text-checkm 0.7 → 0.8
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- checksums.yaml +4 -4
- data/.gitignore +3 -0
- data/.rubocop.yml +93 -56
- data/.ruby-version +1 -1
- data/.travis.yml +2 -0
- data/CHANGELOG.md +5 -0
- data/Gemfile +1 -1
- data/LICENSE.md +1 -1
- data/README.md +7 -8
- data/lib/text/checkm/entry.rb +1 -3
- data/lib/text/checkm/manifest.rb +8 -15
- data/lib/text/checkm/module_info.rb +1 -1
- data/text-checkm.gemspec +12 -9
- data/text-checkm.iml +83 -39
- metadata +49 -35
- data/Gemfile.lock +0 -98
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
|
2
2
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SHA256:
|
3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
|
+
metadata.gz: bcc35642292821b3460859c527401f0d90b93d00d7c8913746b64c030d922c93
|
4
|
+
data.tar.gz: 6d95a7592d6c845035875e2fc468e09baf81c15798c19ffadbf529fcb22f41a8
|
5
5
|
SHA512:
|
6
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-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
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+
metadata.gz: 77ee69c083ab4451743816398933e90cf1e33483a057eee94517685be079b95c9a51230017625e40febfec8a0e3130880e76cc91d4b35bd094708ba3a3344be5
|
7
|
+
data.tar.gz: c67b27ac48cd5bdeb8e4e6d6490f06604d125d2a1e163026971992999dfaf63a93034d477e2ed9809923e2c5313ef6d05b014bd46e77ed97528f00f25fd685ce
|
data/.gitignore
CHANGED
data/.rubocop.yml
CHANGED
@@ -5,10 +5,7 @@ AllCops:
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5
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- 'db/**/*'
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- 'out/**/*'
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- 'node_modules/**/*'
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# Added in RuboCop 0.83
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Layout/EmptyLinesAroundAttributeAccessor:
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Enabled: true
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+
- 'vendor/**/*'
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# Allow one line around block body (Layout/EmptyLines will still disallow two or more)
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Layout/EmptyLinesAroundBlockBody:
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@@ -34,26 +31,6 @@ Layout/MultilineMethodCallIndentation:
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Layout/MultilineOperationIndentation:
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Enabled: false
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Lint/DeprecatedOpenSSLConstant:
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Lint/RaiseException:
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# Added in RuboCop 0.85
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Lint/MixedRegexpCaptureTypes:
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Enabled: true
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Layout/SpaceAroundMethodCallOperator:
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Lint/StructNewOverride:
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Enabled: true
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# We meant to do that
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Naming/MemoizedInstanceVariableName:
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Enabled: False
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@@ -82,10 +59,6 @@ Style/CommentedKeyword:
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Style/Documentation:
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Enabled: false
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Style/ExponentialNotation:
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# Adding more line noise to format strings will not improve them
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Enabled: false
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Style/FrozenStringLiteralComment:
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Enabled: false
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Style/HashTransformValues:
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Enabled: true
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-
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# Requiring the lambda() method just makes wordy calls wordier
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Style/Lambda:
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EnforcedStyle: literal
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@@ -114,18 +75,6 @@ Style/Lambda:
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Style/NumericPredicate:
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Enabled: false
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Style/RedundantFetchBlock:
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Enabled: true
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Style/RedundantRegexpCharacterClass:
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Enabled: true
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# Added in RuboCop 0.85
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Style/RedundantRegexpEscape:
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Enabled: true
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# Don't be unnecessarily redundant
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Style/ReturnNil:
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Enabled: true
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@@ -135,10 +84,98 @@ Style/ReturnNil:
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Style/SingleLineBlockParams:
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Enabled: false
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# Added in RuboCop 0.83
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Style/SlicingWithRange:
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Enabled: true
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-
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# The semantics of `foo&.bar` are a lot less interchangeable with `foo && foo.bar` than RuboCop thinks
|
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Style/SafeNavigation:
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Enabled: false
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+
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############################################################
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+
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Gemspec/DateAssignment: # (new in 1.10)
|
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Enabled: true
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Layout/EmptyLinesAroundAttributeAccessor: # (new in 0.83)
|
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Enabled: true
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Layout/SpaceAroundMethodCallOperator: # (new in 0.82)
|
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Enabled: true
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Layout/SpaceBeforeBrackets: # (new in 1.7)
|
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Enabled: true
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Lint/AmbiguousAssignment: # (new in 1.7)
|
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Enabled: true
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Lint/DeprecatedConstants: # (new in 1.8)
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Enabled: true
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Lint/DeprecatedOpenSSLConstant: # (new in 0.84)
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Enabled: true
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Lint/DuplicateBranch: # (new in 1.3)
|
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Enabled: true
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Lint/DuplicateRegexpCharacterClassElement: # (new in 1.1)
|
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Enabled: true
|
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+
Lint/EmptyBlock: # (new in 1.1)
|
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+
Enabled: true
|
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Lint/EmptyClass: # (new in 1.3)
|
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Enabled: true
|
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+
Lint/LambdaWithoutLiteralBlock: # (new in 1.8)
|
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Enabled: true
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+
Lint/MixedRegexpCaptureTypes: # (new in 0.85)
|
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Enabled: true
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+
Lint/NoReturnInBeginEndBlocks: # (new in 1.2)
|
