text-checkm 0.7 → 0.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f46c51dd805d1e12eb1d3c91aa0f238f9f0760951e585c2b47f4bd03e34fe253
-  data.tar.gz: 68d29caa7df2d95a133f05b301939569819c0c5bd993bedc4a2cc7e94e5a3db0
+  metadata.gz: bcc35642292821b3460859c527401f0d90b93d00d7c8913746b64c030d922c93
+  data.tar.gz: 6d95a7592d6c845035875e2fc468e09baf81c15798c19ffadbf529fcb22f41a8
 SHA512:
-  metadata.gz: 1c99abc9034038707e8edc566cb7cc91996d098840d98dd63305c780667b2f192969191c04b1216169f6804a7701c7a3ca2780b6f8a173303ff564f1f1486f71
-  data.tar.gz: f8e3c007325b03ce145cb477f3bae2317a5d8fa0da89b6b52b80aef2658ec74beada9827e75465d005790e1b32c6da1532cda6530e13a0847bd8d65e7e9b85bc
+  metadata.gz: 77ee69c083ab4451743816398933e90cf1e33483a057eee94517685be079b95c9a51230017625e40febfec8a0e3130880e76cc91d4b35bd094708ba3a3344be5
+  data.tar.gz: c67b27ac48cd5bdeb8e4e6d6490f06604d125d2a1e163026971992999dfaf63a93034d477e2ed9809923e2c5313ef6d05b014bd46e77ed97528f00f25fd685ce

data/.gitignore

@@ -7,6 +7,9 @@
 # Additional IDEA/RubyMine ignores
 .idea/.rakeTasks
 
+# Don't commit Gemfile.lock for libraries
+Gemfile.lock
+
 # Build/test artifacts
 /artifacts/
 

data/.rubocop.yml

@@ -5,10 +5,7 @@ AllCops:
     - 'db/**/*'
     - 'out/**/*'
     - 'node_modules/**/*'
-
-# Added in RuboCop 0.83
-Layout/EmptyLinesAroundAttributeAccessor:
-  Enabled: true
+    - 'vendor/**/*'
 
 # Allow one line around block body (Layout/EmptyLines will still disallow two or more)
 Layout/EmptyLinesAroundBlockBody:
@@ -34,26 +31,6 @@ Layout/MultilineMethodCallIndentation:
 Layout/MultilineOperationIndentation:
   Enabled: false
 
-# Added in RuboCop 0.84
-Lint/DeprecatedOpenSSLConstant:
-  Enabled: true
-
-# Added in RuboCop 0.81
-Lint/RaiseException:
-  Enabled: true
-
-# Added in RuboCop 0.85
-Lint/MixedRegexpCaptureTypes:
-  Enabled: true
-
-# Added in RuboCop 0.82
-Layout/SpaceAroundMethodCallOperator:
-  Enabled: true
-
-# Added in RuboCop 0.81
-Lint/StructNewOverride:
-  Enabled: true
-
 # We meant to do that
 Naming/MemoizedInstanceVariableName:
   Enabled: False
@@ -82,10 +59,6 @@ Style/CommentedKeyword:
 Style/Documentation:
   Enabled: false
 
-# Added in RuboCop 0.82
-Style/ExponentialNotation:
-  Enabled: false
-
 # Adding more line noise to format strings will not improve them
 Style/FormatStringToken:
   Enabled: false
@@ -94,18 +67,6 @@ Style/FormatStringToken:
 Style/FrozenStringLiteralComment:
   Enabled: false
 
-# Added in RuboCop 0.80
-Style/HashEachMethods:
-  Enabled: true
-
-# Added in RuboCop 0.80
-Style/HashTransformKeys:
-  Enabled: true
-
-# Added in RuboCop 0.80
-Style/HashTransformValues:
-  Enabled: true
-
 # Requiring the lambda() method just makes wordy calls wordier
 Style/Lambda:
   EnforcedStyle: literal
@@ -114,18 +75,6 @@ Style/Lambda:
 Style/NumericPredicate:
   Enabled: false
 
-# Added in RuboCop 0.86
-Style/RedundantFetchBlock:
-  Enabled: true
-
-# Added in RuboCop 0.85
-Style/RedundantRegexpCharacterClass:
-  Enabled: true
-
-# Added in RuboCop 0.85
-Style/RedundantRegexpEscape:
-  Enabled: true
-
 # Don't be unnecessarily redundant
 Style/ReturnNil:
   Enabled: true
@@ -135,10 +84,98 @@ Style/ReturnNil:
 Style/SingleLineBlockParams:
   Enabled: false
 
