taxonifi 0.3.2 → 0.3.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7df9c89aa9370f5b09c35f4164eb9238be2b8a0d
-  data.tar.gz: 78c4de112c6e40cdf1e2197402f8f47e9dea6fa0
+  metadata.gz: f6460e1a6db043c95af5f490672d32afb517edae
+  data.tar.gz: 1080653388a1c17919a25c6905f55c5ed2b26a77
 SHA512:
-  metadata.gz: 6de2acff969064aad7a34e73759298630e3640430dff1c8ad3e189c373e0c5fe22c84cb8d56b71910d4711cf5446f344048a8bc4cbcb5c8ea8faec78a1cb8ac4
-  data.tar.gz: ff6a30b825545b759819540d468d37c68ffe700a531023875ed3e5a917dff6cd14859838da84081c87aefa36962d1398ffb6472c9662a47803d03a78d2144152
+  metadata.gz: 6a3973549fb832d1ab0dd5565d00937e86a47e70b924c5148d004586949800172da5e671fb6262f342a9b84c1142c916c147896cc940eff40c1b7ddfd6ca5636
+  data.tar.gz: c2528c8cb4c27fe671252aa0a666fca6da57cf5eab7a1de6406649dfcfc61cefd076ae890797594ec887593031f7278f3ebf732f18236db07a4d795f4ccca730

data/.gitignore

@@ -2,6 +2,8 @@
 # ignore in development script work
 sf
 
+*.gem
+
 vendor
 
 *.xlsx

data/Gemfile.lock

@@ -1,8 +1,10 @@
 PATH
   remote: .
   specs:
-    taxonifi (0.3.2)
+    taxonifi (0.3.3)
+      byebug (~> 4.0)
       rake (~> 10.4)
+      require_all (~> 1.3)
 
 GEM
   remote: https://rubygems.org/
@@ -15,7 +17,11 @@ GEM
     did_you_mean (0.9.8)
       interception
     interception (0.5)
+    json (1.8.2)
     rake (10.4.2)
+    rdoc (4.2.0)
+      json (~> 1.4)
+    require_all (1.3.2)
 
 PLATFORMS
   ruby
@@ -24,6 +30,6 @@ DEPENDENCIES
   awesome_print (~> 1.6)
   builder (~> 3.2)
   bundler (~> 1.9)
-  byebug (~> 4.0)
   did_you_mean (~> 0.9)
+  rdoc (~> 4.2)
   taxonifi!

data/Rakefile

@@ -4,34 +4,7 @@ require 'bundler/gem_tasks'
 require 'rake'
 require 'rake/testtask'
 require 'taxonifi/version'
-
-# require 'rubygems'
-# require 'bundler'
-
-# begin
-#   Bundler.setup(:default, :development)
-# rescue Bundler::BundlerError => e
-#   $stderr.puts e.message
-#   $stderr.puts "Run `bundle install` to install missing gems"
-#   exit e.status_code
-# end
-
-#require 'jeweler'
-
-# Jeweler::Tasks.new do |gem|
-#   # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
-#   gem.name = "taxonifi"
-#   gem.homepage = "http://github.com/SpeciesFile/taxonifi"
-#   gem.license = "MIT"
-#   gem.summary = %Q{A general purpose framework for scripted handling of taxonomic names}
-#   gem.description = %Q{Taxonifi contains simple models and utilties of use in for parsing lists of taxonomic name (life) related metadata}
-#   gem.email = "diapriid@gmail.com"
-#   gem.authors = ["mjy"]
-#   # dependencies defined in Gemfile
-# end
-
-# Jeweler::RubygemsDotOrgTasks.new
-
+require 'taxonifi'
 
 Rake::TestTask.new(:test) do |test|
   test.libs << 'lib' << 'test'
@@ -49,8 +22,8 @@ end
 
 task :default => :test
 
-require 'rdoc/task'
 
+require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
  version = Taxonifi::VERSION 
 

data/lib/{assessor → taxonifi/assessor}/row_assessor.rb

@@ -77,7 +77,9 @@ module Taxonifi
         end
 
         # this far? bad
-        raise RowAssessor::RowAssessorError
+        # raise RowAssessor::RowAssessorError
+
+        raise RowAssessorError
       end
 