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Enabled: true
|
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Lint/NumberedParameterAssignment: # (new in 1.9)
|
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Enabled: true
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+
Lint/OrAssignmentToConstant: # (new in 1.9)
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Enabled: true
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Lint/RaiseException: # (new in 0.81)
|
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Enabled: true
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Lint/RedundantDirGlobSort: # (new in 1.8)
|
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Enabled: true
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Lint/StructNewOverride: # (new in 0.81)
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Enabled: true
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Lint/SymbolConversion: # (new in 1.9)
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Enabled: true
|
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Lint/ToEnumArguments: # (new in 1.1)
|
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Enabled: true
|
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Lint/TripleQuotes: # (new in 1.9)
|
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Enabled: true
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Lint/UnexpectedBlockArity: # (new in 1.5)
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Enabled: true
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Lint/UnmodifiedReduceAccumulator: # (new in 1.1)
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Enabled: true
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Style/ArgumentsForwarding: # (new in 1.1)
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Enabled: true
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Style/CollectionCompact: # (new in 1.2)
|
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Enabled: true
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Style/DocumentDynamicEvalDefinition: # (new in 1.1)
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Enabled: true
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Style/EndlessMethod: # (new in 1.8)
|
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Enabled: true
|
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Style/ExponentialNotation: # (new in 0.82)
|
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Enabled: false
|
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Style/HashConversion: # (new in 1.10)
|
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Enabled: true
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Style/HashEachMethods: # (new in 0.80)
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Enabled: true
|
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Style/HashExcept: # (new in 1.7)
|
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Enabled: true
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Style/HashTransformKeys: # (new in 0.80)
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Enabled: true
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Style/HashTransformValues: # (new in 0.80)
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Enabled: true
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Style/IfWithBooleanLiteralBranches: # (new in 1.9)
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Enabled: true
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Style/NegatedIfElseCondition: # (new in 1.2)
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Enabled: true
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Style/NilLambda: # (new in 1.3)
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Enabled: true
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Style/RedundantArgument: # (new in 1.4)
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Enabled: true
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Style/RedundantFetchBlock: # (new in 0.86)
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Enabled: true
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Style/RedundantRegexpEscape: # (new in 0.85)
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Enabled: true
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Enabled: true
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data/.ruby-version
CHANGED
@@ -1 +1 @@
|
|
1
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-
2.7.
|
1
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+
2.7.2
|
data/.travis.yml
ADDED
data/CHANGELOG.md
CHANGED
@@ -1,3 +1,8 @@
|
|
1
|
+
# 0.8 (5 May 2021)
|
2
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+
|
3
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+
- don't check in `Gemfile.lock`
|
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- set `required_ruby_version` to >= 2.7 in gemspec
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+
|
1
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# 0.7 (22 July 2020)
|
2
7
|
|
3
8
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- fork from [ruby-microservices/checkm@b7a23d6](https://github.com/ruby-microservices/checkm/tree/b7a23d6a72af643cb9554bf16ff49fc27eded827)
|
data/Gemfile
CHANGED
@@ -1,2 +1,2 @@
|
|
1
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-
source '
|
1
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+
source 'https://rubygems.org'
|
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2
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gemspec
|
data/LICENSE.md
CHANGED
@@ -2,7 +2,7 @@
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2
2
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|
3
3
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Copyright © 2010 Chris Beer
|
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|
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-
Copyright ©
|
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+
Copyright © 2021 The Regents of the University of California
|
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6
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|
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7
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Permission is hereby granted, free of charge, to any person obtaining a
|
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8
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copy of this software and associated documentation files (the “Software”),
|
data/README.md
CHANGED
@@ -1,5 +1,8 @@
|
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1
1
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# Text::Checkm
|
2
2
|
|
3
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+
[![Build Status](https://travis-ci.org/dmolesUC/text-checkm.svg?branch=master)](https://travis-ci.org/dmolesUC/text-checkm)
|
4
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+
[![Gem Version](https://img.shields.io/gem/v/text-checkm.svg)](https://github.com/dmolesUC/text-checkm/releases)
|
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+
|
3
6
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Ruby implementation of
|
4
7
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[Checkm](https://confluence.ucop.edu/display/Curation/Checkm), a
|
5
8
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general-purpose text-based file manifest format developed at the
|
@@ -10,14 +13,10 @@ Abrams, and David Loy.
|
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13
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|
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## Copyright
|
12
15
|
|
13
|
-
Based on [checkm](https://github.com/ruby-microservices/checkm/),
|
14
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-
|
15
|
-
|
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-
software](https://security.ucop.edu/resources/open-source-software-licensing.html),
|
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-
this library is based on
|
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-
[ruby-microservices/checkm@b7a23d6](https://github.com/ruby-microservices/checkm/tree/b7a23d6a72af643cb9554bf16ff49fc27eded827),
|
16
|
+
Based on [checkm](https://github.com/ruby-microservices/checkm/), © 2010 Chris Beer.
|
17
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+
(For compliance with [UC policies on the use and creation of open source software](https://security.ucop.edu/resources/open-source-software-licensing.html),
|
18
|
+
this library is based on [ruby-microservices/checkm@b7a23d6](https://github.com/ruby-microservices/checkm/tree/b7a23d6a72af643cb9554bf16ff49fc27eded827),
|
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the last MIT-licensed revision.)
