nexus_parser 1.1.4 → 1.2.0

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Files changed (18) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +9 -0
  3. data/LICENSE +25 -17
  4. data/{README.rdoc → README.md} +7 -5
  5. data/Rakefile +5 -21
  6. data/lib/{lexer.rb → nexus_parser/lexer.rb} +17 -17
  7. data/lib/{parser.rb → nexus_parser/parser.rb} +2 -2
  8. data/lib/{tokens.rb → nexus_parser/tokens.rb} +36 -36
  9. data/lib/nexus_parser/version.rb +5 -0
  10. data/lib/nexus_parser.rb +44 -39
  11. data/nexus_parser.gemspec +49 -50
  12. data/test/MX_test_03.nex +3 -3
  13. data/test/test_nexus_parser.rb +134 -138
  14. metadata +111 -63
  15. data/MIT-LICENSE +0 -20
  16. data/README +0 -13
  17. data/VERSION +0 -1
  18. data/init.rb +0 -1
data/nexus_parser.gemspec CHANGED
@@ -1,60 +1,59 @@
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- # Generated by jeweler
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- # DO NOT EDIT THIS FILE DIRECTLY
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- # Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
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- # -*- encoding: utf-8 -*-
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-
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- Gem::Specification.new do |s|
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- s.name = %q{nexus_parser}
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- s.version = "1.1.4"
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-
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- s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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- s.authors = ["mjy"]
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- s.date = %q{2011-04-12}
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- s.description = %q{A full featured and extensible Nexus file parser in Ruby. }
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- s.email = %q{diapriid@gmail.com}
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- s.extra_rdoc_files = [
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+ # frozen_string_literal: true
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+
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+ require_relative "lib/nexus_parser/version"
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "nexus_parser"
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+ spec.version = NexusParser::VERSION
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+ spec.authors = ["mjy", "kleintom"]
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+ spec.email = ["diapriid@gmail.com"]
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+
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+ spec.summary = "A Nexus file format (phylogenetic inference) parser in Ruby."
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+ spec.description = "A full featured and extensible Nexus file parser in Ruby."
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+ spec.homepage = "http://github.com/mjy/nexus_parser"
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+
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+ spec.metadata["homepage_uri"] = spec.homepage
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+ spec.metadata["source_code_uri"] = spec.homepage
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+
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+ spec.extra_rdoc_files = [
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  "LICENSE",
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- "README",
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- "README.rdoc"
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+ "README.md"
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  ]
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- s.files = [
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+ spec.files = [
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  ".document",
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- ".gitignore",
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- "LICENSE",
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- "MIT-LICENSE",
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- "README",
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- "README.rdoc",
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- "Rakefile",
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- "VERSION",
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- "init.rb",
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- "install.rb",
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- "lib/lexer.rb",
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- "lib/nexus_parser.rb",
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- "lib/parser.rb",
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- "lib/tokens.rb",
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- "nexus_parser.gemspec",
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- "tasks/nexus_parser_tasks.rake",
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- "test/MX_test_03.nex",
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- "test/test.nex",
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- "test/test_nexus_parser.rb",
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- "uninstall.rb"
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+ ".gitignore",
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+ "LICENSE",
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+ "README.md",
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+ "Rakefile",
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+ "install.rb",
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+ "lib/nexus_parser.rb",
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+ "lib/nexus_parser/lexer.rb",
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+ "lib/nexus_parser/parser.rb",
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+ "lib/nexus_parser/tokens.rb",
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+ "lib/nexus_parser/version.rb",
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+ "nexus_parser.gemspec",
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+ "tasks/nexus_parser_tasks.rake",
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+ "test/MX_test_03.nex",
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+ "test/test.nex",
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+ "test/test_nexus_parser.rb",
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+ "uninstall.rb"
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  ]
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- s.homepage = %q{http://github.com/mjy/nexus_parser}
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- s.rdoc_options = ["--charset=UTF-8"]
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- s.require_paths = ["lib"]
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- s.rubygems_version = %q{1.5.3}
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- s.summary = %q{A Nexus file format (phylogenetic inference) parser in Ruby.}
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- s.test_files = [
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+
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+ spec.bindir = "exe"
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+ spec.executables = spec.files.grep(%r{\Aexe/}) { |f| File.basename(f) }
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+ spec.rdoc_options = ["--charset=UTF-8"]
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+ spec.require_paths = ["lib"]
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+
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+ spec.test_files = [
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  "test/test_nexus_parser.rb"
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  ]
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- if s.respond_to? :specification_version then
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- s.specification_version = 3
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+ spec.required_ruby_version = '>= 3.3.0'
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- if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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- else
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- end
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- else
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- end
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+ spec.add_development_dependency 'bundler', '~> 2.0'
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+ spec.add_development_dependency 'rake', '~> 13.0'
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+ spec.add_development_dependency 'rdoc', '~> 6.6.2'
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+ spec.add_development_dependency 'byebug', '~> 11.1'
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+ spec.add_development_dependency 'test-unit'
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  end
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data/test/MX_test_03.nex CHANGED
@@ -9,7 +9,7 @@ BEGIN TAXA;
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  TITLE 'Scharff&Coddington_1997_Araneidae';
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  DIMENSIONS NTAX=10;
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  TAXLABELS
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- Dictyna Uloborus Deinopis Nephila&Herennia 'Nephilengys_cruentata' Meta Leucauge_venusta Pachygnatha 'Theridiosoma_01' Tetragnatha
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+ Dictyna Uloborus Deinopis Nephila&Herennia 'Nephilengys_cruentata' Meta Leucauge_venusta Pachygnatha 'Theridiosoma_01' Tetragnatha
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  ;
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  IDS JC1191fcddc2b128 JC1191fcddc2b129 JC1191fcddc2b130 JC1191fcddc2b131 JC1191fcddc2b132 JC1191fcddc2b133 JC1191fcddc2b134 JC1191fcddc2b135 JC1191fcddc2b137 JC1191fcddc2b136 ;
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  BLOCKID JC1191fcddc0c4;
@@ -21,8 +21,8 @@ BEGIN CHARACTERS;
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  TITLE 'Scharff&Coddington_1997_Araneidae';
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  DIMENSIONS NCHAR=10;
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  FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1 2 3 4 5 6 7 8 9 A";
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- CHARSTATELABELS
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- 1 Tibia_II / norm modified, 2 TII_macrosetae / '= TI' stronger, 3 Femoral_tuber / abs pres 'm-setae', 5 Cymbium / dorsal mesal lateral, 6 Paracymbium / abs pres, 7 Globular_tegulum / abs pres, 8 / entire w_lobe, 9 Conductor_wraps_embolus, 10 Median_apophysis / pres abs ;
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+ CHARSTATELABELS
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+ 1 Tibia_II / norm modified, 2 TII_macrosetae / '= TI' stronger, 3 Femoral_tuber / abs pres 'm-setae', 5 Cymbium / dorsal mesal lateral, 6 Paracymbium / abs pres, 7 Globular_tegulum / abs pres, 8 / entire w_lobe, 9 Conductor_wraps_embolus, 10 Median_apophysis / pres abs ;
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  MATRIX
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  Dictyna 0?00201001
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  Uloborus 0?11000000