flex-station-data 1.0.1 → 1.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/.github/workflows/ruby.yml

@@ -0,0 +1,33 @@
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+# This workflow will download a prebuilt Ruby version, install dependencies and run tests with Rake
+# For more information see: https://github.com/marketplace/actions/setup-ruby-jruby-and-truffleruby
+
+name: Ruby
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+    # To automatically get bug fixes and new Ruby versions for ruby/setup-ruby,
+    # change this to (see https://github.com/ruby/setup-ruby#versioning):
+    # uses: ruby/setup-ruby@v1
+      uses: ruby/setup-ruby@ec106b438a1ff6ff109590de34ddc62c540232e0
+      with:
+        ruby-version: 2.7
+    - name: Install dependencies
+      run: bundle install
+    - name: Run tests
+      run: bundle exec rake

data/.gitignore

@@ -10,3 +10,4 @@
 # rspec failure tracking
 .rspec_status
 .idea/
+.rbenv-gemsets

data/.rubocop.yml

@@ -0,0 +1,106 @@
+Layout/EmptyLinesAroundAttributeAccessor:
+  Enabled: true
+
+Layout/ExtraSpacing:
+  Exclude:
+    - spec/**/*_spec.rb
+
+Layout/HashAlignment:
+  EnforcedHashRocketStyle: table
+  EnforcedColonStyle:      table
+
+Layout/LineLength:
+  Exclude:
+    - spec/**/*_spec.rb
+
+Layout/MultilineMethodCallIndentation:
+  EnforcedStyle: indented
+
+Layout/SpaceAroundMethodCallOperator:
+  Enabled: true
+
+Layout/SpaceInsideArrayLiteralBrackets:
+  Enabled: false
+
+Layout/SpaceInsidePercentLiteralDelimiters:
+  Enabled: false
+
+Lint/DeprecatedOpenSSLConstant:
+  Enabled: true
+
+Lint/MixedRegexpCaptureTypes:
+  Enabled: true
+
+Lint/RaiseException:
+  Enabled: true
+
+Lint/StructNewOverride:
+  Enabled: true
+
+Metrics/BlockLength:
+  Exclude:
+    - spec/**/*_spec.rb
+
+Metrics/MethodLength:
+  Max: 12
+
+Naming/MethodParameterName:
+  Enabled: false
+
+Naming/VariableNumber:
+  EnforcedStyle: snake_case
+
+Style/AccessorGrouping:
+  Enabled: false
+
+Style/BisectedAttrAccessor:
+  Enabled: true
+
+Style/Documentation:
+  Enabled: false
+
+Style/ExponentialNotation:
+  Enabled: false
+
+Style/HashEachMethods:
+  Enabled: false
+
+Style/HashTransformKeys:
+  Enabled: true
+
+Style/HashTransformValues:
+  Enabled: true
+
+Style/PercentLiteralDelimiters:
+  Exclude:
+    - flex-station-data.gemspec
+
+Style/RedundantAssignment:
+  Enabled: true
+
+Style/RedundantFetchBlock:
+  Enabled: true
+
+Style/RedundantPercentQ:
+  Exclude:
+    - flex-station-data.gemspec
+
+Style/RedundantRegexpCharacterClass:
+  Enabled: true
+
+Style/RedundantRegexpEscape:
+  Enabled: true
+
+Style/SlicingWithRange:
+  Enabled: true
+
+Style/StringLiterals:
+  EnforcedStyle: double_quotes
+
+Style/SymbolArray:
+  Exclude:
+    - spec/**/*_spec.rb
+
+Style/WordArray:
+  Exclude:
+    - spec/**/*_spec.rb

data/.ruby-version

@@ -1 +1 @@
-2.5.6
+2.7.1

data/CHANGELOG.md

@@ -1,3 +1,9 @@
+# 1.0.2
+
+* Update to Ruby 2.7.1
+* Introduce Rubocop
+* Added "Ruby" GitHub workflow
+
 # 1.0.1
 
 * Miscellaneous refactoring.