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-
Subsequent work ©
|
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+
Subsequent work © 2021 the Regents of the University of California. See
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[LICENSE.md](LICENSE.md) for more details.
|
23
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-
|
data/lib/text/checkm/entry.rb
CHANGED
@@ -26,12 +26,10 @@ module Text
|
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26
26
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@manifest = manifest
|
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end
|
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-
# rubocop:disable Style/MethodMissingSuper
|
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def method_missing(sym, *_args)
|
31
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# TODO: something less extreme
|
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31
|
@values[@fields.index(sym.to_s.downcase) || BASE_FIELDS.index(sym.to_s.downcase)]
|
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|
end
|
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-
# rubocop:enable Style/MethodMissingSuper
|
35
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|
36
34
|
def respond_to_missing?(sym, *)
|
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35
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@fields.include?(sym.to_s.downcase) || BASE_FIELDS.include?(sym.to_s.downcase)
|
@@ -70,7 +68,7 @@ module Text
|
|
70
68
|
def valid_multilevel?
|
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69
|
return true unless sourcefileorurl =~ /^@/
|
72
70
|
|
73
|
-
Manifest.parse(
|
71
|
+
Manifest.parse(File.read(source), path: File.dirname(source))
|
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72
|
end
|
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73
|
end
|
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end
|
data/lib/text/checkm/manifest.rb
CHANGED
@@ -7,10 +7,7 @@ module Text
|
|
7
7
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Manifest.new str, args
|
8
8
|
end
|
9
9
|
|
10
|
-
attr_reader :version
|
11
|
-
attr_reader :entries
|
12
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-
attr_reader :fields
|
13
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-
attr_reader :path
|
10
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+
attr_reader :version, :entries, :fields, :path
|
14
11
|
|
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# rubocop:disable Metrics/MethodLength
|
16
13
|
def initialize(checkm, args = {})
|
@@ -66,23 +63,22 @@ module Text
|
|
66
63
|
def parse_lines
|
67
64
|
@lines.each do |line|
|
68
65
|
case line
|
66
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+
when /^$/
|
67
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+
# do nothing
|
69
68
|
when /^#%/
|
70
69
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parse_header line
|
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when /^#/
|
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parse_comment line
|
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-
when
|
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-
|
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-
when /^@/
|
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-
parse_line line
|
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+
# when /^@/
|
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+
# parse_line line
|
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else
|
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parse_line line
|
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end
|
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end
|
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end
|
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-
|
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|
# rubocop:enable Metrics/MethodLength
|
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|
|
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-
# rubocop:disable Metrics/MethodLength
|
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|
+
# rubocop:disable Metrics/MethodLength
|
86
82
|
def parse_header(line)
|
87
83
|
case line
|
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|
when /^#%checkm/
|
@@ -94,14 +90,11 @@ module Text
|
|
94
90
|
list = line.split('|')
|
95
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|
list.shift
|
96
92
|
@fields = list.map { |v| v.strip.downcase }
|
97
|
-
when /^#%prefix/
|
98
|
-
# do nothing
|
99
|
-
when /^#%profile/
|
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|
+
when /^#%prefix/, /^#%profile/
|
100
94
|
# do nothing
|
101
95
|
end
|
102
96
|
end
|
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|
-
|
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|
-
# rubocop:enable Metrics/MethodLength, Metrics/CyclomaticComplexity
|
97
|
+
# rubocop:enable Metrics/MethodLength
|
105
98
|
|
106
99
|
def parse_comment(_line)
|
107
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|
# do nothing
|
@@ -7,7 +7,7 @@ module Text
|
|
7
7
|
SUMMARY = 'Ruby implementation of the Checkm text manifest format'.freeze
|
8
8
|
DESCRIPTION = 'A Ruby implementation of the Checkm checksum-based text manifest format'.freeze
|
9
9
|
LICENSE = 'MIT'.freeze
|
10
|
-
VERSION = '0.
|
10
|
+
VERSION = '0.8'.freeze
|
11
11
|
HOMEPAGE = 'https://github.com/dmolesUC/checkm'.freeze
|
12
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|
|
13
13
|
private_class_method :new
|
data/text-checkm.gemspec
CHANGED
@@ -16,14 +16,17 @@ Gem::Specification.new do |spec|
|
|
16
16
|
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
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|
spec.require_paths = ['lib']
|
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|
|
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-
spec.
|
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|
-
|
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|
-
spec.add_development_dependency '
|
22
|
-
spec.add_development_dependency '
|
19
|
+
spec.required_ruby_version = '>= 2.7'
|
20
|
+
|
21
|
+
spec.add_development_dependency 'bundle-audit', '~> 0.1'
|
22
|
+
spec.add_development_dependency 'ci_reporter_rspec', '~> 1.0'
|
23
|
+
spec.add_development_dependency 'colorize', '~> 0.8'
|
24
|
+
spec.add_development_dependency 'irb', '~> 1.3' # workaroundfor https://github.com/bundler/bundler/issues/6929
|
23
25
|
spec.add_development_dependency 'listen', '>= 3.0.5', '< 3.2'
|
24
|
-
spec.add_development_dependency 'rake', '
|
25
|
-
spec.add_development_dependency 'rspec-support'
|
26
|
-
spec.add_development_dependency 'rubocop', '
|
27
|
-
spec.add_development_dependency '
|
28
|
-
spec.add_development_dependency 'simplecov
|
26
|
+
spec.add_development_dependency 'rake', '~> 13.0'
|
27
|
+
spec.add_development_dependency 'rspec-support', '~> 3.10'
|
28
|
+
spec.add_development_dependency 'rubocop', '1.14'
|
29
|
+
spec.add_development_dependency 'rubocop-rake', '0.5'
|
30
|
+
spec.add_development_dependency 'simplecov', '~> 0.21'
|
31
|
+
spec.add_development_dependency 'simplecov-rcov', '~> 0.2'
|
29
32
|
end
|
data/text-checkm.iml
CHANGED
@@ -1,51 +1,95 @@
|
|
1
1
|
<?xml version="1.0" encoding="UTF-8"?>
|
2
2
|
<module type="RUBY_MODULE" version="4">
|
3
|
+
<component name="ModuleRunConfigurationManager">
|
4
|
+
<shared />
|
5
|
+
</component>
|
3
6
|
<component name="NewModuleRootManager" inherit-compiler-output="true">
|
4
7
|
<exclude-output />
|
5
8
|
<content url="file://$MODULE_DIR$" />
|
6
|
-
<orderEntry type="jdk" jdkName="RVM: ruby-2.7.