       # Return the column representing the parent of the name

data/lib/{assessor → taxonifi}/assessor.rb

@@ -1,7 +1,6 @@
 module Taxonifi
 
-  require File.expand_path(File.join(File.dirname(__FILE__), 'base'))
-  require File.expand_path(File.join(File.dirname(__FILE__), 'row_assessor'))
+  Dir[File.join(__dir__, 'assessor', '*.rb')].each {|file| require file }
 
   class AssessorError < StandardError; end
 

data/lib/taxonifi/base.rb

@@ -0,0 +1,5 @@
+module Taxonifi
+  class ModelError < StandardError; end
+  module Model
+  end
+end

data/lib/{lumper → taxonifi/lumper}/name_index.rb

@@ -1,5 +1,3 @@
-require File.expand_path(File.join(File.dirname(__FILE__), '../taxonifi'))
-
 module Taxonifi::Lumper
   class NameIndex
     attr_accessor :index

data/lib/{lumper → taxonifi}/lumper.rb

@@ -1,16 +1,10 @@
-require File.expand_path(File.join(File.dirname(__FILE__), '../taxonifi'))
-
 # The lumper lumps! Tools for recognizing and using 
 # combinations of column types. 
 module Taxonifi::Lumper 
-
   # Define groups of columns/fields and include
   # functionality to determine whether your
   # columns match a given set.
   module Lumps
-    Dir.glob( File.expand_path(File.join(File.dirname(__FILE__), "lumps/*.rb") )) do |file|
-      require file
-    end
   end
 
   class LumperError < StandardError; end

data/lib/{model → taxonifi/model}/base.rb

@@ -1,9 +1,6 @@
 module Taxonifi
-  class ModelError < StandardError; end
   module Model
 
-    require File.expand_path(File.join(File.dirname(__FILE__), 'shared_class_methods'))
-
     # A base class for all Taxonifi::Models that represent
     # "individuals" (as opposed to collections of indviduals).  
     class Base 

data/lib/{model → taxonifi/model}/name_collection.rb

@@ -1,3 +1,6 @@
+
+require File.expand_path(File.join(File.dirname(__FILE__), 'collection'))
+
 module Taxonifi
   class NameCollectionError < StandardError; end
   module Model

data/lib/{splitter → taxonifi}/splitter.rb

@@ -14,12 +14,6 @@ module Taxonifi
 
     class SplitterError < StandardError; end
 
-    require File.expand_path(File.join(File.dirname(__FILE__), 'tokens'))
-    require File.expand_path(File.join(File.dirname(__FILE__), 'parser'))
-    require File.expand_path(File.join(File.dirname(__FILE__), 'lexer'))
-    require File.expand_path(File.join(File.dirname(__FILE__), 'builder'))
-
-
     # stub, we might not need
     class Splitter
       def initialize 

data/lib/{utils → taxonifi/utils}/array.rb

@@ -1,5 +1,3 @@
-require File.expand_path(File.join(File.dirname(__FILE__), '../taxonifi'))
-
 # Generic Array methods
 module Taxonifi::Utils
   module Array

data/lib/{utils → taxonifi/utils}/hash.rb

@@ -1,6 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), '../taxonifi'))
-
-# Generic Array methods
+# Generic Has methods
 module Taxonifi::Utils
   module Hash 
 

data/lib/taxonifi/version.rb

@@ -1,3 +1,3 @@
 module Taxonifi 
-  VERSION = "0.3.2"
+  VERSION = "0.3.3"
 end

data/lib/taxonifi.rb

@@ -1,5 +1,6 @@
 require 'csv'
 require 'fileutils'
+require 'require_all'
 
 # Everything in Taxonifi is in here.
 module Taxonifi
@@ -27,18 +28,10 @@ module Taxonifi
       species
       subspecies
       variety
-  }
 
-  require File.expand_path(File.join(File.dirname(__FILE__), 'splitter/splitter'))
-  require File.expand_path(File.join(File.dirname(__FILE__), 'assessor/assessor'))
-  require File.expand_path(File.join(File.dirname(__FILE__), 'export/export'))
+  }
 
-  # TODO use **/*.rb syntax
-  %w{model utils lumper}.each do |dir|
-    Dir.glob( File.expand_path(File.join(File.dirname(__FILE__), "#{dir}/*.rb") )) do |file|
-      require file
-    end
-  end
+  require_rel 'taxonifi'
 
 
 end

data/taxonifi.gemspec

@@ -28,19 +28,14 @@ Gem::Specification.new do |s|
   s.rubygems_version = "2.4.5"
 
   s.add_dependency "rake", '~> 10.4'
+  s.add_dependency "byebug", "~> 4.0"
+  s.add_dependency "require_all", "~> 1.3"
 
   s.add_development_dependency "bundler", "~> 1.9"
   s.add_development_dependency 'awesome_print', '~> 1.6'
   s.add_development_dependency 'did_you_mean', '~> 0.9'
-  s.add_development_dependency "byebug", "~> 4.0"
-  # s.add_development_dependency "rdoc", "~> 4.2"
-
+  s.add_development_dependency "rdoc", "~> 4.2"
   s.add_development_dependency "builder", "~> 3.2"
 