data/Gemfile

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 source "https://rubygems.org"
 
 # Specify your gem's dependencies in flex-station-data.gemspec

data/Gemfile.lock

@@ -1,48 +1,70 @@
 PATH
   remote: .
   specs:
-    flex-station-data (1.0.1)
+    flex-station-data (1.0.2)
       activesupport
       linefit
 
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.0.0)
+    activesupport (6.0.3.2)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
-      zeitwerk (~> 2.1, >= 2.1.8)
-    coderay (1.1.2)
-    concurrent-ruby (1.1.5)
-    diff-lcs (1.3)
-    i18n (1.6.0)
+      zeitwerk (~> 2.2, >= 2.2.2)
+    ast (2.4.1)
+    coderay (1.1.3)
+    concurrent-ruby (1.1.6)
+    diff-lcs (1.4.4)
+    i18n (1.8.3)
       concurrent-ruby (~> 1.0)
     linefit (0.3.4)
-    method_source (0.9.2)
-    minitest (5.11.3)
-    pry (0.12.2)
-      coderay (~> 1.1.0)
-      method_source (~> 0.9.0)
-    rake (10.5.0)
-    rspec (3.8.0)
-      rspec-core (~> 3.8.0)
-      rspec-expectations (~> 3.8.0)
-      rspec-mocks (~> 3.8.0)
-    rspec-core (3.8.2)
-      rspec-support (~> 3.8.0)
-    rspec-expectations (3.8.4)
+    method_source (1.0.0)
+    minitest (5.14.1)
+    parallel (1.19.2)
+    parser (2.7.1.4)
+      ast (~> 2.4.1)
+    pry (0.13.1)
+      coderay (~> 1.1)
+      method_source (~> 1.0)
+    rainbow (3.0.0)
+    rake (13.0.1)
+    regexp_parser (1.7.1)
+    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 (~> 3.8.0)
-    rspec-mocks (3.8.1)
+      rspec-support (~> 3.9.0)
+    rspec-mocks (3.9.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.8.0)
-    rspec-support (3.8.2)
+      rspec-support (~> 3.9.0)
+    rspec-support (3.9.3)
+    rubocop (0.87.1)
+      parallel (~> 1.10)
+      parser (>= 2.7.1.1)
+      rainbow (>= 2.2.2, < 4.0)
+      regexp_parser (>= 1.7)
+      rexml
+      rubocop-ast (>= 0.1.0, < 1.0)
+      ruby-progressbar (~> 1.7)
+      unicode-display_width (>= 1.4.0, < 2.0)
+    rubocop-ast (0.1.0)
+      parser (>= 2.7.0.1)
+    rubocop-rspec (1.42.0)
+      rubocop (>= 0.87.0)
+    ruby-progressbar (1.10.1)
     thread_safe (0.3.6)
-    tzinfo (1.2.5)
+    tzinfo (1.2.7)
       thread_safe (~> 0.1)
-    zeitwerk (2.1.9)
+    unicode-display_width (1.7.0)
+    zeitwerk (2.3.1)
 
 PLATFORMS
   ruby
@@ -51,8 +73,9 @@ DEPENDENCIES
   bundler (~> 2.0)
   flex-station-data!
   pry
-  rake (~> 10.0)
+  rake (~> 13.0)
   rspec (~> 3.8)
+  rubocop-rspec
 
 BUNDLED WITH
-   2.0.2
+   2.1.4

data/Rakefile

@@ -1,6 +1,10 @@
+# frozen_string_literal: true
+
 require "bundler/gem_tasks"
 require "rspec/core/rake_task"
+require "rubocop/rake_task"
 
 RSpec::Core::RakeTask.new(:spec)
+RuboCop::RakeTask.new(:rubocop)
 
