:minor: 2
-:patch: 0
-:major: 0
View
96 biodiversity.gemspec
@@ -1,22 +1,80 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE
+# Instead, edit Jeweler::Tasks in Rakefile, and run `rake gemspec`
+# -*- encoding: utf-8 -*-
+
Gem::Specification.new do |s|
- s.name = 'biodiversity'
- s.version = '0.5.6'
- s.date = '2009-8-11'
-
- s.summary = "scientific species name parser\n\nExecutable is nnparse"
- s.description = "Biodiversity library provides a parser tool for scientific species names"
-
- s.authors = ['Dmitry Mozzherin']
- s.email = 'dmozzherin {et} eol {dt} org'
- s.homepage = 'http://github.com/dimus/biodiversity/wikis'
-
- s.has_rdoc = false
-
- s.add_dependency 'treetop', ['>= 1.2.4']
- s.add_dependency 'json', ['>= 1.1.3'] if RUBY_VERSION.split(".")[0..1].join('').to_i < 19
+ s.name = %q{biodiversity}
+ s.version = "0.5.6"
+
+ s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+ s.authors = ["Dmitry Mozzherin"]
+ s.date = %q{2009-08-12}
+ s.default_executable = %q{nnparse}
+ s.description = %q{TODO: longer description of your gem}
+ s.email = %q{dmozzherin@gmail.com}
+ s.executables = ["nnparse"]
+ s.extra_rdoc_files = [
+ "LICENSE",
+ "README.rdoc"
+ ]
+ s.files = [
+ ".document",
+ ".gitignore",
+ "LICENSE",
+ "README.rdoc",
+ "Rakefile",
+ "VERSION",
+ "bin/nnparse",
+ "biodiversity.gemspec",
+ "conf/environment.rb",
+ "lib/biodiversity.rb",
+ "lib/biodiversity/guid.rb",
+ "lib/biodiversity/guid/lsid.rb",
+ "lib/biodiversity/parser.rb",
+ "lib/biodiversity/parser/scientific_name_canonical.rb",
+ "lib/biodiversity/parser/scientific_name_canonical.treetop",
+ "lib/biodiversity/parser/scientific_name_clean.rb",
+ "lib/biodiversity/parser/scientific_name_clean.treetop",
+ "lib/biodiversity/parser/scientific_name_dirty.rb",
+ "lib/biodiversity/parser/scientific_name_dirty.treetop",
+ "spec/guid/lsid.spec.rb",
+ "spec/parser/scientific_name.spec.rb",
+ "spec/parser/scientific_name_canonical.spec.rb",
+ "spec/parser/scientific_name_clean.spec.rb",
+ "spec/parser/scientific_name_dirty.spec.rb",
+ "spec/parser/spec_helper.rb",
+ "spec/parser/test_data.txt"
+ ]
+ s.homepage = %q{http://github.com/dimus/biodiversity}
+ s.rdoc_options = ["--charset=UTF-8"]
+ s.require_paths = ["lib"]
+ s.rubygems_version = %q{1.3.5}
+ s.summary = %q{TODO: one-line summary of your gem}
+ s.test_files = [
+ "spec/biodiversity_spec.rb",
+ "spec/guid/lsid.spec.rb",
+ "spec/parser/scientific_name.spec.rb",
+ "spec/parser/scientific_name_canonical.spec.rb",
+ "spec/parser/scientific_name_clean.spec.rb",
+ "spec/parser/scientific_name_dirty.spec.rb",
+ "spec/parser/spec_helper.rb",
+ "spec/spec_helper.rb"
+ ]
+
+ if s.respond_to? :specification_version then
+ current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+ s.specification_version = 3
- s.bindir = "bin"
- s.executables << 'nnparse'
-
- s.files = %w(LICENSE README.rdoc Rakefile conf conf/environment.rb spec/parser spec/parser/scientific_name.spec.rb spec/parser/scientific_name_canonical.spec.rb spec/parser/scientific_name_clean.spec.rb spec/parser/scientific_name_clean.spec.rb spec/parser/scientific_name_dirty.spec.rb spec/guid spec/guid/lsid.spec.rb lib/biodiversity lib/biodiversity/parser lib/biodiversity/guid.rb lib/biodiversity/guid lib/biodiversity/guid/lsid.rb lib/biodiversity/parser/scientific_name_clean.rb lib/biodiversity/parser/scientific_name_canonical.rb lib/biodiversity/parser/scientific_name_dirty.rb lib/biodiversity/parser/scientific_name_canonical.treetop lib/biodiversity/parser/scientific_name_clean.treetop lib/biodiversity/parser/scientific_name_dirty.treetop lib/biodiversity/parser.rb lib/biodiversity.rb bin/nnparse)
+ if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+ s.add_runtime_dependency(%q<treetop>, [">= 0"])
+ s.add_development_dependency(%q<rspec>, [">= 0"])
+ else
+ s.add_dependency(%q<treetop>, [">= 0"])
+ s.add_dependency(%q<rspec>, [">= 0"])
+ end
+ else
+ s.add_dependency(%q<treetop>, [">= 0"])
+ s.add_dependency(%q<rspec>, [">= 0"])
+ end
end
View
0 spec/biodiversity_spec.rb
No changes.
View
0 spec/spec_helper.rb
No changes.

0 comments on commit 12935ab

Please sign in to comment.