flex-station-data 0.3.0 → 1.0.2

checksums.yaml

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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

@@ -9,3 +9,5 @@
 
 # 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

@@ -0,0 +1 @@
+2.7.1

data/CHANGELOG.md

@@ -1,7 +1,29 @@
+# 1.0.2
+
+* Update to Ruby 2.7.1
+* Introduce Rubocop
+* Added "Ruby" GitHub workflow
+
+# 1.0.1
+
+* Miscellaneous refactoring.
+
+# 1.0.0
+
+* Removed option for sample data report and verbose linear regression report.
+
+# 0.3.2
+
+* Internal refactoring
+
+# 0.3.1
+
+* Fixed bug
+
 # 0.3.0
 
 * The linear regression analysis report now produces a summary report of the
-  regression for each sample. The sample data can by added by sSpecifying the
+  regression for each sample. The sample data can by added by specifying the
   `--verbose` option.
 
 # 0.2.0

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 (0.3.0)
+    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/README.md

@@ -2,8 +2,6 @@
 
 Tools for reading and analyzing data from the FlexStation microplate reader.
 
-Currently this is somewhere between alpha and beta.
-
 ## Installation
 
 Add this line to your application's Gemfile:
@@ -28,51 +26,40 @@ To update your installation, use:
 
 ## Usage
 
-### Viewing the sample data
-
-To view the sample results from a set of plate readings, use the following
+To perform a linear regression analysis on the sample data, use the following
 command:
 
-    $ flex-station sample-data <source file> [--threshold=<threshold>]
+    $ flex-station linear-regression <source file> [--threshold=<threshold>] [--min-r-squared=<minimum R²>]
 
 Where `source file` is the file that you got from the reader. You can specify
 multiple source files. The `threshold` setting is optional. If provided,
 samples with values that are below the `threshold` value will be skipped.
 `threshold` must be a number.
 
+If a `--min-r-squared` value is given, samples with a R² value that falls
+below the threshold will be flagged as "poor fits." If no `--min-r-squared` is
+specified, a default of 0.75 will be used.
+
 The output is in CSV format. You'll probably want to save it to a file. You
 can do that by piping the output to a file:
 
-    $ flex-station sample-data source-data.csv --threshold=300 > sample-data.csv
-
-### Performing linear regression analysis on the sample data
-
-To perform a linear regression analysis on the sample data, use the following
-command:
-
-    $ flex-station-data liinear-regression <source file> [--threshold=<threshold>] [--verbose] [--min-r-squared=<mininmum R²>]
-
-Note that the `source file` and `threshold` options are the same as for the
-`sample-data` command above. If a `--min-r-squared` value is given, samples
-with a R² value that falls below the threshold will be flagged as "poor fits."
-If no `--min-r-squared` is specified, a default of 0.75 will be used.
-
-By default the linear regression tool will produce a summary report giving the
-slope, intercept, and R² values for each sample. However if `--verbose` is
-specified, it will also include the sample data and regressions for each well.
-
-As with the sample data tool, you will probably want to pipe the output to a file:
-
     $ flex-station linear-regression source-data.csv --threshold=300 > linear-regression.csv
 
 ## Contributing
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/johncarney/flex-station-data. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+Bug reports and pull requests are welcome on GitHub at
+https://github.com/johncarney/flex-station-data. This project is intended to
+be a safe, welcoming space for collaboration, and contributors are expected to
+adhere to the [Contributor Covenant](http://contributor-covenant.org) code of
+conduct.
 
 ## License
 
-The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+The gem is available as open source under the terms of the
+[MIT License](https://opensource.org/licenses/MIT).
 
 ## Code of Conduct
 
-Everyone interacting in the FlexStationData project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/johncarney/flex-station-data/blob/master/CODE_OF_CONDUCT.md).
+Everyone interacting in the FlexStationData project’s codebases, issue
+trackers, chat rooms and mailing lists is expected to follow the
+[code of conduct](https://github.com/johncarney/flex-station-data/blob/master/CODE_OF_CONDUCT.md).

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

@@ -1,16 +1,38 @@
 #!/usr/bin/env ruby
+# frozen_string_literal: true
 
 require "pathname"
+require "flex_station_data/concerns/callable"
 
-case command = ARGV.first
-when "sample-data"
-  system(Pathname(__dir__).join("flex-station-sample-data").to_path, *ARGV.drop(1))
-when "linear-regression"
-  system(Pathname(__dir__).join("flex-station-linear-regression").to_path, *ARGV.drop(1))
-when nil
-  $stderr.puts "USAGE: flex-station <command>"
-  exit(1)
-else
-  $stderr.puts "Unrecognised command: #{command}"
-  exit(1)
+class App
+  include FlexStationData::Concerns::Callable[:run]
+
+  attr_reader :command, :args
+
+  def initialize(command = "help", *args)
+    @command = command
+    @args    = args
+  end
+
+  def dir_path
+    Pathname(__dir__)
+  end
+
+  def linear_regression_path
+    dir_path.join("flex-station-linear-regression")
+  end
+
+  def run
+    case command
+    when "linear-regression"
+      exec(linear_regression_path.to_path, *args)
+    when "help", "--help"
+      puts "USAGE: flex-station <command>"
+    else
+      warn "Unrecognised command: #{command}"
+      exit(1)
+    end
+  end
 end
+
+App.run(*ARGV)