text-checkm 0.7

data/spec/spec_helper.rb

@@ -0,0 +1,23 @@
+# ------------------------------------------------------------
+# Simplecov
+
+require 'colorize'
+require 'simplecov' if ENV['COVERAGE']
+
+# ------------------------------------------------------------
+# RSpec
+
+RSpec.configure do |config|
+  config.color = true
+  config.tty = true
+  config.formatter = :documentation
+  config.mock_with :rspec do |mocks|
+    mocks.verify_partial_doubles = true
+  end
+  config.shared_context_metadata_behavior = :apply_to_host_groups
+end
+
+# ------------------------------------------------------------
+# Code under test
+
+require 'text/checkm'

data/text-checkm.gemspec

@@ -0,0 +1,29 @@
+require_relative 'lib/text/checkm/module_info'
+
+Gem::Specification.new do |spec|
+  spec.name = Text::Checkm::ModuleInfo::NAME
+  spec.author = Text::Checkm::ModuleInfo::AUTHOR
+  spec.email = Text::Checkm::ModuleInfo::AUTHOR_EMAIL
+  spec.summary = Text::Checkm::ModuleInfo::SUMMARY
+  spec.description = Text::Checkm::ModuleInfo::DESCRIPTION
+  spec.license = Text::Checkm::ModuleInfo::LICENSE
+  spec.version = Text::Checkm::ModuleInfo::VERSION
+  spec.homepage = Text::Checkm::ModuleInfo::HOMEPAGE
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+
+  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.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'
+end

data/text-checkm.iml

@@ -0,0 +1,51 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="RUBY_MODULE" version="4">
+  <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="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" />
+  </component>
+  <component name="RModuleSettingsStorage">
+    <LOAD_PATH number="2" string0="$MODULE_DIR$/lib" string1="$MODULE_DIR$/spec" />
+    <I18N_FOLDERS number="0" />
+  </component>
+</module>

metadata

@@ -0,0 +1,236 @@
+--- !ruby/object:Gem::Specification
+name: text-checkm
+version: !ruby/object:Gem::Version
+  version: '0.7'
+platform: ruby
+authors:
+- David Moles
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2020-07-23 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'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: ci_reporter_rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: colorize
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: irb
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: listen
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.5
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.5
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  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'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '0.86'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '0.86'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.16.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.16.1
+- !ruby/object:Gem::Dependency
+  name: simplecov-rcov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A Ruby implementation of the Checkm checksum-based text manifest format
+email: dmoles@berkeley.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".document"
+- ".gitignore"
+- ".idea/$CACHE_FILE$"
+- ".idea/.gitignore"
+- ".idea/go.imports.xml"
+- ".idea/inspectionProfiles/Project_Default.xml"
+- ".idea/inspectionProfiles/profiles_settings.xml"
+- ".idea/misc.xml"
+- ".idea/modules.xml"
+- ".idea/vcs.xml"
+- ".rubocop.yml"
+- ".ruby-version"
+- ".simplecov"
+- CHANGELOG.md
+- Gemfile
+- Gemfile.lock
+- LICENSE.md
+- README.md
+- Rakefile
+- SPEC.txt
+- lib/text/checkm.rb
+- lib/text/checkm/checksum.rb
+- lib/text/checkm/entry.rb
+- lib/text/checkm/manifest.rb
+- lib/text/checkm/module_info.rb
+- rakelib/bundle.rake
+- rakelib/coverage.rake
+- rakelib/rubocop.rake
+- spec/.rubocop.yml
+- spec/data/merritt-manifest.checkm
+- spec/data/myfirst.checkm
+- spec/data/test_1/1
+- spec/data/two-level-manifest.checkm
+- spec/lib/text/checkm/checksum_spec.rb
+- spec/lib/text/checkm/entry_spec.rb
+- spec/lib/text/checkm/manifest_spec.rb
+- spec/spec_helper.rb
+- text-checkm.gemspec
+- text-checkm.iml
+homepage: https://github.com/dmolesUC/checkm
+licenses:
+- MIT
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.2
+signing_key:
+specification_version: 4
+summary: Ruby implementation of the Checkm text manifest format
+test_files:
+- spec/.rubocop.yml
+- spec/data/merritt-manifest.checkm
+- spec/data/myfirst.checkm
+- spec/data/test_1/1
+- spec/data/two-level-manifest.checkm
+- spec/lib/text/checkm/checksum_spec.rb
+- spec/lib/text/checkm/entry_spec.rb
+- spec/lib/text/checkm/manifest_spec.rb
+- spec/spec_helper.rb