|
9
|
+
<orderEntry type="jdk" jdkName="RVM: ruby-2.7.2" jdkType="RUBY_SDK" />
|
7
10
|
<orderEntry type="sourceFolder" forTests="false" />
|
8
|
-
<orderEntry type="library" scope="PROVIDED" name="ast (v2.4.
|
9
|
-
<orderEntry type="library" scope="PROVIDED" name="builder (v3.2.4, RVM: ruby-2.7.
|
10
|
-
<orderEntry type="library" scope="PROVIDED" name="bundle-audit (v0.1.0, RVM: ruby-2.7.
|
11
|
-
<orderEntry type="library" scope="PROVIDED" name="bundler (v2.1.
|
12
|
-
<orderEntry type="library" scope="PROVIDED" name="bundler-audit (v0.
|
13
|
-
<orderEntry type="library" scope="PROVIDED" name="ci_reporter (v2.0.0, RVM: ruby-2.7.
|
14
|
-
<orderEntry type="library" scope="PROVIDED" name="ci_reporter_rspec (v1.0.0, RVM: ruby-2.7.
|
15
|
-
<orderEntry type="library" scope="PROVIDED" name="colorize (v0.8.1, RVM: ruby-2.7.
|
16
|
-
<orderEntry type="library" scope="PROVIDED" name="diff-lcs (v1.4.4, RVM: ruby-2.7.
|
17
|
-
<orderEntry type="library" scope="PROVIDED" name="docile (v1.3.
|
18
|
-
<orderEntry type="library" scope="PROVIDED" name="ffi (v1.
|
19
|
-
<orderEntry type="library" scope="PROVIDED" name="io-console (v0.5.
|
20
|
-
<orderEntry type="library" scope="PROVIDED" name="irb (v1.
|
21
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
22
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
23
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
24
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
25
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
26
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
27
|
-
<orderEntry type="library" scope="PROVIDED" name="rb-
|
28
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
29
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
30
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
31
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
32
|
-
<orderEntry type="library" scope="PROVIDED" name="rspec (v3.
|
33
|
-
<orderEntry type="library" scope="PROVIDED" name="rspec-
|
34
|
-
<orderEntry type="library" scope="PROVIDED" name="rspec-
|
35
|
-
<orderEntry type="library" scope="PROVIDED" name="rspec-
|
36
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
37
|
-
<orderEntry type="library" scope="PROVIDED" name="rubocop (
|
38
|
-
<orderEntry type="library" scope="PROVIDED" name="rubocop-
|
39
|
-
<orderEntry type="library" scope="PROVIDED" name="ruby-progressbar (v1.
|
40
|
-
<orderEntry type="library" scope="PROVIDED" name="ruby_dep (v1.5.0, RVM: ruby-2.7.
|
41
|
-
<orderEntry type="library" scope="PROVIDED" name="simplecov (v0.
|
42
|
-
<orderEntry type="library" scope="PROVIDED" name="simplecov-html (v0.
|
43
|
-
<orderEntry type="library" scope="PROVIDED" name="simplecov-rcov (v0.2.3, RVM: ruby-2.7.
