mumuki-r-runner 0.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/lib/metadata_hook.rb +24 -0
- data/lib/query_hook.rb +48 -0
- data/lib/r_runner.rb +15 -0
- data/lib/test_hook.rb +48 -0
- data/lib/try_hook.rb +47 -0
- data/lib/version.rb +3 -0
- metadata +133 -0
checksums.yaml
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---
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SHA256:
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metadata.gz: 16dac79ec3a5bf8a0f39be4ea303b2a2ce76c6e880740ce6506b0f7d34900cd8
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data.tar.gz: 61edafb16a21bbf9f4e8c205dd12aa563512c0a1d1006f710f6c19d50d1595ac
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SHA512:
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metadata.gz: b3994020d6d9e97170d7735d7d79c135f32527d2b77d10113a5026d531dd35f5087d7eff923717d85598a46d688e6c73a4468a957428954316f8beaa7730fda5
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data.tar.gz: 6dddb828be0def8f2f9d65a3c152d4be2c6f8cc2e26526b894dbffd4eab117d216514e39b27a4e555b54eba4b67125f9b39d032423006f78ede02a611f2a5987
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class RMetadataHook < Mumukit::Hook
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def metadata
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{language: {
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name: 'r',
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icon: {type: 'devicon', name: 'r'},
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version: '3.6.1',
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extension: 'R',
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ace_mode: 'R'
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},
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test_framework: {
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name: 'testthat',
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version: '2.3.1', # FIXME fix version using devtools
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test_extension: '.R',
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template: <<R
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test_that("{{ test_template_sample_description }}", {
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expect_true( TRUE )
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})
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R
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}}
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end
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end
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data/lib/query_hook.rb
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class RQueryHook < Mumukit::Templates::FileHook
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with_error_patterns
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isolated true
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def tempfile_extension
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'.R'
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end
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def compile_file_content(r)
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"#{compile_file_header(r)}\n#{compile_query(r.query)}"
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end
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def compile_file_header(r)
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<<R
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#{r.extra}
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#{r.content}
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#{compile_cookie(r.cookie)}
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R
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end
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def compile_query(query)
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query
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end
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def compile_cookie(cookie)
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return if cookie.blank?
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compile_statements(cookie).join "\n"
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end
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def command_line(filename)
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"Rscript #{filename}"
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end
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private
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def compile_statements(cookie)
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cookie.map { |query| "invisible(tryCatch({ #{query} }, error = function(e) {}))" }
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end
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def error_patterns
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[
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Mumukit::ErrorPattern::Errored.new(/(?=Execution halted\n$)/)
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]
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end
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end
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data/lib/r_runner.rb
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require 'mumukit'
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require 'nokogiri'
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Mumukit.runner_name = 'r'
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Mumukit.configure do |config|
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config.docker_image = 'mumuki/mumuki-r-worker:0.1'
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config.structured = true
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config.stateful = true
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end
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require_relative './version'
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require_relative './metadata_hook'
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require_relative './test_hook'
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require_relative './query_hook'
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require_relative './try_hook'
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data/lib/test_hook.rb
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class RTestHook < Mumukit::Templates::FileHook
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isolated true
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structured true
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def compile_file_content(request)
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<<R
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#{request.extra}
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#{request.content}
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#{request.test}
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R
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end
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def tempfile_extension
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'.R'
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end
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def command_line(filename)
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%Q{R -q -e testthat::test_file('#{filename}',reporter='junit')} #TODO use
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end
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def post_process_file(file, result, status)
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if status.failed?
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[result, :errored]
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else
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super
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end
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end
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def to_structured_result(result)
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clean_xml = result.gsub(/^>.+$/, '')
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transform(Nokogiri::XML(clean_xml).xpath('//testcase'))
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end
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def transform(examples)
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examples.map do |it|
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failure = it.at('failure', 'error')
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if failure
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[it['name'].gsub('_', ' '), :failed, failure.content]
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else
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[it['name'].gsub('_', ' '), :passed, '']
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end
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end
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end
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def cleanup_raw_result(result)
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super(result.gsub 'tmpmumuki', '/tmp/mumuki')
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end
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end
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data/lib/try_hook.rb
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class RTryHook < Mumukit::Templates::TryHook
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isolated true
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attr_reader :query_hook
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def initialize(config = nil)
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super config
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@query_hook = RQueryHook.new
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end
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def compile_file_content(r)
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<<R
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#{@query_hook.compile_file_header(r)}
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cat("#{query_separator}", fill = TRUE);
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#{@query_hook.compile_query(r.query)}
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cat("#{goal_separator}", fill = TRUE);
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#{@query_hook.compile_query(r.goal.with_indifferent_access[:query] || 'NULL')}
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R
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end
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delegate :tempfile_extension, to: :query_hook
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delegate :command_line, to: :query_hook
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def query_separator
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'!!!MUMUKI-QUERY-START!!!'
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end
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def goal_separator
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'!!!MUMUKI-GOAL-START!!!'
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end
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def to_structured_results(_file, result, status)
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/#{query_separator}
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?(.*)
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#{goal_separator}
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?(.*)
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/m =~ result
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{
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query: to_query_result($1, status),
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goal: $2,
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status: status
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}
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end
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def to_query_result(result, status)
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{ result: result, status: status }
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end
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end
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data/lib/version.rb
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metadata
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--- !ruby/object:Gem::Specification
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name: mumuki-r-runner
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version: !ruby/object:Gem::Version
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version: 0.1.0
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platform: ruby
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authors:
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- Franco Leonardo Bulgarelli
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2020-02-06 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: mumukit
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.30'
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.30'
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '2.0'
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.0'
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3.4'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3.4'
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- !ruby/object:Gem::Dependency
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name: codeclimate-test-reporter
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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- !ruby/object:Gem::Dependency
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name: mumukit-bridge
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3.5'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3.5'
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description:
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email:
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- franco@mumuki.org
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executables: []
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extensions: []
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extra_rdoc_files: []
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files:
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- lib/metadata_hook.rb
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- lib/query_hook.rb
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- lib/r_runner.rb
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- lib/test_hook.rb
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- lib/try_hook.rb
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- lib/version.rb
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homepage: http://github.com/mumuki/mumuki-r-runner
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licenses:
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- MIT
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metadata: {}
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post_install_message:
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rdoc_options: []
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require_paths:
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- lib
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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- - ">="
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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rubygems_version: 3.0.3
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signing_key:
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specification_version: 4
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summary: R Runner for Mumuki
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test_files: []
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