taxonifi 0.5.5 → 0.6.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: c1007d26c853d41b9042410d3f206779ff70bcd7a5fbf0073709d33c6577d30e
+  metadata.gz: 3ea1c5278c07b5da29b0d47833aa5049ea1bf1a67d8ee0e0457e24642c6afe33
+  data.tar.gz: 4e3b2e214b36f2dd861321e9539ff15d0075d4713563b5b170332c55ed51eb37
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+  metadata.gz: 29a4108207df9f6087a1cc741b226e72ec9273907d5a2e999a316d7fe194a45ccb6c13c9d7594744e510a47939dcc8ccc566bce48798547bd7917e4cdf2dac7d
+  data.tar.gz: cbf0e3345cfee7110b79eff07152ba828f69a20be204aba2c7460597b7295fea61aa6791770ad5a90348e9afa28a50d225e68e885912929880fcb5bb295b1dbc

data/.github/workflows/ruby.yml

@@ -0,0 +1,41 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
+# For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
+
+name: Ruby
+
+on:
+  push:
+    branches: [ master, ruby3 ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        ruby: [2.6, 2.7, 3.0]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+    # To automatically get bug fixes and new Ruby versions for ruby/setup-ruby,
+    # change this to (see https://github.com/ruby/setup-ruby#versioning):
+    # uses: ruby/setup-ruby@v1
+      uses: ruby/setup-ruby@fdcfbcf14ec9672f6f615cb9589a1bc5dd69d262
+      with:
+        ruby-version: ${{ matrix.ruby }}
+    - name: Install dependencies
+      run: bundle install
+    - name: Show environment
+      run: gem environment
+    - name: Run tests
+      run: bundle exec rake
+    - name: Checking install works
+      run: rake install

data/.ruby-version

@@ -1 +1 @@
-2.6.5
+3.0.2

data/Gemfile.lock

@@ -1,20 +1,24 @@
 PATH
   remote: .
   specs:
-    taxonifi (0.5.5)
+    taxonifi (0.6.0)
       require_all (~> 3.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    awesome_print (1.8.0)
+    awesome_print (1.9.2)
     builder (3.2.4)
-    byebug (11.1.1)
-    power_assert (1.1.5)
-    rake (13.0.1)
-    rdoc (6.2.1)
+    byebug (11.1.3)
+    power_assert (2.0.1)
+    psych (4.0.3)
+      stringio
+    rake (13.0.6)
+    rdoc (6.4.0)
+      psych (>= 4.0.0)
     require_all (3.0.0)
-    test-unit (3.3.5)
+    stringio (3.0.1)
+    test-unit (3.3.9)
       power_assert
 
 PLATFORMS
@@ -31,4 +35,4 @@ DEPENDENCIES
   test-unit (~> 3.3.5)
 
 BUNDLED WITH
-   2.1.4
+   2.2.22

data/README.md

@@ -112,11 +112,11 @@ The following is an example that translates a DwC style input format as exported
 require 'taxonifi'
 file = File.expand_path(File.join(File.dirname(__FILE__), 'file_fixtures/Lygaeoidea-csv.tsv'))
 
-csv = CSV.read(file, { 
+csv = CSV.read(file,
   headers: true,
   col_sep: "\t",
   header_converters: :downcase
-} ) 
+)
 
 nc = Taxonifi::Lumper::Lumps::ParentChildNameCollection.name_collection(csv)
 e = Taxonifi::Export::SpeciesFile.new(:nc => nc, :authorized_user_id => 1)
@@ -131,10 +131,10 @@ Reading files
 taxonifi feeds on Ruby's CSV. read your files with header true, and downcased, e.g.:
 
 ```
-csv = CSV.read('input/my_data.tab',  { 
+csv = CSV.read('input/my_data.tab',
               headers: true,
               header_converters: :downcase,
-              col_sep: "\t"  } ) 
+              col_sep: "\t")
 ```
 
 # Code organization

data/lib/taxonifi/assessor/row_assessor.rb

@@ -79,6 +79,7 @@ module Taxonifi
         # this far? bad
         # raise RowAssessor::RowAssessorError
 
