bio-nexml 1.0.0 → 1.1.0

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metadata CHANGED
@@ -1,79 +1,72 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: bio-nexml
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- version: !ruby/object:Gem::Version
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- hash: 23
3
+ version: !ruby/object:Gem::Version
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+ version: 1.1.0
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5
  prerelease:
6
- segments:
7
- - 1
8
- - 0
9
- - 0
10
- version: 1.0.0
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6
  platform: ruby
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- authors:
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+ authors:
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8
  - Rutger Vos
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9
  - Anurag Priyam
15
10
  autorequire:
16
11
  bindir: bin
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12
  cert_chain: []
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-
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- date: 2011-09-21 00:00:00 Z
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- dependencies:
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- - !ruby/object:Gem::Dependency
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+ date: 2012-05-09 00:00:00.000000000Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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16
  name: bio
23
- prerelease: false
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- requirement: &id001 !ruby/object:Gem::Requirement
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+ requirement: &78329210 !ruby/object:Gem::Requirement
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  none: false
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- requirements:
27
- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 5
30
- segments:
31
- - 1
32
- - 4
33
- - 1
19
+ requirements:
20
+ - - ! '>='
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+ - !ruby/object:Gem::Version
34
22
  version: 1.4.1
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23
  type: :runtime
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- version_requirements: *id001
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- - !ruby/object:Gem::Dependency
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- name: libxml-ruby
39
24
  prerelease: false
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- requirement: &id002 !ruby/object:Gem::Requirement
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+ version_requirements: *78329210
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+ - !ruby/object:Gem::Dependency
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+ name: libxml-ruby
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+ requirement: &78370740 !ruby/object:Gem::Requirement
41
29
  none: false
42
- requirements:
43
- - - ">="
44
- - !ruby/object:Gem::Version
45
- hash: 27
46
- segments:
47
- - 1
48
- - 1
49
- - 4
30
+ requirements:
31
+ - - =
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+ - !ruby/object:Gem::Version
50
33
  version: 1.1.4
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34
  type: :runtime
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- version_requirements: *id002
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+ prerelease: false
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+ version_requirements: *78370740
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37
  description: This plugin reads, writes and generates NeXML
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- email:
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+ email:
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39
  - rutgeraldo@gmail.com
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40
  - anurag08priyam@gmail.com
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41
  executables: []
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-
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42
  extensions: []
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-
61
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  extra_rdoc_files: []
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-
63
- files:
44
+ files:
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+ - .gitignore
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+ - .travis.yml
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+ - Gemfile
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+ - LICENSE.txt
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+ - README.mkd
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+ - Rakefile
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+ - TODO.txt
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+ - VERSION
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+ - bio-nexml.gemspec
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+ - lib/bio-nexml.rb
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+ - lib/bio/db/nexml.rb
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+ - lib/bio/db/nexml/mapper.rb
64
57
  - lib/bio/db/nexml/mapper/framework.rb
65
58
  - lib/bio/db/nexml/mapper/inflection.rb
66
59
  - lib/bio/db/nexml/mapper/repository.rb
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- - lib/bio/db/nexml/mapper.rb
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60
  - lib/bio/db/nexml/matrix.rb
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  - lib/bio/db/nexml/parser.rb
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+ - lib/bio/db/nexml/schema/README.txt
70
63
  - lib/bio/db/nexml/schema/abstract.xsd
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+ - lib/bio/db/nexml/schema/characters/README.txt
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65
  - lib/bio/db/nexml/schema/characters/abstractcharacters.xsd
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66
  - lib/bio/db/nexml/schema/characters/characters.xsd
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  - lib/bio/db/nexml/schema/characters/continuous.xsd
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68
  - lib/bio/db/nexml/schema/characters/dna.xsd
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  - lib/bio/db/nexml/schema/characters/protein.xsd
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- - lib/bio/db/nexml/schema/characters/README.txt
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  - lib/bio/db/nexml/schema/characters/restriction.xsd
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  - lib/bio/db/nexml/schema/characters/rna.xsd
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  - lib/bio/db/nexml/schema/characters/standard.xsd
@@ -81,58 +74,53 @@ files:
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  - lib/bio/db/nexml/schema/external/xhtml-datatypes-1.xsd
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  - lib/bio/db/nexml/schema/external/xlink.xsd
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  - lib/bio/db/nexml/schema/external/xml.xsd
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+ - lib/bio/db/nexml/schema/meta/README.txt
84
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  - lib/bio/db/nexml/schema/meta/annotations.xsd
85
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  - lib/bio/db/nexml/schema/meta/meta.xsd
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- - lib/bio/db/nexml/schema/meta/README.txt
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  - lib/bio/db/nexml/schema/nexml.xsd
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- - lib/bio/db/nexml/schema/README.txt
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  - lib/bio/db/nexml/schema/taxa/README.txt
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  - lib/bio/db/nexml/schema/taxa/taxa.xsd
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+ - lib/bio/db/nexml/schema/trees/README.txt
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84
  - lib/bio/db/nexml/schema/trees/abstracttrees.xsd
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85
  - lib/bio/db/nexml/schema/trees/network.xsd
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- - lib/bio/db/nexml/schema/trees/README.txt
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  - lib/bio/db/nexml/schema/trees/tree.xsd
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  - lib/bio/db/nexml/schema/trees/trees.xsd
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  - lib/bio/db/nexml/taxa.rb
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  - lib/bio/db/nexml/trees.rb
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  - lib/bio/db/nexml/writer.rb
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- - lib/bio/db/nexml.rb