-
-  # Travis
-
-
-
 end
 

data/test/helper.rb

@@ -1,25 +1,12 @@
 require 'rubygems'
-require 'bundler'
-require 'byebug'
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/taxonifi'))
 
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
+require 'bundler/setup'
+Bundler.setup
 
+require 'byebug'
 require 'test/unit'
-#require 'shoulda'
 
-
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-
-class Test::Unit::TestCase
-end
+require File.expand_path(File.join(File.dirname(__FILE__), '../lib/taxonifi'))
 
 # TODO: rename to reflect format
 def generic_csv_with_names

data/test/test_export_prolog.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/export/export')) 
+require 'helper'
 
 class Test_ExportProlog < Test::Unit::TestCase
 
@@ -8,7 +7,6 @@ class Test_ExportProlog < Test::Unit::TestCase
     assert foo = e.export
   end 
 
-
 end 
 
 

data/test/test_exporter.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/export/export')) 
+require 'helper'
 
 class Test_TaxonifiExports < Test::Unit::TestCase
 

data/test/test_lumper_clump.rb

@@ -1,7 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/lumper/clump')) 
-
-# Builder construction
+require 'helper'
 
 class Test_TaxonifiLumperClump < Test::Unit::TestCase
 

data/test/test_lumper_geogs.rb

@@ -1,6 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-
-# Builder construction
+require 'helper'
 
 class Test_TaxonifiLumperGeogs < Test::Unit::TestCase
 

data/test/test_lumper_hierarchical_collection.rb

@@ -1,7 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/lumper/lumper')) 
-
-# Builder construction
+require 'helper'
 
 class Test_TaxonifiLumperHierarchicalCollection < Test::Unit::TestCase
 

data/test/test_lumper_names.rb

@@ -1,7 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/lumper/lumper')) 
-
-# Builder construction
+require 'helper'
 
 class Test_TaxonifiLumperNames < Test::Unit::TestCase
 

data/test/test_lumper_parent_child_name_collection.rb

@@ -1,4 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
+require 'helper'
 
 class Test_TaxonifiLumperParentChildNameCollection < Test::Unit::TestCase
 

data/test/test_lumper_refs.rb

@@ -1,7 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper')) 
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/lumper/lumper')) 
-
-# Builder construction
+require 'helper'
 
 class Test_TaxonifiLumperRefs < Test::Unit::TestCase
 

data/test/test_obo_nomenclature.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/export/export')) 
+require 'helper'
 
 class Test_TaxonifiExportOboNomenclature < Test::Unit::TestCase
 

data/test/test_parser.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/splitter/parser')) 
+require 'helper'
 
 class Test_TaxonifiSplitterParser < Test::Unit::TestCase
   # TODO: this could also go to builder related tests

data/test/test_splitter.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/splitter/splitter')) 
+require 'helper'
 
 class SplitterTest < Test::Unit::TestCase
   def test_truth

data/test/test_splitter_tokens.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/splitter/splitter')) 
+require 'helper'
 
 class Test_TaxonifiSplitterLexer < Test::Unit::TestCase
 

data/test/test_taxonifi.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/taxonifi'))
+require 'helper'
 
 class TestTaxonifi < Test::Unit::TestCase
 
@@ -7,5 +6,4 @@ class TestTaxonifi < Test::Unit::TestCase
     assert Taxonifi::RANKS
   end
 
-
 end

data/test/test_taxonifi_accessor.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/assessor/assessor')) 
+require 'helper'
 
 class Test_TaxonifiAccessor < Test::Unit::TestCase
 

data/test/test_taxonifi_base.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/model/base')) 
+require 'helper'
 
 class TestTaxonifiBase < Test::Unit::TestCase
 

data/test/test_taxonifi_geog.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/model/name')) 
+require 'helper'
 
 class TestTaxonifiGeog < Test::Unit::TestCase
 

data/test/test_taxonifi_name.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/model/name')) 
+require 'helper'
 
 class TestTaxonifiName < Test::Unit::TestCase
 

data/test/test_taxonifi_name_collection.rb

@@ -1,4 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
+require 'helper'
 