-# Added in RuboCop 0.83
-Style/SlicingWithRange:
-  Enabled: true
-
 # The semantics of `foo&.bar` are a lot less interchangeable with `foo && foo.bar` than RuboCop thinks
 Style/SafeNavigation:
   Enabled: false
+
+############################################################
+
+Gemspec/DateAssignment: # (new in 1.10)
+  Enabled: true
+Layout/EmptyLinesAroundAttributeAccessor: # (new in 0.83)
+    Enabled: true
+Layout/SpaceAroundMethodCallOperator: # (new in 0.82)
+    Enabled: true
+Layout/SpaceBeforeBrackets: # (new in 1.7)
+  Enabled: true
+Lint/AmbiguousAssignment: # (new in 1.7)
+  Enabled: true
+Lint/DeprecatedConstants: # (new in 1.8)
+  Enabled: true
+Lint/DeprecatedOpenSSLConstant: # (new in 0.84)
+    Enabled: true
+Lint/DuplicateBranch: # (new in 1.3)
+  Enabled: true
+Lint/DuplicateRegexpCharacterClassElement: # (new in 1.1)
+  Enabled: true
+Lint/EmptyBlock: # (new in 1.1)
+  Enabled: true
+Lint/EmptyClass: # (new in 1.3)
+  Enabled: true
+Lint/LambdaWithoutLiteralBlock: # (new in 1.8)
+  Enabled: true
+Lint/MixedRegexpCaptureTypes: # (new in 0.85)
+    Enabled: true
+Lint/NoReturnInBeginEndBlocks: # (new in 1.2)
+  Enabled: true
+Lint/NumberedParameterAssignment: # (new in 1.9)
+  Enabled: true
+Lint/OrAssignmentToConstant: # (new in 1.9)
+  Enabled: true
+Lint/RaiseException: # (new in 0.81)
+    Enabled: true
+Lint/RedundantDirGlobSort: # (new in 1.8)
+  Enabled: true
+Lint/StructNewOverride: # (new in 0.81)
+    Enabled: true
+Lint/SymbolConversion: # (new in 1.9)
+  Enabled: true
+Lint/ToEnumArguments: # (new in 1.1)
+  Enabled: true
+Lint/TripleQuotes: # (new in 1.9)
+  Enabled: true
+Lint/UnexpectedBlockArity: # (new in 1.5)
+  Enabled: true
+Lint/UnmodifiedReduceAccumulator: # (new in 1.1)
+  Enabled: true
+Style/ArgumentsForwarding: # (new in 1.1)
+  Enabled: true
+Style/CollectionCompact: # (new in 1.2)
+  Enabled: true
+Style/DocumentDynamicEvalDefinition: # (new in 1.1)
+  Enabled: true
+Style/EndlessMethod: # (new in 1.8)
+  Enabled: true
+Style/ExponentialNotation: # (new in 0.82)
+    Enabled: false
+Style/HashConversion: # (new in 1.10)
+  Enabled: true
+Style/HashEachMethods: # (new in 0.80)
+    Enabled: true
+Style/HashExcept: # (new in 1.7)
+  Enabled: true
+Style/HashTransformKeys: # (new in 0.80)
+    Enabled: true
+Style/HashTransformValues: # (new in 0.80)
+    Enabled: true
+Style/IfWithBooleanLiteralBranches: # (new in 1.9)
+  Enabled: true
+Style/NegatedIfElseCondition: # (new in 1.2)
+  Enabled: true
+Style/NilLambda: # (new in 1.3)
+  Enabled: true
+Style/RedundantArgument: # (new in 1.4)
+  Enabled: true
+Style/RedundantFetchBlock: # (new in 0.86)
+    Enabled: true
+Style/RedundantRegexpCharacterClass: # (new in 0.85)
+    Enabled: true
+Style/RedundantRegexpEscape: # (new in 0.85)
+    Enabled: true
+Style/SlicingWithRange: # (new in 0.83)
+    Enabled: true
+Style/StringChars: # (new in 1.12)
+  Enabled: true
+Style/SwapValues: # (new in 1.1)
+  Enabled: true
+

data/.ruby-version

@@ -1 +1 @@
-2.7.0
+2.7.2

data/.travis.yml

@@ -0,0 +1,2 @@
+language: ruby
+

data/CHANGELOG.md

@@ -1,3 +1,8 @@
+# 0.8 (5 May 2021)
+
+- don't check in `Gemfile.lock`
+- set `required_ruby_version` to >= 2.7 in gemspec
+
 # 0.7 (22 July 2020)
 