|
44
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
45
|
-
<orderEntry type="library" scope="PROVIDED" name="
|
11
|
+
<orderEntry type="library" scope="PROVIDED" name="ast (v2.4.2, RVM: ruby-2.7.2) [gem]" level="application" />
|
12
|
+
<orderEntry type="library" scope="PROVIDED" name="builder (v3.2.4, RVM: ruby-2.7.2) [gem]" level="application" />
|
13
|
+
<orderEntry type="library" scope="PROVIDED" name="bundle-audit (v0.1.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
14
|
+
<orderEntry type="library" scope="PROVIDED" name="bundler (v2.1.4, RVM: ruby-2.7.2) [gem]" level="application" />
|
15
|
+
<orderEntry type="library" scope="PROVIDED" name="bundler-audit (v0.8.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
16
|
+
<orderEntry type="library" scope="PROVIDED" name="ci_reporter (v2.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
17
|
+
<orderEntry type="library" scope="PROVIDED" name="ci_reporter_rspec (v1.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
18
|
+
<orderEntry type="library" scope="PROVIDED" name="colorize (v0.8.1, RVM: ruby-2.7.2) [gem]" level="application" />
|
19
|
+
<orderEntry type="library" scope="PROVIDED" name="diff-lcs (v1.4.4, RVM: ruby-2.7.2) [gem]" level="application" />
|
20
|
+
<orderEntry type="library" scope="PROVIDED" name="docile (v1.3.5, RVM: ruby-2.7.2) [gem]" level="application" />
|
21
|
+
<orderEntry type="library" scope="PROVIDED" name="ffi (v1.15.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
22
|
+
<orderEntry type="library" scope="PROVIDED" name="io-console (v0.5.9, RVM: ruby-2.7.2) [gem]" level="application" />
|
23
|
+
<orderEntry type="library" scope="PROVIDED" name="irb (v1.3.5, RVM: ruby-2.7.2) [gem]" level="application" />
|
24
|
+
<orderEntry type="library" scope="PROVIDED" name="listen (v3.1.5, RVM: ruby-2.7.2) [gem]" level="application" />
|
25
|
+
<orderEntry type="library" scope="PROVIDED" name="parallel (v1.20.1, RVM: ruby-2.7.2) [gem]" level="application" />
|
26
|
+
<orderEntry type="library" scope="PROVIDED" name="parser (v3.0.1.1, RVM: ruby-2.7.2) [gem]" level="application" />
|
27
|
+
<orderEntry type="library" scope="PROVIDED" name="rainbow (v3.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
28
|
+
<orderEntry type="library" scope="PROVIDED" name="rake (v13.0.3, RVM: ruby-2.7.2) [gem]" level="application" />
|
29
|
+
<orderEntry type="library" scope="PROVIDED" name="rb-fsevent (v0.10.4, RVM: ruby-2.7.2) [gem]" level="application" />
|
30
|
+
<orderEntry type="library" scope="PROVIDED" name="rb-inotify (v0.10.1, RVM: ruby-2.7.2) [gem]" level="application" />
|
31
|
+
<orderEntry type="library" scope="PROVIDED" name="regexp_parser (v2.1.1, RVM: ruby-2.7.2) [gem]" level="application" />
|
32
|
+
<orderEntry type="library" scope="PROVIDED" name="reline (v0.2.5, RVM: ruby-2.7.2) [gem]" level="application" />
|
33
|
+
<orderEntry type="library" scope="PROVIDED" name="rexml (v3.2.5, RVM: ruby-2.7.2) [gem]" level="application" />
|
34
|
+
<orderEntry type="library" scope="PROVIDED" name="rspec (v3.10.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
35
|
+
<orderEntry type="library" scope="PROVIDED" name="rspec-core (v3.10.1, RVM: ruby-2.7.2) [gem]" level="application" />
|
36
|
+
<orderEntry type="library" scope="PROVIDED" name="rspec-expectations (v3.10.1, RVM: ruby-2.7.2) [gem]" level="application" />
|
37
|
+
<orderEntry type="library" scope="PROVIDED" name="rspec-mocks (v3.10.2, RVM: ruby-2.7.2) [gem]" level="application" />
|
38
|
+
<orderEntry type="library" scope="PROVIDED" name="rspec-support (v3.10.2, RVM: ruby-2.7.2) [gem]" level="application" />
|
39
|
+
<orderEntry type="library" scope="PROVIDED" name="rubocop (v1.14.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
40
|
+
<orderEntry type="library" scope="PROVIDED" name="rubocop-ast (v1.5.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
41
|
+
<orderEntry type="library" scope="PROVIDED" name="rubocop-rake (v0.5.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
42
|
+
<orderEntry type="library" scope="PROVIDED" name="ruby-progressbar (v1.11.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
43
|
+
<orderEntry type="library" scope="PROVIDED" name="ruby_dep (v1.5.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
44
|
+
<orderEntry type="library" scope="PROVIDED" name="simplecov (v0.21.2, RVM: ruby-2.7.2) [gem]" level="application" />
|
45
|
+
<orderEntry type="library" scope="PROVIDED" name="simplecov-html (v0.12.3, RVM: ruby-2.7.2) [gem]" level="application" />
|
46
|
+