+        # TODO: add an error message that can be relayed on here and elsewhere
         raise RowAssessorError
       end
 

data/lib/taxonifi/version.rb

@@ -1,3 +1,3 @@
 module Taxonifi 
-  VERSION = "0.5.5"
+  VERSION = "0.6.0"
 end

data/taxonifi.gemspec

@@ -29,7 +29,7 @@ Gem::Specification.new do |s|
   s.metadata = { "source_code_uri" => "https://github.com/SpeciesFileGroup/taxonifi" }
 
   s.add_dependency "require_all", "~> 3.0"
-  s.required_ruby_version = '~> 2.6'
+  s.required_ruby_version = '>= 2.6', '< 4'
 
   s.add_development_dependency "rake", '~> 13.0'
   s.add_development_dependency "byebug", "~> 11"

data/test/helper.rb

@@ -22,16 +22,16 @@ def generic_csv_with_names
     csv << [6, "3", "Foo bar stuff (Guy, 1921)", "species", "Foo bar blorf (Guy, 1921)"] # initial subspecies rank data had rank blank, assuming they will be called species
   end
 
-  @csv = CSV.parse(@csv_string, {headers: true})
+  @csv = CSV.parse(@csv_string, headers: true)
 end
 
 def names
   file = File.expand_path(File.join(File.dirname(__FILE__), 'file_fixtures/names.csv'))
 
-  csv = CSV.read(file, { 
+  csv = CSV.read(file,
     headers: true,
     col_sep: ",",
     header_converters: :downcase
-  } ) 
+  )
   nc = Taxonifi::Lumper.create_name_collection(csv: csv, initial_id: 1) 
 end

data/test/test_exporter.rb

@@ -16,11 +16,11 @@ class Test_TaxonifiExports < Test::Unit::TestCase
   def test_big_file
     file = File.expand_path(File.join(File.dirname(__FILE__), 'file_fixtures/Lygaeoidea.csv'))
 
-    csv = CSV.read(file, { 
+    csv = CSV.read(file,
       headers: true,
       col_sep: ",",
       header_converters: :downcase
-    } ) 
+    )
 
     nc = Taxonifi::Lumper::Lumps::ParentChildNameCollection.name_collection(csv)
     nc.generate_ref_collection(1)
@@ -32,11 +32,11 @@ class Test_TaxonifiExports < Test::Unit::TestCase
   def test_little_file_linkages
     file = File.expand_path(File.join(File.dirname(__FILE__), 'file_fixtures/Fossil.csv'))
 
-    csv = CSV.read(file, { 
+    csv = CSV.read(file,
       headers: true,
       col_sep: ",",
       header_converters: :downcase
-    } ) 
+    )
 
     nc = Taxonifi::Lumper.create_name_collection(:csv => csv, :initial_id => 1) 
     rc = Taxonifi::Lumper.create_ref_collection(:csv => csv) 

data/test/test_lumper_clump.rb

@@ -9,7 +9,7 @@ class Test_TaxonifiLumperClump < Test::Unit::TestCase
       csv << ["Fooidae", "Foo", "bar", "Smith", "1854"]
     end
 
-    @csv = CSV.parse(@csv_string, {headers: true})
+    @csv = CSV.parse(@csv_string, headers: true)
   end
 
   def test_new_clump_without_params_can_be_created

data/test/test_lumper_geogs.rb

@@ -23,7 +23,7 @@ class Test_TaxonifiLumperGeogs < Test::Unit::TestCase
     # The name_index looks like
     # {:country => {"Canada" => 0, "USA" => 2, "Utopia" => 5} ... etc.
 
-    @csv = CSV.parse(@csv_string, {headers: true})
+    @csv = CSV.parse(@csv_string, headers: true)
   end
 
   def _create_a_collection

data/test/test_lumper_hierarchical_collection.rb

@@ -9,7 +9,7 @@ class Test_TaxonifiLumperHierarchicalCollection < Test::Unit::TestCase
       csv << %w{a b c}
     end
 
-    @csv = CSV.parse(@csv_string, {headers: true})
+    @csv = CSV.parse(@csv_string, headers: true)
   end
 
   def test_that_create_hierarchical_collection_creates_collection
@@ -48,7 +48,7 @@ class Test_TaxonifiLumperHierarchicalCollection < Test::Unit::TestCase
       csv <<  @headers
       csv << ["a", nil, "c"]
     end
-    csv = CSV.parse(csv_string, {headers: true})
+    csv = CSV.parse(csv_string, headers: true)
     c = Taxonifi::Lumper.create_hierarchical_collection(csv, %w{a b c})
     assert_equal nil, c.collection.first.parent
     assert_equal "a", c.collection[1].parent.name
@@ -61,7 +61,7 @@ class Test_TaxonifiLumperHierarchicalCollection < Test::Unit::TestCase
       csv << ["a", "b", "d"]
       csv << ["e", "b", "f"]
     end
-    csv = CSV.parse(csv_string, {headers: true})
+    csv = CSV.parse(csv_string, headers: true)
     c = Taxonifi::Lumper.create_hierarchical_collection(csv, %w{a b c})
     assert_equal %w{a b c d e b f}, c.collection.collect{|o| o.name}
     assert_equal 7, c.collection.size

data/test/test_lumper_names.rb

@@ -9,7 +9,7 @@ class Test_TaxonifiLumperNames < Test::Unit::TestCase
       csv << ["Fooidae", "Foo", "bar", "Smith", "1854"]
     end
 