 - fork from [ruby-microservices/checkm@b7a23d6](https://github.com/ruby-microservices/checkm/tree/b7a23d6a72af643cb9554bf16ff49fc27eded827)

data/Gemfile

@@ -1,2 +1,2 @@
-source 'http://rubygems.org'
+source 'https://rubygems.org'
 gemspec

data/LICENSE.md

@@ -2,7 +2,7 @@
 
 Copyright © 2010 Chris Beer
 
-Copyright © 2020 The Regents of the University of California
+Copyright © 2021 The Regents of the University of California
 
 Permission is hereby granted, free of charge, to any person obtaining a
 copy of this software and associated documentation files (the “Software”),

data/README.md

@@ -1,5 +1,8 @@
 # Text::Checkm
 
+[![Build Status](https://travis-ci.org/dmolesUC/text-checkm.svg?branch=master)](https://travis-ci.org/dmolesUC/text-checkm)
+[![Gem Version](https://img.shields.io/gem/v/text-checkm.svg)](https://github.com/dmolesUC/text-checkm/releases)
+
 Ruby implementation of
 [Checkm](https://confluence.ucop.edu/display/Curation/Checkm), a
 general-purpose text-based file manifest format developed at the
@@ -10,14 +13,10 @@ Abrams, and David Loy.
 
 ## Copyright
 
-Based on [checkm](https://github.com/ruby-microservices/checkm/), copyright
-© 2010 Chris Beer. (For compliance with [UC policies on the use and
-creation of open source
-software](https://security.ucop.edu/resources/open-source-software-licensing.html),
-this library is based on
-[ruby-microservices/checkm@b7a23d6](https://github.com/ruby-microservices/checkm/tree/b7a23d6a72af643cb9554bf16ff49fc27eded827),
+Based on [checkm](https://github.com/ruby-microservices/checkm/), © 2010 Chris Beer.
+(For compliance with [UC policies on the use and creation of open source software](https://security.ucop.edu/resources/open-source-software-licensing.html),
+this library is based on [ruby-microservices/checkm@b7a23d6](https://github.com/ruby-microservices/checkm/tree/b7a23d6a72af643cb9554bf16ff49fc27eded827),
 the last MIT-licensed revision.)
 
-Subsequent work © 2020 the Regents of the University of California. See
+Subsequent work © 2021 the Regents of the University of California. See
 [LICENSE.md](LICENSE.md) for more details.
-

data/lib/text/checkm/entry.rb

@@ -26,12 +26,10 @@ module Text
         @manifest = manifest
       end
 
-      # rubocop:disable Style/MethodMissingSuper
       def method_missing(sym, *_args)
         # TODO: something less extreme
         @values[@fields.index(sym.to_s.downcase) || BASE_FIELDS.index(sym.to_s.downcase)]
       end
-      # rubocop:enable Style/MethodMissingSuper
 
       def respond_to_missing?(sym, *)
         @fields.include?(sym.to_s.downcase) || BASE_FIELDS.include?(sym.to_s.downcase)
@@ -70,7 +68,7 @@ module Text
       def valid_multilevel?
         return true unless sourcefileorurl =~ /^@/
 
-        Manifest.parse(URI.open(source).read, path: File.dirname(source))
+        Manifest.parse(File.read(source), path: File.dirname(source))
       end
     end
   end

data/lib/text/checkm/manifest.rb

@@ -7,10 +7,7 @@ module Text
         Manifest.new str, args
       end
 
-      attr_reader :version
-      attr_reader :entries
-      attr_reader :fields
-      attr_reader :path
+      attr_reader :version, :entries, :fields, :path
 
       # rubocop:disable Metrics/MethodLength
       def initialize(checkm, args = {})
@@ -66,23 +63,22 @@ module Text
       def parse_lines
         @lines.each do |line|
           case line
+          when /^$/
+            # do nothing
           when /^#%/
             parse_header line
           when /^#/
             parse_comment line
-          when /^$/
-            # do nothing
-          when /^@/
-            parse_line line
+          # when /^@/
+          #   parse_line line
           else
             parse_line line
           end
         end
       end
-
       # rubocop:enable Metrics/MethodLength
 