<orderEntry type="library" scope="PROVIDED" name="simplecov-rcov (v0.2.3, RVM: ruby-2.7.2) [gem]" level="application" />
|
47
|
+
<orderEntry type="library" scope="PROVIDED" name="simplecov_json_formatter (v0.1.3, RVM: ruby-2.7.2) [gem]" level="application" />
|
48
|
+
<orderEntry type="library" scope="PROVIDED" name="thor (v1.1.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
49
|
+
<orderEntry type="library" scope="PROVIDED" name="unicode-display_width (v2.0.0, RVM: ruby-2.7.2) [gem]" level="application" />
|
46
50
|
</component>
|
47
51
|
<component name="RModuleSettingsStorage">
|
48
52
|
<LOAD_PATH number="2" string0="$MODULE_DIR$/lib" string1="$MODULE_DIR$/spec" />
|
49
53
|
<I18N_FOLDERS number="0" />
|
50
54
|
</component>
|
55
|
+
<component name="RakeTasksCache">
|
56
|
+
<option name="myRootTask">
|
57
|
+
<RakeTaskImpl id="rake">
|
58
|
+
<subtasks>
|
59
|
+
<RakeTaskImpl id="bundle">
|
60
|
+
<subtasks>
|
61
|
+
<RakeTaskImpl description="Updates the ruby-advisory-db then runs bundle-audit" fullCommand="bundle:audit" id="audit" />
|
62
|
+
</subtasks>
|
63
|
+
</RakeTaskImpl>
|
64
|
+
<RakeTaskImpl description="Run all specs in spec directory, with coverage" fullCommand="coverage" id="coverage" />
|
65
|
+
<RakeTaskImpl description="Run tests, check test coverage, check code style" fullCommand="default" id="default" />
|
66
|
+
<RakeTaskImpl description="Run RuboCop with auto-correct, and output results to console" fullCommand="ra" id="ra" />
|
67
|
+
<RakeTaskImpl description="Run rubocop with HTML output" fullCommand="rubocop" id="rubocop" />
|
68
|
+
<RakeTaskImpl id="rubocop">
|
69
|
+
<subtasks>
|
70
|
+
<RakeTaskImpl description="Auto-correct RuboCop offenses" fullCommand="rubocop:auto_correct" id="auto_correct" />
|
71
|
+
</subtasks>
|
72
|
+
</RakeTaskImpl>
|
73
|
+
<RakeTaskImpl description="Run all tests" fullCommand="spec" id="spec" />
|
74
|
+
<RakeTaskImpl id="spec">
|
75
|
+
<subtasks>
|
76
|
+
<RakeTaskImpl description="Run all tests" fullCommand="spec:all" id="all" />
|
77
|
+
</subtasks>
|
78
|
+
</RakeTaskImpl>
|
79
|
+
<RakeTaskImpl id="ci">
|
80
|
+
<subtasks>
|
81
|
+
<RakeTaskImpl id="setup">
|
82
|
+
<subtasks>
|
83
|
+
<RakeTaskImpl description="" fullCommand="ci:setup:rspec" id="rspec" />
|
84
|
+
<RakeTaskImpl description="" fullCommand="ci:setup:rspecbase" id="rspecbase" />
|
85
|
+
<RakeTaskImpl description="" fullCommand="ci:setup:rspecdoc" id="rspecdoc" />
|
86
|
+
<RakeTaskImpl description="" fullCommand="ci:setup:spec_report_cleanup" id="spec_report_cleanup" />
|
87
|
+
</subtasks>
|
88
|
+
</RakeTaskImpl>
|
89
|
+
</subtasks>
|
90
|
+
</RakeTaskImpl>
|
91
|
+
</subtasks>
|
92
|
+
</RakeTaskImpl>
|
93
|
+
</option>
|
94
|
+
</component>
|
51
95
|
</module>
|
metadata
CHANGED
@@ -1,71 +1,71 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: text-checkm
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: '0.
|
4
|
+
version: '0.8'
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- David Moles
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2021-05-05 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundle-audit
|
15
15
|
requirement: !ruby/object:Gem::Requirement
|
16
16
|
requirements:
|
17
|
-
- - "
|
17
|
+
- - "~>"
|
18
18
|
- !ruby/object:Gem::Version
|
19
|
-
version: '0'
|
19
|
+
version: '0.1'
|
20
20
|
type: :development
|
21
21
|
prerelease: false
|
22
22
|
version_requirements: !ruby/object:Gem::Requirement
|
23
23
|
requirements:
|
24
|
-
- - "
|
24
|
+
- - "~>"
|
25
25
|
- !ruby/object:Gem::Version
|
26
|
-
version: '0'
|
26
|
+
version: '0.1'
|
27
27
|
- !ruby/object:Gem::Dependency
|
28
28
|
name: ci_reporter_rspec
|
29
29
|
requirement: !ruby/object:Gem::Requirement
|
30
30
|
requirements:
|
31
|
-
- - "
|
31
|
+
- - "~>"
|
32
32
|
- !ruby/object:Gem::Version
|
33
|
-
version: '0'
|
33
|
+
version: '1.0'
|
34
34
|
type: :development
|
35
35
|
prerelease: false
|
36
36
|
version_requirements: !ruby/object:Gem::Requirement
|
37
37
|
requirements:
|
38
|
-
- - "
|
38
|
+
- - "~>"
|
39
39
|
- !ruby/object:Gem::Version
|
40
|
-
version: '0'
|
40
|
+
version: '1.0'
|
41
41
|
- !ruby/object:Gem::Dependency
|
42
42
|
name: colorize
|
43
43
|
requirement: !ruby/object:Gem::Requirement
|
44
44
|
requirements:
|
45
|
-
- - "
|
45
|
+
- - "~>"
|
46
46
|
- !ruby/object:Gem::Version
|
47
|
-
version: '0'
|
47
|
+
version: '0.8'
|
48
48
|
type: :development
|
49
49
|
prerelease: false
|
50
50
|
version_requirements: !ruby/object:Gem::Requirement
|
51
51
|
requirements:
|
52
|
-
- - "
|
52
|
+
- - "~>"
|
53
53
|
- !ruby/object:Gem::Version
|
54
|
-
version: '0'
|
54
|
+
version: '0.8'
|
55