-    @csv = CSV.parse(@csv_string, {headers: true})
+    @csv = CSV.parse(@csv_string, headers: true)
   end
 
   def test_that_setup_setups
@@ -69,7 +69,7 @@ class Test_TaxonifiLumperNames < Test::Unit::TestCase
     # 1 3 6
     # 0 4 7
 
-    csv = CSV.parse(string, {headers: true})
+    csv = CSV.parse(string, headers: true)
     nc = Taxonifi::Lumper.create_name_collection(:csv => csv)
 
     assert_equal nc.collection[2], nc.collection[5].parent
@@ -93,7 +93,7 @@ class Test_TaxonifiLumperNames < Test::Unit::TestCase
     # 2  bar
     # 3  foo 
 
-    csv = CSV.parse(string, {headers: true})
+    csv = CSV.parse(string, headers: true)
     nc = Taxonifi::Lumper.create_name_collection(:csv => csv)
     assert_equal 2, nc.collection[3].authors.size
     assert_equal 'Smith', nc.collection[3].authors.first.last_name
@@ -125,7 +125,7 @@ class Test_TaxonifiLumperNames < Test::Unit::TestCase
     # 1  Foo
     # 2  bar
 
-    csv = CSV.parse(string, {headers: true})
+    csv = CSV.parse(string, headers: true)
     nc = Taxonifi::Lumper.create_name_collection(:csv => csv)
     assert_equal nil, nc.collection[2].properties['foo']
     assert_equal "1", nc.collection[2].properties['bar']          # !!! everything converted to String
@@ -149,7 +149,7 @@ class Test_TaxonifiLumperNames < Test::Unit::TestCase
     # 5  varblorf 
     # 6  varbliff 
 
-    csv = CSV.parse(string, {headers: true})
+    csv = CSV.parse(string, headers: true)
     nc = Taxonifi::Lumper.create_name_collection(:csv => csv)
 
     assert_equal nc.collection[1], nc.collection[2].parent

data/test/test_lumper_parent_child_name_collection.rb

@@ -14,7 +14,7 @@ class Test_TaxonifiLumperParentChildNameCollection < Test::Unit::TestCase
       csv << [5, "0", "Bidae", "Family", nil ]
     end
 
-    @csv = CSV.parse(@csv_string, {headers: true})
+    @csv = CSV.parse(@csv_string, headers: true)
   end
 
   def create_a_collection
@@ -54,7 +54,7 @@ class Test_TaxonifiLumperParentChildNameCollection < Test::Unit::TestCase
     # csv <<    [7,  3,   'Neortholomus (Neortholomus) blorf (Say, 1832)','species'] 
     # csv <<    [8,  3,   'Neortholomus (Neortholomus) blorf (Say, 1832)','species']
     end
-    csv = CSV.parse(csv_string, {headers: true})
+    csv = CSV.parse(csv_string, headers: true)
 
     nc = Taxonifi::Lumper::Lumps::ParentChildNameCollection.name_collection(csv)
    

data/test/test_lumper_refs.rb

@@ -9,7 +9,7 @@ class Test_TaxonifiLumperRefs < Test::Unit::TestCase
       csv << ["Smith J. and Barnes S.", "2012", "Bar and foo", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)" ]
     end
 
-    @csv = CSV.parse(@csv_string, {headers: true})
+    @csv = CSV.parse(@csv_string, headers: true)
   end
 
   def test_available_lumps
@@ -23,7 +23,7 @@ class Test_TaxonifiLumperRefs < Test::Unit::TestCase
         csv << ["Smith J. and Barnes S."]
       end
 