-      # rubocop:disable Metrics/MethodLength, Metrics/CyclomaticComplexity
+      # rubocop:disable Metrics/MethodLength
       def parse_header(line)
         case line
         when /^#%checkm/
@@ -94,14 +90,11 @@ module Text
           list = line.split('|')
           list.shift
           @fields = list.map { |v| v.strip.downcase }
-        when /^#%prefix/
-          # do nothing
-        when /^#%profile/
+        when /^#%prefix/, /^#%profile/
           # do nothing
         end
       end
-
-      # rubocop:enable Metrics/MethodLength, Metrics/CyclomaticComplexity
+      # rubocop:enable Metrics/MethodLength
 
       def parse_comment(_line)
         # do nothing

data/lib/text/checkm/module_info.rb

@@ -7,7 +7,7 @@ module Text
       SUMMARY = 'Ruby implementation of the Checkm text manifest format'.freeze
       DESCRIPTION = 'A Ruby implementation of the Checkm checksum-based text manifest format'.freeze
       LICENSE = 'MIT'.freeze
-      VERSION = '0.7'.freeze
+      VERSION = '0.8'.freeze
       HOMEPAGE = 'https://github.com/dmolesUC/checkm'.freeze
 
       private_class_method :new

data/text-checkm.gemspec

@@ -16,14 +16,17 @@ Gem::Specification.new do |spec|
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ['lib']
 
-  spec.add_development_dependency 'bundle-audit'
-  spec.add_development_dependency 'ci_reporter_rspec'
-  spec.add_development_dependency 'colorize'
-  spec.add_development_dependency 'irb' # workaroundfor https://github.com/bundler/bundler/issues/6929
+  spec.required_ruby_version = '>= 2.7'
+
+  spec.add_development_dependency 'bundle-audit', '~> 0.1'
+  spec.add_development_dependency 'ci_reporter_rspec', '~> 1.0'
+  spec.add_development_dependency 'colorize', '~> 0.8'
+  spec.add_development_dependency 'irb', '~> 1.3' # workaroundfor https://github.com/bundler/bundler/issues/6929
   spec.add_development_dependency 'listen', '>= 3.0.5', '< 3.2'
-  spec.add_development_dependency 'rake', '>= 13.0'
-  spec.add_development_dependency 'rspec-support'
-  spec.add_development_dependency 'rubocop', '0.86'
-  spec.add_development_dependency 'simplecov', '~> 0.16.1'
-  spec.add_development_dependency 'simplecov-rcov'
+  spec.add_development_dependency 'rake', '~> 13.0'
+  spec.add_development_dependency 'rspec-support', '~> 3.10'
+  spec.add_development_dependency 'rubocop', '1.14'
+  spec.add_development_dependency 'rubocop-rake', '0.5'
+  spec.add_development_dependency 'simplecov', '~> 0.21'
+  spec.add_development_dependency 'simplecov-rcov', '~> 0.2'
 end