-task :default => :spec
+task default: %i[ rubocop spec ]

data/bin/flex-station

@@ -1,4 +1,5 @@
 #!/usr/bin/env ruby
+# frozen_string_literal: true
 
 require "pathname"
 require "flex_station_data/concerns/callable"
@@ -28,7 +29,7 @@ class App
     when "help", "--help"
       puts "USAGE: flex-station <command>"
     else
-      $stderr.puts "Unrecognised command: #{command}"
+      warn "Unrecognised command: #{command}"
       exit(1)
     end
   end

data/bin/flex-station-linear-regression

@@ -1,4 +1,5 @@
 #!/usr/bin/env ruby
+# frozen_string_literal: true
 
 require "flex_station_data/concerns/callable"
 require "flex_station_data/services/load_plates"
@@ -27,11 +28,15 @@ module FlexStationData
     end
 
     def threshold
-      Float(option(:threshold)) rescue nil
+      Float(option(:threshold))
+    rescue ArgumentError, TypeError
+      nil
     end
 
     def min_r_squared
-      Float(option("min-r-squared")) rescue 0.75
+      Float(option("min-r-squared"))
+    rescue ArgumentError, TypeError
+      0.75
     end
 
     def files
@@ -57,7 +62,7 @@ module FlexStationData
 
     def clean_values(values)
       values.each_with_object([]) do |value, memo|
-        memo << ((value != memo.compact.last) ? value : nil)
+        memo << (value != memo.compact.last ? value : nil)
       end
     end
 

data/flex-station-data.gemspec

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 lib = File.expand_path("lib", __dir__)
 $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
 require "flex_station_data/version"
@@ -21,19 +23,20 @@ Gem::Specification.new do |spec|
 
   # Specify which files should be added to the gem when it is released.
   # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
-  spec.files = Dir.chdir(File.expand_path('..', __FILE__)) do
+  spec.files = Dir.chdir(File.expand_path(__dir__)) do
     `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
   end
   spec.bindir        = "bin"
   spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
 
-  spec.required_ruby_version = ">= 2.5.6"
+  spec.required_ruby_version = ">= 2.7.1"
 
   spec.add_development_dependency "bundler", "~> 2.0"
-  spec.add_development_dependency "rake", "~> 10.0"
-  spec.add_development_dependency "rspec", "~> 3.8"
   spec.add_development_dependency "pry"
+  spec.add_development_dependency "rake", "~> 13.0"
+  spec.add_development_dependency "rspec", "~> 3.8"
+  spec.add_development_dependency "rubocop-rspec"
 
   spec.add_runtime_dependency "activesupport"
   spec.add_runtime_dependency "linefit"

data/lib/flex_station_data.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/version"
 
 module FlexStationData

data/lib/flex_station_data/concerns/callable.rb

@@ -1,33 +1,33 @@
+# frozen_string_literal: true
+
 module FlexStationData
   module Concerns
     module Callable
       class << self
-        def [](verb)
-          @@__callable_modules[verb] ||= Module.new.tap { |mod| __make_callable(mod, verb) }
+        def included(base)
+          base.include with(:call)
         end
 
-        private
-
-        def __make_callable(mod, verb)
-          class_methods = Module.new do
-            define_method verb do |*args, &block|
-              new(*args).send(verb, &block)
-            end
+        def with(verb)
+          callable_modules[verb.to_sym] ||= Module.new do
+            define_singleton_method(:included) do |base|
+              base.define_singleton_method(verb) do |*args|
+                new(*args).public_send(verb)
+              end
 
-            define_method :to_proc do
-              Proc.new(&method(verb))
+              base.define_singleton_method(:to_proc) do
+                method(verb).to_proc
+              end
             end
           end
-
-          mod.singleton_class.define_method :included do |base|
-            base.extend class_methods
-          end
         end
-      end
 