-     csv = CSV.parse(csv_string, {headers: true})
+     csv = CSV.parse(csv_string, headers: true)
 
      assert_equal [:citation_basic, :citation_small], Taxonifi::Lumper.intersecting_lumps(csv.headers)
      assert_equal [], Taxonifi::Lumper.available_lumps(csv.headers)
@@ -56,7 +56,7 @@ class Test_TaxonifiLumperRefs < Test::Unit::TestCase
       csv << ["Smith J. and Barnes S.", "2012", "Bar and foo", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)" ]
       csv << ["Smith J. and Barnes S.", "2012", "Bar and foo", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)" ]
     end
-    csv = CSV.parse(csv_string, {headers: true})
+    csv = CSV.parse(csv_string, headers: true)
     rc = Taxonifi::Lumper.create_ref_collection(:csv => csv)
     assert_equal 1, rc.collection.size
   end
@@ -68,7 +68,7 @@ class Test_TaxonifiLumperRefs < Test::Unit::TestCase
       csv << ["Smith J. and Barnes S.", "2012", "Bar and foo", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)" ]
       csv << ["Smith J. and Bartes S.", "2012", "Bar and foo", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)" ]
     end
-    csv = CSV.parse(csv_string, {headers: true})
+    csv = CSV.parse(csv_string, headers: true)
     rc = Taxonifi::Lumper.create_ref_collection(:csv => csv)
     assert_equal 2, rc.collection.size
   end
@@ -79,7 +79,7 @@ class Test_TaxonifiLumperRefs < Test::Unit::TestCase
       csv << ["Smith J. and Barnes S.", "2012", "Bar and foo", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)" ]
       csv << ["Smith J.", "2012", "Foo and bar", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)" ]
     end
-    csv = CSV.parse(csv_string, {headers: true})
+    csv = CSV.parse(csv_string, headers: true)
     rc = Taxonifi::Lumper.create_ref_collection(:csv => csv)
     assert_equal "Foo and bar", rc.object_from_row(1).title
   end
@@ -90,7 +90,7 @@ class Test_TaxonifiLumperRefs < Test::Unit::TestCase
       csv << ["Smith J. and Barnes S.", "2012", "Bar and foo", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)", "foo value", 1 ]
       csv << ["Smith J.", "2012", "Foo and bar", "Journal of Foo", "2", "3", "2-3, 190", nil, "2", "4", "2(4)", nil, "bar value" ]
     end
-    csv = CSV.parse(csv_string, {headers: true})
+    csv = CSV.parse(csv_string, headers: true)
     rc = Taxonifi::Lumper.create_ref_collection(:csv => csv)
   
     assert_equal "foo value", rc.collection.first.properties['foo'] 

data/test/test_taxonifi_accessor.rb

@@ -14,7 +14,7 @@ class Test_TaxonifiAccessor < Test::Unit::TestCase
       csv << ["Fooidae", "Bar",    nil,     "bar",   nil,      "varbar", "Smith",  "1854"]   # 5
     end
 
-    @csv = CSV.parse(@csv_string, {headers: true, header_converters: :downcase})
+    @csv = CSV.parse(@csv_string, headers: true, header_converters: :downcase)
   end
 
   def test_first_available
@@ -46,7 +46,7 @@ class Test_TaxonifiAccessor < Test::Unit::TestCase
         csv <<  headers
         csv << ["Smith J. and Barnes S."]
       end
-     csv = CSV.parse(csv_string, {headers: true})
+     csv = CSV.parse(csv_string, headers: true)
      assert_equal [:citation_basic, :citation_small],  Taxonifi::Assessor::RowAssessor.intersecting_lumps_with_data(csv.first)
   end 
 
@@ -57,7 +57,7 @@ class Test_TaxonifiAccessor < Test::Unit::TestCase
         csv << ["Smith J. and Barnes S.", 1912, "Foo", "Bar", "3(4)", "1-2"]
       end
 
-     csv = CSV.parse(csv_string, {headers: true})
+     csv = CSV.parse(csv_string, headers: true)
 
      assert_equal [:citation_small],  Taxonifi::Assessor::RowAssessor.lumps_with_data(csv.first)
   end

metadata

@@ -1,11 +1,11 @@
 --- !ruby/object:Gem::Specification
 name: taxonifi
 version: !ruby/object:Gem::Version
-  version: 0.5.5
+  version: 0.6.0
 platform: ruby
 authors:
 - Matt Yoder
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
 date: 2013-03-27 00:00:00.000000000 Z
@@ -132,6 +132,7 @@ extra_rdoc_files:
 - README.md
 files:
 - ".document"
+- ".github/workflows/ruby.yml"
 - ".gitignore"
 - ".ruby-version"
 - ".travis.yml"
@@ -206,23 +207,26 @@ licenses:
 - MIT
 metadata:
   source_code_uri: https://github.com/SpeciesFileGroup/taxonifi
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - "~>"
+  - - ">="
     - !ruby/object:Gem::Version
       version: '2.6'
+  - - "<"
+    - !ruby/object:Gem::Version
+      version: '4'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.6
-signing_key: 
+rubygems_version: 3.2.22
+signing_key:
 specification_version: 4
 summary: A general purpose framework for scripted handling of taxonomic names or other
   heirarchical metadata.