55
|
- !ruby/object:Gem::Dependency
|
56
56
|
name: irb
|
57
57
|
requirement: !ruby/object:Gem::Requirement
|
58
58
|
requirements:
|
59
|
-
- - "
|
59
|
+
- - "~>"
|
60
60
|
- !ruby/object:Gem::Version
|
61
|
-
version: '
|
61
|
+
version: '1.3'
|
62
62
|
type: :development
|
63
63
|
prerelease: false
|
64
64
|
version_requirements: !ruby/object:Gem::Requirement
|
65
65
|
requirements:
|
66
|
-
- - "
|
66
|
+
- - "~>"
|
67
67
|
- !ruby/object:Gem::Version
|
68
|
-
version: '
|
68
|
+
version: '1.3'
|
69
69
|
- !ruby/object:Gem::Dependency
|
70
70
|
name: listen
|
71
71
|
requirement: !ruby/object:Gem::Requirement
|
@@ -90,72 +90,86 @@ dependencies:
|
|
90
90
|
name: rake
|
91
91
|
requirement: !ruby/object:Gem::Requirement
|
92
92
|
requirements:
|
93
|
-
- - "
|
93
|
+
- - "~>"
|
94
94
|
- !ruby/object:Gem::Version
|
95
95
|
version: '13.0'
|
96
96
|
type: :development
|
97
97
|
prerelease: false
|
98
98
|
version_requirements: !ruby/object:Gem::Requirement
|
99
99
|
requirements:
|
100
|
-
- - "
|
100
|
+
- - "~>"
|
101
101
|
- !ruby/object:Gem::Version
|
102
102
|
version: '13.0'
|
103
103
|
- !ruby/object:Gem::Dependency
|
104
104
|
name: rspec-support
|
105
105
|
requirement: !ruby/object:Gem::Requirement
|
106
106
|
requirements:
|
107
|
-
- - "
|
107
|
+
- - "~>"
|
108
108
|
- !ruby/object:Gem::Version
|
109
|
-
version: '
|
109
|
+
version: '3.10'
|
110
110
|
type: :development
|
111
111
|
prerelease: false
|
112
112
|
version_requirements: !ruby/object:Gem::Requirement
|
113
113
|
requirements:
|
114
|
-
- - "
|
114
|
+
- - "~>"
|
115
115
|
- !ruby/object:Gem::Version
|
116
|
-
version: '
|
116
|
+
version: '3.10'
|
117
117
|
- !ruby/object:Gem::Dependency
|
118
118
|
name: rubocop
|
119
119
|
requirement: !ruby/object:Gem::Requirement
|
120
120
|
requirements:
|
121
121
|
- - '='
|
122
122
|
- !ruby/object:Gem::Version
|
123
|
-
version: '
|
123
|
+
version: '1.14'
|
124
|
+
type: :development
|
125
|
+
prerelease: false
|
126
|
+
version_requirements: !ruby/object:Gem::Requirement
|
127
|
+
requirements:
|
128
|
+
- - '='
|
129
|
+
- !ruby/object:Gem::Version
|
130
|
+
version: '1.14'
|
131
|
+
- !ruby/object:Gem::Dependency
|
132
|
+
name: rubocop-rake
|
133
|
+
requirement: !ruby/object:Gem::Requirement
|
134
|
+
requirements:
|
135
|
+
- - '='
|
136
|
+
- !ruby/object:Gem::Version
|
137
|
+
version: '0.5'
|
124
138
|
type: :development
|
125
139
|
prerelease: false
|
126
140
|
version_requirements: !ruby/object:Gem::Requirement
|
127
141
|
requirements:
|
128
142
|
- - '='
|
129
143
|
- !ruby/object:Gem::Version
|
130
|
-
version: '0.
|
144
|
+
version: '0.5'
|
131
145
|
- !ruby/object:Gem::Dependency
|
132
146
|
name: simplecov
|
133
147
|
requirement: !ruby/object:Gem::Requirement
|
134
148
|
requirements:
|
135
149
|
- - "~>"
|
136
150
|
- !ruby/object:Gem::Version
|
137
|
-
version: 0.
|
151
|
+
version: '0.21'
|
138
152
|
type: :development
|
139
153
|
prerelease: false
|
140
154
|
version_requirements: !ruby/object:Gem::Requirement
|
141
155
|
requirements:
|
142
156
|
- - "~>"
|
143
157
|
- !ruby/object:Gem::Version
|
144
|
-
version: 0.
|
158
|
+
version: '0.21'
|
145
159
|
- !ruby/object:Gem::Dependency
|
146
160
|
name: simplecov-rcov
|
147
161
|
requirement: !ruby/object:Gem::Requirement
|
148
162
|
requirements:
|
149
|
-
- - "
|
163
|
+
- - "~>"
|
150
164
|
- !ruby/object:Gem::Version
|
151
|
-
version: '0'
|
165
|
+
version: '0.2'
|
152
166
|
type: :development
|
153
167
|
prerelease: false
|
154
168
|
version_requirements: !ruby/object:Gem::Requirement
|
155
169
|
requirements:
|
156
|
-
- - "
|
170
|
+
- - "~>"
|
157
171
|
- !ruby/object:Gem::Version
|
158
|
-
version: '0'
|
172
|
+
version: '0.2'
|
159
173
|
description: A Ruby implementation of the Checkm checksum-based text manifest format
|
160
174
|
email: dmoles@berkeley.edu
|
161
175
|
executables: []
|
@@ -175,9 +189,9 @@ files:
|
|
175
189
|
- ".rubocop.yml"
|
176
190
|
- ".ruby-version"
|
177
191
|
- ".simplecov"
|
192
|
+
- ".travis.yml"
|
178
193
|
- CHANGELOG.md
|
179
194
|
- Gemfile
|
180
|
-
- Gemfile.lock
|
181
195
|
- LICENSE.md
|
182
196
|
- README.md
|
183
197
|
- Rakefile
|
@@ -213,14 +227,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
|
213
227
|
requirements:
|
214
228
|
- - ">="
|
215
229
|
- !ruby/object:Gem::Version
|
216
|
-
version: '
|
230
|
+
version: '2.7'
|
217
231
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
218
232
|
requirements:
|
219
233
|
- - ">="
|
220
234
|
- !ruby/object:Gem::Version
|
221
235
|
version: '0'
|
222
236
|
requirements: []
|
223
|
-
rubygems_version: 3.1.
