bio-miga/miga

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lib/miga/taxonomy.rb

Summary

Maintainability
A
1 hr
Test Coverage
A
100%

Class has too many lines. [111/100]
Open

class MiGA::Taxonomy < MiGA::MiGA
  include MiGA::Taxonomy::Base

  ##
  # Taxonomic hierarchy Hash.
Severity: Minor
Found in lib/miga/taxonomy.rb by rubocop

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

Method has too many lines. [13/10]
Open

  def <<(value)
    case value
    when Hash
      value.each do |r, n|
        next if n.nil? || n == ''
Severity: Minor
Found in lib/miga/taxonomy.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 << is too high. [15.84/15]
Open

  def <<(value)
    case value
    when Hash
      value.each do |r, n|
        next if n.nil? || n == ''
Severity: Minor
Found in lib/miga/taxonomy.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 sorted_ranks has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def sorted_ranks(force_ranks = false, with_namespace = false)
    @@KNOWN_RANKS.map do |r|
      next if
        (r == :ns && !with_namespace) || (ranks[r].nil? && !force_ranks)

Severity: Minor
Found in lib/miga/taxonomy.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

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

  def initialize_by_ranks(str, ranks)
    ranks = ranks.split(/\s+/) unless ranks.is_a? Array
    str = str.split(/\s+/) unless str.is_a? Array
    unless ranks.size == str.size
      raise "Unequal number of ranks and names: #{ranks} => #{str}"
Severity: Minor
Found in lib/miga/taxonomy.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

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

  def <<(value)
    case value
    when Hash
      value.each do |r, n|
        next if n.nil? || n == ''
Severity: Minor
Found in lib/miga/taxonomy.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

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

  def add_alternative(tax, replace = true)
    return if tax.nil?
    raise 'Unsupported taxonomy class.' unless tax.is_a? MiGA::Taxonomy

    alt_ns = alternative(tax.namespace)
Severity: Minor
Found in lib/miga/taxonomy.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

Use alias fetch [] instead of alias :fetch :[].
Open

  alias :fetch :[]
Severity: Minor
Found in lib/miga/taxonomy.rb by rubocop

This cop enforces the use of either #alias or #alias_method depending on configuration. It also flags uses of alias :symbol rather than alias bareword.

Example: EnforcedStyle: prefer_alias (default)

# bad
alias_method :bar, :foo
alias :bar :foo

# good
alias bar foo

Example: EnforcedStyle: preferaliasmethod

# bad
alias :bar :foo
alias bar foo

# good
alias_method :bar, :foo

Line is too long. [81/80]
Open

      " #{str} ".scan(/(?<= )([A-Za-z]+):([^:]*) /) { |r, n| self << { r => n } }
Severity: Minor
Found in lib/miga/taxonomy.rb by rubocop

Missing magic comment # frozen_string_literal: true.
Open

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