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- - lib/bio-nexml.rb
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- - LICENSE.txt
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- - README.rdoc
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+ - test/data/nexml/test.xml
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  - test/test_bio-nexml.rb
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- homepage: http://rvosa.github.com/bio-nexml/
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- licenses:
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+ - test/unit/bio/db/nexml/tc_factory.rb
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+ - test/unit/bio/db/nexml/tc_mapper.rb
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+ - test/unit/bio/db/nexml/tc_matrix.rb
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+ - test/unit/bio/db/nexml/tc_parser.rb
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+ - test/unit/bio/db/nexml/tc_taxa.rb
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+ - test/unit/bio/db/nexml/tc_trees.rb
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+ - test/unit/bio/db/nexml/tc_writer.rb
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+ homepage: https://github.com/nexml/bio-nexml
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+ licenses:
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  - MIT
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  post_install_message:
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  rdoc_options: []
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-
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- require_paths:
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+ require_paths:
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  - lib
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- required_ruby_version: !ruby/object:Gem::Requirement
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+ required_ruby_version: !ruby/object:Gem::Requirement
113
108
  none: false
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- requirements:
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- - - ">="
116
- - !ruby/object:Gem::Version
117
- hash: 3
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- segments:
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- - 0
120
- version: "0"
121
- required_rubygems_version: !ruby/object:Gem::Requirement
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+ requirements:
110
+ - - ! '>='
111
+ - !ruby/object:Gem::Version
112
+ version: '0'
113
+ required_rubygems_version: !ruby/object:Gem::Requirement
122
114
  none: false
123
- requirements:
124
- - - ">="
125
- - !ruby/object:Gem::Version
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- hash: 3
127
- segments:
128
- - 0
129
- version: "0"
115
+ requirements:
116
+ - - ! '>='
117
+ - !ruby/object:Gem::Version
118
+ version: '0'
130
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  requirements: []
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-
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  rubyforge_project:
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- rubygems_version: 1.8.7
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+ rubygems_version: 1.8.10
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  signing_key:
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  specification_version: 3
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  summary: BioRuby plugin for reading and writing NeXML (http://nexml.org)
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- test_files:
125
+ test_files:
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  - test/test_bio-nexml.rb
@@ -1,53 +0,0 @@
1
- = bio-nexml
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-
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- NeXML is a file format for phylogenetic data. It is inspired by the modular
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- architecture of the commonly-used NEXUS file format (hence the name) in that
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- a NeXML instance document can contain:
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- * sets of Operational Taxonomic Units (OTUs), i.e. the tips in phylogenetic
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- trees, and that which comparative observations are made on. Often these are
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- species ("taxa").
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- * sets of phylogenetic trees (or reticulate trees, i.e. networks)
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- * sets of comparative data, i.e. molecular sequences, morphological categorical
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- data, continuous data, and other types.
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-
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- The elements in a NeXML document can be annotated using RDFa
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- (http://en.wikipedia.org/wiki/RDFa), which means that every object that can
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- be parsed out of a NeXML document must be an object that, in turn, can be
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- annotated with predicates (and their namespaces) and other objects (with,
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- perhaps, their own namespaces). The advantage over previous file formats is
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- that we can retain all metadata for all objects within one file, regardless
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- where the metadata come from.
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-
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- NeXML can be transformed to RDF using an XSL stylesheet. As such, NeXML forms
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- an intermediate format between traditional flat file formats (with predictable
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- structure but no semantics) and RDF (with loose structure, but lots of
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- semantics) that is both easy to work with, yet ready for the Semantic Web.
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-
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- To learn more, visit http://www.nexml.org
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-
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- == Getting Started
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-
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- https://www.nescent.org/wg_phyloinformatics/NeXML_and_RDF_API_for_BioRuby
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-
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- It is not complete, but definitely enough to get started.
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-
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- == Contributing to bio-nexml
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-
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- * Check out the latest master to make sure the feature hasn't been implemented
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- or the bug hasn't been fixed yet
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- * Check out the issue tracker to make sure someone already hasn't requested it
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- and/or contributed it
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- * Fork the project
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- * Start a feature/bugfix branch
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- * Commit and push until you are happy with your contribution
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- * Make sure to add tests for it. This is important so I don't break it in a
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- future version unintentionally.
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- * Please try not to mess with the Rakefile, version, or history. If you want to
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- have your own version, or is otherwise necessary, that is fine, but please
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- isolate to its own commit so I can cherry-pick around it.
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-
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- == Copyright
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-
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- Copyright (c) 2011 rvosa. See LICENSE.txt for
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- further details.
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-