bio-miga/miga

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lib/miga/cli/action/tax_test.rb

Summary

Maintainability
A
55 mins
Test Coverage

Assignment Branch Condition size for query_probability_distributions is too high. [32.2/15]
Open

  def query_probability_distributions(d, cr)
    cli.say 'Querying probability distributions'
    tax = closest_relative_tax(cr)
    if %w[intax both].include? cli[:test]
      r = test_closest_relative(cr, tax, :intax)
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Assignment Branch Condition size for closest_relative_tax is too high. [22.83/15]
Open

  def closest_relative_tax(cr)
    cli.puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
    p = cli.load_project
    if cli[:ref_project]
      if (ref = p.option(:ref_project)).nil?
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [17/10]
Open

  def query_probability_distributions(d, cr)
    cli.say 'Querying probability distributions'
    tax = closest_relative_tax(cr)
    if %w[intax both].include? cli[:test]
      r = test_closest_relative(cr, tax, :intax)
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [16/10]
Open

  def closest_relative_tax(cr)
    cli.puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
    p = cli.load_project
    if cli[:ref_project]
      if (ref = p.option(:ref_project)).nil?
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method has too many lines. [12/10]
Open

  def parse_cli
    cli.defaults = { test: 'both', ref_project: false }
    cli.parse do |opt|
      cli.opt_object(opt, [:project, :dataset])
      opt.on(
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method closest_relative_tax has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
Open

  def closest_relative_tax(cr)
    cli.puts "Closest relative: #{cr[0]} with AAI: #{cr[1]}."
    p = cli.load_project
    if cli[:ref_project]
      if (ref = p.option(:ref_project)).nil?
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb - About 55 mins to fix

Cognitive Complexity

Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

A method's cognitive complexity is based on a few simple rules:

  • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
  • Code is considered more complex for each "break in the linear flow of the code"
  • Code is considered more complex when "flow breaking structures are nested"

Further reading

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::TaxTest < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks for missing top-level documentation of classes and modules. Classes with no body are exempt from the check and so are namespace modules - modules that have nothing in their bodies except classes, other modules, or constant definitions.

The documentation requirement is annulled if the class or module has a "#:nodoc:" comment next to it. Likewise, "#:nodoc: all" does the same for all its children.

Example:

# bad
class Person
  # ...
end

# good
# Description/Explanation of Person class
class Person
  # ...
end

Use || instead of or.
Open

    if cr.nil? or cr.empty?
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions, or in all contexts.

Example: EnforcedStyle: always (default)

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

Unused method argument - d. If it's necessary, use _ or _d as an argument name to indicate that it won't be used.
Open

  def query_probability_distributions(d, cr)
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks for unused method arguments.

Example:

# bad

def some_method(used, unused, _unused_but_allowed)
  puts used
end

Example:

# good

def some_method(used, _unused, _unused_but_allowed)
  puts used
end

Use %i or %I for an array of symbols.
Open

      cli.opt_object(opt, [:project, :dataset])
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop can check for array literals made up of symbols that are not using the %i() syntax.

Alternatively, it checks for symbol arrays using the %i() syntax on projects which do not want to use that syntax.

Configuration option: MinSize If set, arrays with fewer elements than this value will not trigger the cop. For example, a MinSize of3` will not enforce a style on an array of 2 or fewer elements.

Example: EnforcedStyle: percent (default)

# good
%i[foo bar baz]

# bad
[:foo, :bar, :baz]

Example: EnforcedStyle: brackets

# good
[:foo, :bar, :baz]

# bad
%i[foo bar baz]

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop is designed to help upgrade to Ruby 3.0. It will add the comment # frozen_string_literal: true to the top of files to enable frozen string literals. Frozen string literals may be default in Ruby 3.0. The comment will be added below a shebang and encoding comment. The frozen string literal comment is only valid in Ruby 2.3+.

Example: EnforcedStyle: when_needed (default)

# The `when_needed` style will add the frozen string literal comment
# to files only when the `TargetRubyVersion` is set to 2.3+.
# bad
module Foo
  # ...
end

# good
# frozen_string_literal: true

module Foo
  # ...
end

Example: EnforcedStyle: always

# The `always` style will always add the frozen string literal comment
# to a file, regardless of the Ruby version or if `freeze` or `<<` are
# called on a string literal.
# bad
module Bar
  # ...
end

# good
# frozen_string_literal: true

module Bar
  # ...
end

Example: EnforcedStyle: never

# The `never` will enforce that the frozen string literal comment does
# not exist in a file.
# bad
# frozen_string_literal: true

module Baz
  # ...
end

# good
module Baz
  # ...
end

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