data/text-checkm.iml

@@ -1,51 +1,95 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <module type="RUBY_MODULE" version="4">
+  <component name="ModuleRunConfigurationManager">
+    <shared />
+  </component>
   <component name="NewModuleRootManager" inherit-compiler-output="true">
     <exclude-output />
     <content url="file://$MODULE_DIR$" />
-    <orderEntry type="jdk" jdkName="RVM: ruby-2.7.0" jdkType="RUBY_SDK" />
+    <orderEntry type="jdk" jdkName="RVM: ruby-2.7.2" jdkType="RUBY_SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="library" scope="PROVIDED" name="ast (v2.4.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="builder (v3.2.4, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="bundle-audit (v0.1.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="bundler (v2.1.2, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="bundler-audit (v0.7.0.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="ci_reporter (v2.0.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="ci_reporter_rspec (v1.0.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="colorize (v0.8.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="diff-lcs (v1.4.4, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="docile (v1.3.2, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="ffi (v1.13.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="io-console (v0.5.6, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="irb (v1.2.4, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="json (v2.3.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="listen (v3.1.5, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="parallel (v1.19.2, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="parser (v2.7.1.4, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rainbow (v3.0.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rake (v13.0.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rb-fsevent (v0.10.4, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rb-inotify (v0.10.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="regexp_parser (v1.7.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="reline (v0.1.4, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rexml (v3.2.4, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rspec (v3.9.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rspec-core (v3.9.2, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rspec-expectations (v3.9.2, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rspec-mocks (v3.9.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rspec-support (v3.9.3, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rubocop (v0.86.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="rubocop-ast (v0.2.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="ruby-progressbar (v1.10.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="ruby_dep (v1.5.0, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="simplecov (v0.16.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="simplecov-html (v0.10.2, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="simplecov-rcov (v0.2.3, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="thor (v1.0.1, RVM: ruby-2.7.0) [gem]" level="application" />
-    <orderEntry type="library" scope="PROVIDED" name="unicode-display_width (v1.7.0, RVM: ruby-2.7.0) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ast (v2.4.2, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="builder (v3.2.4, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="bundle-audit (v0.1.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="bundler (v2.1.4, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="bundler-audit (v0.8.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ci_reporter (v2.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ci_reporter_rspec (v1.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="colorize (v0.8.1, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="diff-lcs (v1.4.4, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="docile (v1.3.5, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ffi (v1.15.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="io-console (v0.5.9, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="irb (v1.3.5, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="listen (v3.1.5, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="parallel (v1.20.1, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="parser (v3.0.1.1, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rainbow (v3.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rake (v13.0.3, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rb-fsevent (v0.10.4, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rb-inotify (v0.10.1, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="regexp_parser (v2.1.1, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="reline (v0.2.5, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rexml (v3.2.5, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rspec (v3.10.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rspec-core (v3.10.1, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rspec-expectations (v3.10.1, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rspec-mocks (v3.10.2, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rspec-support (v3.10.2, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rubocop (v1.14.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rubocop-ast (v1.5.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="rubocop-rake (v0.5.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ruby-progressbar (v1.11.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="ruby_dep (v1.5.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="simplecov (v0.21.2, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="simplecov-html (v0.12.3, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="simplecov-rcov (v0.2.3, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="simplecov_json_formatter (v0.1.3, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="thor (v1.1.0, RVM: ruby-2.7.2) [gem]" level="application" />
+    <orderEntry type="library" scope="PROVIDED" name="unicode-display_width (v2.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
   </component>
   <component name="RModuleSettingsStorage">
     <LOAD_PATH number="2" string0="$MODULE_DIR$/lib" string1="$MODULE_DIR$/spec" />
     <I18N_FOLDERS number="0" />
   </component>
+  <component name="RakeTasksCache">
+    <option name="myRootTask">
+      <RakeTaskImpl id="rake">
+        <subtasks>
+          <RakeTaskImpl id="bundle">
+            <subtasks>
+              <RakeTaskImpl description="Updates the ruby-advisory-db then runs bundle-audit" fullCommand="bundle:audit" id="audit" />
+            </subtasks>
+          </RakeTaskImpl>
+          <RakeTaskImpl description="Run all specs in spec directory, with coverage" fullCommand="coverage" id="coverage" />
+          <RakeTaskImpl description="Run tests, check test coverage, check code style" fullCommand="default" id="default" />
+          <RakeTaskImpl description="Run RuboCop with auto-correct, and output results to console" fullCommand="ra" id="ra" />
+          <RakeTaskImpl description="Run rubocop with HTML output" fullCommand="rubocop" id="rubocop" />
+          <RakeTaskImpl id="rubocop">
+            <subtasks>
+              <RakeTaskImpl description="Auto-correct RuboCop offenses" fullCommand="rubocop:auto_correct" id="auto_correct" />
+            </subtasks>
+          </RakeTaskImpl>
+          <RakeTaskImpl description="Run all tests" fullCommand="spec" id="spec" />
+          <RakeTaskImpl id="spec">
+            <subtasks>
+              <RakeTaskImpl description="Run all tests" fullCommand="spec:all" id="all" />
+            </subtasks>
+          </RakeTaskImpl>
+          <RakeTaskImpl id="ci">
+            <subtasks>
+              <RakeTaskImpl id="setup">
+                <subtasks>
+                  <RakeTaskImpl description="" fullCommand="ci:setup:rspec" id="rspec" />
+                  <RakeTaskImpl description="" fullCommand="ci:setup:rspecbase" id="rspecbase" />
+                  <RakeTaskImpl description="" fullCommand="ci:setup:rspecdoc" id="rspecdoc" />
+                  <RakeTaskImpl description="" fullCommand="ci:setup:spec_report_cleanup" id="spec_report_cleanup" />
+                </subtasks>
+              </RakeTaskImpl>
+            </subtasks>
+          </RakeTaskImpl>
+        </subtasks>
+      </RakeTaskImpl>
+    </option>
+  </component>
 </module>

