bio-nexml 1.0.0 → 1.1.0

metadata

@@ -1,79 +1,72 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: bio-nexml
-version: !ruby/object:Gem::Version 
-  hash: 23
+version: !ruby/object:Gem::Version
+  version: 1.1.0
   prerelease: 
-  segments: 
-  - 1
-  - 0
-  - 0
-  version: 1.0.0
 platform: ruby
-authors: 
+authors:
 - Rutger Vos
 - Anurag Priyam
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2011-09-21 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-05-09 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: bio
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: &78329210 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 1
-        - 4
-        - 1
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
         version: 1.4.1
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: libxml-ruby
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: *78329210
+- !ruby/object:Gem::Dependency
+  name: libxml-ruby
+  requirement: &78370740 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 27
-        segments: 
-        - 1
-        - 1
-        - 4
+    requirements:
+    - - =
+      - !ruby/object:Gem::Version
         version: 1.1.4
   type: :runtime
-  version_requirements: *id002
+  prerelease: false
+  version_requirements: *78370740
 description: This plugin reads, writes and generates NeXML
-email: 
+email:
 - rutgeraldo@gmail.com
 - anurag08priyam@gmail.com
 executables: []
-
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
+- .gitignore
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.mkd
+- Rakefile
+- TODO.txt
+- VERSION
+- bio-nexml.gemspec
+- lib/bio-nexml.rb
+- lib/bio/db/nexml.rb
+- lib/bio/db/nexml/mapper.rb
 - lib/bio/db/nexml/mapper/framework.rb
 - lib/bio/db/nexml/mapper/inflection.rb
 - lib/bio/db/nexml/mapper/repository.rb
-- lib/bio/db/nexml/mapper.rb
 - lib/bio/db/nexml/matrix.rb
 - lib/bio/db/nexml/parser.rb
+- lib/bio/db/nexml/schema/README.txt
 - lib/bio/db/nexml/schema/abstract.xsd
+- lib/bio/db/nexml/schema/characters/README.txt
 - lib/bio/db/nexml/schema/characters/abstractcharacters.xsd
 - lib/bio/db/nexml/schema/characters/characters.xsd
 - lib/bio/db/nexml/schema/characters/continuous.xsd
 - lib/bio/db/nexml/schema/characters/dna.xsd
 - lib/bio/db/nexml/schema/characters/protein.xsd
-- lib/bio/db/nexml/schema/characters/README.txt
 - lib/bio/db/nexml/schema/characters/restriction.xsd
 - lib/bio/db/nexml/schema/characters/rna.xsd
 - lib/bio/db/nexml/schema/characters/standard.xsd
@@ -81,58 +74,53 @@ files:
 - lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd
 - lib/bio/db/nexml/schema/external/xlink.xsd
 - lib/bio/db/nexml/schema/external/xml.xsd
+- lib/bio/db/nexml/schema/meta/README.txt
 - lib/bio/db/nexml/schema/meta/annotations.xsd
 - lib/bio/db/nexml/schema/meta/meta.xsd
-- lib/bio/db/nexml/schema/meta/README.txt
 - lib/bio/db/nexml/schema/nexml.xsd
-- lib/bio/db/nexml/schema/README.txt
 - lib/bio/db/nexml/schema/taxa/README.txt
 - lib/bio/db/nexml/schema/taxa/taxa.xsd
+- lib/bio/db/nexml/schema/trees/README.txt
 - lib/bio/db/nexml/schema/trees/abstracttrees.xsd
 - lib/bio/db/nexml/schema/trees/network.xsd
-- lib/bio/db/nexml/schema/trees/README.txt
 - lib/bio/db/nexml/schema/trees/tree.xsd
 - lib/bio/db/nexml/schema/trees/trees.xsd
 - lib/bio/db/nexml/taxa.rb
 - lib/bio/db/nexml/trees.rb
 - lib/bio/db/nexml/writer.rb
-- lib/bio/db/nexml.rb
-- lib/bio-nexml.rb
-- LICENSE.txt
-- README.rdoc
+- test/data/nexml/test.xml
 - test/test_bio-nexml.rb
-homepage: http://rvosa.github.com/bio-nexml/
-licenses: 
+- test/unit/bio/db/nexml/tc_factory.rb
+- test/unit/bio/db/nexml/tc_mapper.rb
+- test/unit/bio/db/nexml/tc_matrix.rb
+- test/unit/bio/db/nexml/tc_parser.rb
+- test/unit/bio/db/nexml/tc_taxa.rb
+- test/unit/bio/db/nexml/tc_trees.rb
+- test/unit/bio/db/nexml/tc_writer.rb
+homepage: https://github.com/nexml/bio-nexml
+licenses:
 - MIT
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.7
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
 summary: BioRuby plugin for reading and writing NeXML (http://nexml.org)
-test_files: 
+test_files:
 - test/test_bio-nexml.rb

data/README.rdoc

@@ -1,53 +0,0 @@
-= bio-nexml
-
-NeXML is a file format for phylogenetic data. It is inspired by the modular
-architecture of the commonly-used NEXUS file format (hence the name) in that
-a NeXML instance document can contain:
-* sets of Operational Taxonomic Units (OTUs), i.e. the tips in phylogenetic
-  trees, and that which comparative observations are made on. Often these are
-  species ("taxa").
-* sets of phylogenetic trees (or reticulate trees, i.e. networks)
-* sets of comparative data, i.e. molecular sequences, morphological categorical
-  data, continuous data, and other types.
-
-The elements in a NeXML document can be annotated using RDFa
-(http://en.wikipedia.org/wiki/RDFa), which means that every object that can
-be parsed out of a NeXML document must be an object that, in turn, can be
-annotated with predicates (and their namespaces) and other objects (with,
-perhaps, their own namespaces). The advantage over previous file formats is
-that we can retain all metadata for all objects within one file, regardless
-where the metadata come from.
-
-NeXML can be transformed to RDF using an XSL stylesheet. As such, NeXML forms
-an intermediate format between traditional flat file formats (with predictable
-structure but no semantics) and RDF (with loose structure, but lots of
-semantics) that is both easy to work with, yet ready for the Semantic Web.
-
-To learn more, visit http://www.nexml.org
-
-== Getting Started
-
-https://www.nescent.org/wg_phyloinformatics/NeXML_and_RDF_API_for_BioRuby
-
-It is not complete, but definitely enough to get started.
-
-== Contributing to bio-nexml
- 
-* Check out the latest master to make sure the feature hasn't been implemented
-  or the bug hasn't been fixed yet
-* Check out the issue tracker to make sure someone already hasn't requested it
-  and/or contributed it
-* Fork the project
-* Start a feature/bugfix branch
-* Commit and push until you are happy with your contribution
-* Make sure to add tests for it. This is important so I don't break it in a
-  future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to
-  have your own version, or is otherwise necessary, that is fine, but please
-  isolate to its own commit so I can cherry-pick around it.
-
-== Copyright
-
-Copyright (c) 2011 rvosa. See LICENSE.txt for
-further details.
-