bio-miga/miga

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lib/miga/tax_dist.rb

Summary

Maintainability
A
3 hrs
Test Coverage
A
100%

Method has too many lines. [22/10]
Open

    def aai_pvalues(aai, test, opts = {})
      y = {}
      Zlib::GzipReader.open(aai_path(test, opts)) do |fh|
        keys = nil
        fh.each_line do |ln|
Severity: Minor
Found in lib/miga/tax_dist.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.

Assignment Branch Condition size for aai_pvalues is too high. [24.1/15]
Open

    def aai_pvalues(aai, test, opts = {})
      y = {}
      Zlib::GzipReader.open(aai_path(test, opts)) do |fh|
        keys = nil
        fh.each_line do |ln|
Severity: Minor
Found in lib/miga/tax_dist.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 aai_taxtest(aai, test, opts = {})
      meaning = {
        most_likely: [0.00, 0.01],
        probably: [0.01, 0.10],
        possibly_even: [0.10, 0.50]
Severity: Minor
Found in lib/miga/tax_dist.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 aai_pvalues has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

    def aai_pvalues(aai, test, opts = {})
      y = {}
      Zlib::GzipReader.open(aai_path(test, opts)) do |fh|
        keys = nil
        fh.each_line do |ln|
Severity: Minor
Found in lib/miga/tax_dist.rb - About 2 hrs 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

Assignment Branch Condition size for aai_taxtest is too high. [16.09/15]
Open

    def aai_taxtest(aai, test, opts = {})
      meaning = {
        most_likely: [0.00, 0.01],
        probably: [0.01, 0.10],
        possibly_even: [0.10, 0.50]
Severity: Minor
Found in lib/miga/tax_dist.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 aai_taxtest has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
Open

    def aai_taxtest(aai, test, opts = {})
      meaning = {
        most_likely: [0.00, 0.01],
        probably: [0.01, 0.10],
        possibly_even: [0.10, 0.50]
Severity: Minor
Found in lib/miga/tax_dist.rb - About 45 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

Method aai_path has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

    def aai_path(test, opts = {})
      opts[:engine] ||= :blast
      engine = opts[:engine].to_s.downcase.to_sym
      test = test.to_s.downcase.to_sym
      return nil unless %i[intax novel].include? test
Severity: Minor
Found in lib/miga/tax_dist.rb - About 25 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 magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/tax_dist.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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