metadata

@@ -1,71 +1,71 @@
 --- !ruby/object:Gem::Specification
 name: text-checkm
 version: !ruby/object:Gem::Version
-  version: '0.7'
+  version: '0.8'
 platform: ruby
 authors:
 - David Moles
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-07-23 00:00:00.000000000 Z
+date: 2021-05-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundle-audit
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.1'
 - !ruby/object:Gem::Dependency
   name: ci_reporter_rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: colorize
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.8'
 - !ruby/object:Gem::Dependency
   name: irb
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.3'
 - !ruby/object:Gem::Dependency
   name: listen
   requirement: !ruby/object:Gem::Requirement
@@ -90,72 +90,86 @@ dependencies:
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '13.0'
 - !ruby/object:Gem::Dependency
   name: rspec-support
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.10'
 - !ruby/object:Gem::Dependency
   name: rubocop
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '0.86'
+        version: '1.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '1.14'
+- !ruby/object:Gem::Dependency
+  name: rubocop-rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '0.5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '0.86'
+        version: '0.5'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.16.1
+        version: '0.21'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.16.1
+        version: '0.21'
 - !ruby/object:Gem::Dependency
   name: simplecov-rcov
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '0.2'
 description: A Ruby implementation of the Checkm checksum-based text manifest format
 email: dmoles@berkeley.edu
 executables: []
@@ -175,9 +189,9 @@ files:
 - ".rubocop.yml"
 - ".ruby-version"
 - ".simplecov"
+- ".travis.yml"
 - CHANGELOG.md
 - Gemfile
-- Gemfile.lock
 - LICENSE.md
 - README.md
 - Rakefile
@@ -213,14 +227,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '0'
+      version: '2.7'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
+rubygems_version: 3.1.4
 signing_key:
 specification_version: 4
 summary: Ruby implementation of the Checkm text manifest format

data/Gemfile.lock

@@ -1,98 +0,0 @@
-PATH
-  remote: .
-  specs:
-    text-checkm (0.7)
-
-GEM
-  remote: http://rubygems.org/
-  specs:
-    ast (2.4.1)
-    builder (3.2.4)
-    bundle-audit (0.1.0)
-      bundler-audit
-    bundler-audit (0.7.0.1)
-      bundler (>= 1.2.0, < 3)
-      thor (>= 0.18, < 2)
-    ci_reporter (2.0.0)
-      builder (>= 2.1.2)
-    ci_reporter_rspec (1.0.0)
-      ci_reporter (~> 2.0)
-      rspec (>= 2.14, < 4)
-    colorize (0.8.1)
-    diff-lcs (1.4.4)
-    docile (1.3.2)
-    ffi (1.13.1)
-    io-console (0.5.6)
-    irb (1.2.4)
-      reline (>= 0.0.1)
-    json (2.3.1)
-    listen (3.1.5)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-      ruby_dep (~> 1.2)
-    parallel (1.19.2)
-    parser (2.7.1.4)
-      ast (~> 2.4.1)
-    rainbow (3.0.0)
-    rake (13.0.1)
-    rb-fsevent (0.10.4)
-    rb-inotify (0.10.1)
-      ffi (~> 1.0)
-    regexp_parser (1.7.1)
-    reline (0.1.4)
-      io-console (~> 0.5)
-    rexml (3.2.4)
-    rspec (3.9.0)
-      rspec-core (~> 3.9.0)
-      rspec-expectations (~> 3.9.0)
-      rspec-mocks (~> 3.9.0)
-    rspec-core (3.9.2)
-      rspec-support (~> 3.9.3)
-    rspec-expectations (3.9.2)
-      diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.9.0)
-    rspec-mocks (3.9.1)
-      diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.9.0)
-    rspec-support (3.9.3)
-    rubocop (0.86.0)
-      parallel (~> 1.10)
-      parser (>= 2.7.0.1)
-      rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.7)
-      rexml
-      rubocop-ast (>= 0.0.3, < 1.0)
-      ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 1.4.0, < 2.0)
-    rubocop-ast (0.2.0)
-      parser (>= 2.7.0.1)
-    ruby-progressbar (1.10.1)
-    ruby_dep (1.5.0)
-    simplecov (0.16.1)
-      docile (~> 1.1)
-      json (>= 1.8, < 3)
-      simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.2)
-    simplecov-rcov (0.2.3)
-      simplecov (>= 0.4.1)
-    thor (1.0.1)
-    unicode-display_width (1.7.0)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  bundle-audit
-  ci_reporter_rspec
-  colorize
-  irb
-  listen (>= 3.0.5, < 3.2)
-  rake (>= 13.0)
-  rspec-support
-  rubocop (= 0.86)
-  simplecov (~> 0.16.1)
-  simplecov-rcov
-  text-checkm!
-
-BUNDLED WITH
-   2.1.2