bio-miga/miga

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lib/miga/project/result.rb

Summary

Maintainability
A
25 mins
Test Coverage
A
97%

Module has too many lines. [109/100]
Open

module MiGA::Project::Result
  include MiGA::Project::Base
  include MiGA::Common::WithResult

  ##
Severity: Minor
Found in lib/miga/project/result.rb by rubocop

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

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

  def add_result_clade_finding(base, _opts)
    if result_files_exist?(base, %w[.empty])
      r = MiGA::Result.new("#{base}.json")
      r.add_file(:empty, 'miga-project.empty')
      return r
Severity: Minor
Found in lib/miga/project/result.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. [13/10]
Open

  def add_result_subclades(base, _opts)
    if result_files_exist?(base, %w[.empty])
      r = MiGA::Result.new("#{base}.json")
      r.add_file(:empty, 'miga-project.empty')
      return r
Severity: Minor
Found in lib/miga/project/result.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. [13/10]
Open

  def add_result_ogs(base, _opts)
    if result_files_exist?(base, %w[.empty])
      r = MiGA::Result.new("#{base}.json")
      r.add_file(:empty, 'miga-project.empty')
      return r
Severity: Minor
Found in lib/miga/project/result.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. [11/10]
Open

  def add_result_distances(base, _opts)
    return nil unless result_files_exist?(base, ['.txt']) &&
      (result_files_exist?(base, ['.rds']) ||
       result_files_exist?(base, ['.rda']))

Severity: Minor
Found in lib/miga/project/result.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 add_result_clade_finding is too high. [15.65/15]
Open

  def add_result_clade_finding(base, _opts)
    if result_files_exist?(base, %w[.empty])
      r = MiGA::Result.new("#{base}.json")
      r.add_file(:empty, 'miga-project.empty')
      return r
Severity: Minor
Found in lib/miga/project/result.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 add_result_clade_finding has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
Open

  def add_result_clade_finding(base, _opts)
    if result_files_exist?(base, %w[.empty])
      r = MiGA::Result.new("#{base}.json")
      r.add_file(:empty, 'miga-project.empty')
      return r
Severity: Minor
Found in lib/miga/project/result.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

Align the operands of a condition in an unless statement spanning multiple lines.
Open

      (result_files_exist?(base, ['.rds']) ||
       result_files_exist?(base, ['.rda']))
Severity: Minor
Found in lib/miga/project/result.rb by rubocop

This cop checks the indentation of the right hand side operand in binary operations that span more than one line.

Example:

# bad
if a +
b
  something
end

# good
if a +
   b
  something
end

Put empty method definitions on a single line.
Open

  def inactivate!(reason = nil)
  end
Severity: Minor
Found in lib/miga/project/result.rb by rubocop

This cop checks for the formatting of empty method definitions. By default it enforces empty method definitions to go on a single line (compact style), but it can be configured to enforce the end to go on its own line (expanded style).

Note: A method definition is not considered empty if it contains comments.

Example: EnforcedStyle: compact (default)

# bad
def foo(bar)
end

def self.foo(bar)
end

# good
def foo(bar); end

def foo(bar)
  # baz
end

def self.foo(bar); end

Example: EnforcedStyle: expanded

# bad
def foo(bar); end

def self.foo(bar); end

# good
def foo(bar)
end

def self.foo(bar)
end

Missing magic comment # frozen_string_literal: true.
Open

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