 class TestTaxonifiNameCollection < Test::Unit::TestCase
 

data/test/test_taxonifi_ref.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/model/ref')) 
+require 'helper'
 
 class TestTaxonifiRef < Test::Unit::TestCase
 

data/test/test_taxonifi_ref_collection.rb

@@ -1,5 +1,4 @@
 require 'helper'
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/model/ref_collection')) 
 
 class TestTaxonifiRefCollection < Test::Unit::TestCase
 

data/test/test_taxonifi_species_name.rb

@@ -1,5 +1,4 @@
-require File.expand_path(File.join(File.dirname(__FILE__), 'helper'))
-require File.expand_path(File.join(File.dirname(__FILE__), '../lib/model/species_name')) 
+require 'helper'
 
 class TestTaxonifiSpeciesName < Test::Unit::TestCase
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: taxonifi
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 0.3.3
 platform: ruby
 authors:
 - mjy
@@ -24,6 +24,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '10.4'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.0'
+- !ruby/object:Gem::Dependency
+  name: require_all
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -67,19 +95,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0.9'
 - !ruby/object:Gem::Dependency
-  name: byebug
+  name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '4.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '4.2'
 - !ruby/object:Gem::Dependency
   name: builder
   requirement: !ruby/object:Gem::Requirement
@@ -111,40 +139,41 @@ files:
 - LICENSE.txt
 - README.md
 - Rakefile
-- lib/assessor/assessor.rb
-- lib/assessor/base.rb
-- lib/assessor/row_assessor.rb
-- lib/export/export.rb
-- lib/export/format/base.rb
-- lib/export/format/obo_nomenclature.rb
-- lib/export/format/prolog.rb
-- lib/export/format/species_file.rb
-- lib/lumper/clump.rb
-- lib/lumper/lumper.rb
-- lib/lumper/lumps/parent_child_name_collection.rb
-- lib/lumper/name_index.rb
-- lib/model/author_year.rb
-- lib/model/base.rb
-- lib/model/collection.rb
-- lib/model/generic_object.rb
-- lib/model/geog.rb
-- lib/model/geog_collection.rb
-- lib/model/name.rb
-- lib/model/name_collection.rb
-- lib/model/person.rb
-- lib/model/ref.rb
-- lib/model/ref_collection.rb
-- lib/model/shared_class_methods.rb
-- lib/model/species_name.rb
-- lib/splitter/builder.rb
-- lib/splitter/lexer.rb
-- lib/splitter/parser.rb
-- lib/splitter/splitter.rb
-- lib/splitter/tokens.rb
 - lib/taxonifi.rb
+- lib/taxonifi/assessor.rb
+- lib/taxonifi/assessor/base.rb
+- lib/taxonifi/assessor/row_assessor.rb
+- lib/taxonifi/base.rb
+- lib/taxonifi/export.rb
+- lib/taxonifi/export/format/base.rb
+- lib/taxonifi/export/format/obo_nomenclature.rb
+- lib/taxonifi/export/format/prolog.rb
+- lib/taxonifi/export/format/species_file.rb
+- lib/taxonifi/lumper.rb
+- lib/taxonifi/lumper/clump.rb
+- lib/taxonifi/lumper/lumps/parent_child_name_collection.rb
+- lib/taxonifi/lumper/name_index.rb
+- lib/taxonifi/model/author_year.rb
+- lib/taxonifi/model/base.rb
+- lib/taxonifi/model/collection.rb
+- lib/taxonifi/model/generic_object.rb
+- lib/taxonifi/model/geog.rb
+- lib/taxonifi/model/geog_collection.rb
+- lib/taxonifi/model/name.rb
+- lib/taxonifi/model/name_collection.rb
+- lib/taxonifi/model/person.rb
+- lib/taxonifi/model/ref.rb
+- lib/taxonifi/model/ref_collection.rb
+- lib/taxonifi/model/shared_class_methods.rb
+- lib/taxonifi/model/species_name.rb
+- lib/taxonifi/splitter.rb
+- lib/taxonifi/splitter/builder.rb
+- lib/taxonifi/splitter/lexer.rb
+- lib/taxonifi/splitter/parser.rb
+- lib/taxonifi/splitter/tokens.rb
+- lib/taxonifi/utils/array.rb
+- lib/taxonifi/utils/hash.rb
 - lib/taxonifi/version.rb
-- lib/utils/array.rb
-- lib/utils/hash.rb
 - taxonifi.gemspec
 - test/file_fixtures/Fossil.csv
 - test/file_fixtures/Lygaeoidea.csv