-      __make_callable(self, :call)
+        alias [] with
 
-      @@__callable_modules = { call: self }
+        def callable_modules
+          @callable_modules ||= {}
+        end
+      end
     end
   end
 end

data/lib/flex_station_data/concerns/presenter.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_relative "callable"
 
 module FlexStationData

data/lib/flex_station_data/concerns/service.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require_relative "callable"
 
 module FlexStationData

data/lib/flex_station_data/default_sample_map.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module FlexStationData
   class DefaultSampleMap
     attr_reader :rows, :columns, :wells_per_sample
@@ -20,7 +22,7 @@ module FlexStationData
       row_label = ("A".ord + row).chr
       base_column = (column * wells_per_sample) + 1
       (0...wells_per_sample).map do |column_offset|
-        [ row_label, base_column +column_offset ].join("")
+        [ row_label, base_column + column_offset ].join("")
       end
     end
 

data/lib/flex_station_data/linear_regression.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "active_support/core_ext"
 require "linefit"
 

data/lib/flex_station_data/plate.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/sample"
 
 module FlexStationData

data/lib/flex_station_data/presenters/plate_hash.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/presenters/sample_hash"
 
 module FlexStationData

data/lib/flex_station_data/presenters/plates_hash.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/presenters/plate_hash"
 
 module FlexStationData

data/lib/flex_station_data/presenters/sample_hash.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/concerns/presenter"
 require "flex_station_data/services/sample_quality"
 require "flex_station_data/presenters/sample_regression_hash"

data/lib/flex_station_data/presenters/sample_regression_hash.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/concerns/presenter"
 require "flex_station_data/linear_regression"
 

data/lib/flex_station_data/sample.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "matrix"
 
 require "flex_station_data/services/compute_mean"

data/lib/flex_station_data/services/compute_mean.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "active_support/core_ext"
 
 require "flex_station_data/concerns/service"

data/lib/flex_station_data/services/load_plates.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "csv"
 require "active_support/core_ext"
 

data/lib/flex_station_data/services/parse_plate.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "active_support/core_ext"
 
 require "flex_station_data/services/parse_plate_readings"

data/lib/flex_station_data/services/parse_plate_readings.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "active_support/core_ext"
 require "matrix"
 
@@ -51,7 +53,9 @@ module FlexStationData
       end
 
       def parse_value(v)
-        return Float(v) rescue v.presence
+        Float(v)
+      rescue ArgumentError, TypeError
+        v.presence
       end
 
       def parse_row(row)
@@ -86,7 +90,7 @@ module FlexStationData
 
     def wells_matrix
       well_row_count = matrix.row_count / times.size
-      Matrix[*well_values.column_vectors.map { |col| col.to_a.each_slice(well_row_count).to_a.transpose }.transpose ]
+      Matrix[*well_values.column_vectors.map { |col| col.to_a.each_slice(well_row_count).to_a.transpose }.transpose]
     end
 
     attr_reader :plate_data

data/lib/flex_station_data/services/parse_sample_map.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "matrix"
 require "active_support/core_ext"
 

data/lib/flex_station_data/services/sample_quality.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "flex_station_data/services/value_quality"
 
 module FlexStationData

data/lib/flex_station_data/services/value_quality.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "singleton"
 require "active_support/core_ext"
 

data/lib/flex_station_data/version.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 module FlexStationData
-  VERSION = "1.0.1"
+  VERSION = "1.0.2"
 end

data/lib/flex_station_data/wells.rb

@@ -1,3 +1,5 @@
+# frozen_string_literal: true
+
 require "matrix"
 
 module FlexStationData

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: flex-station-data
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.0.2
 platform: ruby
 authors:
 - John Carney
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-09-26 00:00:00.000000000 Z
+date: 2020-07-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -24,20 +24,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  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: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '13.0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -53,7 +67,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '3.8'
 - !ruby/object:Gem::Dependency
-  name: pry
+  name: rubocop-rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -103,8 +117,10 @@ executables:
 extensions: []
 extra_rdoc_files: []
 files:
+- ".github/workflows/ruby.yml"
 - ".gitignore"
 - ".rspec"
+- ".rubocop.yml"
 - ".ruby-version"
 - CHANGELOG.md
 - CODE_OF_CONDUCT.md
@@ -151,15 +167,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.5.6
+      version: 2.7.1
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.6.2
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: Data analysis tool for FlexStation microplate reader