|
237
|
+
rubygems_version: 3.1.4
|
224
238
|
signing_key:
|
225
239
|
specification_version: 4
|
226
240
|
summary: Ruby implementation of the Checkm text manifest format
|
data/Gemfile.lock
DELETED
@@ -1,98 +0,0 @@
|
|
1
|
-
PATH
|
2
|
-
remote: .
|
3
|
-
specs:
|
4
|
-
text-checkm (0.7)
|
5
|
-
|
6
|
-
GEM
|
7
|
-
remote: http://rubygems.org/
|
8
|
-
specs:
|
9
|
-
ast (2.4.1)
|
10
|
-
builder (3.2.4)
|
11
|
-
bundle-audit (0.1.0)
|
12
|
-
bundler-audit
|
13
|
-
bundler-audit (0.7.0.1)
|
14
|
-
bundler (>= 1.2.0, < 3)
|
15
|
-
thor (>= 0.18, < 2)
|
16
|
-
ci_reporter (2.0.0)
|
17
|
-
builder (>= 2.1.2)
|
18
|
-
ci_reporter_rspec (1.0.0)
|
19
|
-
ci_reporter (~> 2.0)
|
20
|
-
rspec (>= 2.14, < 4)
|
21
|
-
colorize (0.8.1)
|
22
|
-
diff-lcs (1.4.4)
|
23
|
-
docile (1.3.2)
|
24
|
-
ffi (1.13.1)
|
25
|
-
io-console (0.5.6)
|
26
|
-
irb (1.2.4)
|
27
|
-
reline (>= 0.0.1)
|
28
|
-
json (2.3.1)
|
29
|
-
listen (3.1.5)
|
30
|
-
rb-fsevent (~> 0.9, >= 0.9.4)
|
31
|
-
rb-inotify (~> 0.9, >= 0.9.7)
|
32
|
-
ruby_dep (~> 1.2)
|
33
|
-
parallel (1.19.2)
|
34
|
-
parser (2.7.1.4)
|
35
|
-
ast (~> 2.4.1)
|
36
|
-
rainbow (3.0.0)
|
37
|
-
rake (13.0.1)
|
38
|
-
rb-fsevent (0.10.4)
|
39
|
-
rb-inotify (0.10.1)
|
40
|
-
ffi (~> 1.0)
|
41
|
-
regexp_parser (1.7.1)
|
42
|
-
reline (0.1.4)
|
43
|
-
io-console (~> 0.5)
|
44
|
-
rexml (3.2.4)
|
45
|
-
rspec (3.9.0)
|
46
|
-
rspec-core (~> 3.9.0)
|
47
|
-
rspec-expectations (~> 3.9.0)
|
48
|
-
rspec-mocks (~> 3.9.0)
|
49
|
-
rspec-core (3.9.2)
|
50
|
-
rspec-support (~> 3.9.3)
|
51
|
-
rspec-expectations (3.9.2)
|
52
|
-
diff-lcs (>= 1.2.0, < 2.0)
|
53
|
-
rspec-support (~> 3.9.0)
|
54
|
-
rspec-mocks (3.9.1)
|
55
|
-
diff-lcs (>= 1.2.0, < 2.0)
|
56
|
-
rspec-support (~> 3.9.0)
|
57
|
-
rspec-support (3.9.3)
|
58
|
-
rubocop (0.86.0)
|
59
|
-
parallel (~> 1.10)
|
60
|
-
parser (>= 2.7.0.1)
|
61
|
-
rainbow (>= 2.2.2, < 4.0)
|
62
|
-
regexp_parser (>= 1.7)
|
63
|
-
rexml
|
64
|
-
rubocop-ast (>= 0.0.3, < 1.0)
|
65
|
-
ruby-progressbar (~> 1.7)
|
66
|
-
unicode-display_width (>= 1.4.0, < 2.0)
|
67
|
-
rubocop-ast (0.2.0)
|
68
|
-
parser (>= 2.7.0.1)
|
69
|
-
ruby-progressbar (1.10.1)
|
70
|
-
ruby_dep (1.5.0)
|
71
|
-
simplecov (0.16.1)
|
72
|
-
docile (~> 1.1)
|
73
|
-
json (>= 1.8, < 3)
|
74
|
-
simplecov-html (~> 0.10.0)
|
75
|
-
simplecov-html (0.10.2)
|
76
|
-
simplecov-rcov (0.2.3)
|
77
|
-
simplecov (>= 0.4.1)
|
78
|
-
thor (1.0.1)
|
79
|
-
unicode-display_width (1.7.0)
|
80
|
-
|
81
|
-
PLATFORMS
|
82
|
-
ruby
|
83
|
-
|
84
|
-
DEPENDENCIES
|
85
|
-
bundle-audit
|
86
|
-
ci_reporter_rspec
|
87
|
-
colorize
|
88
|
-
irb
|
89
|
-
listen (>= 3.0.5, < 3.2)
|
90
|
-
rake (>= 13.0)
|
91
|
-
rspec-support
|
92
|
-
rubocop (= 0.86)
|
93
|
-
simplecov (~> 0.16.1)
|
94
|
-
simplecov-rcov
|
95
|
-
text-checkm!
|
96
|
-
|
97
|
-
BUNDLED WITH
|
98
|
-
2.1.2
|