bio-miga/miga

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Avoid the use of Perl-style backrefs.
Open

        stats[:"#{$1}_pvalue"] = $3.to_f unless $1 == 'root'
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Redundant self detected.
Open

    self.load if self.metadata.nil?
Severity: Minor
Found in lib/miga/project.rb by rubocop

This cop checks for redundant uses of self.

The usage of self is only needed when:

  • Sending a message to same object with zero arguments in presence of a method name clash with an argument or a local variable.

  • Calling an attribute writer to prevent an local variable assignment.

Note, with using explicit self you can only send messages with public or protected scope, you cannot send private messages this way.

Note we allow uses of self with operators because it would be awkward otherwise.

Example:

# bad
def foo(bar)
  self.baz
end

# good
def foo(bar)
  self.bar  # Resolves name clash with the argument.
end

def foo
  bar = 1
  self.bar  # Resolves name clash with the local variable.
end

def foo
  %w[x y z].select do |bar|
    self.bar == bar  # Resolves name clash with argument of the block.
  end
end

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

        ('%.1f%% (%s/%s)' % vals)
Severity: Minor
Found in lib/miga/common.rb by rubocop

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Use snake_case for variable names.
Open

  @@OPTIONS = {
Severity: Minor
Found in lib/miga/project/base.rb by rubocop

This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.

Example: EnforcedStyle: snake_case (default)

# bad
fooBar = 1

# good
foo_bar = 1

Example: EnforcedStyle: camelCase

# bad
foo_bar = 1

# good
fooBar = 1

Use snake_case for method names.
Open

  def self.FULL_VERSION
Severity: Minor
Found in lib/miga/version.rb by rubocop

This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.

Example: EnforcedStyle: snake_case (default)

# bad
def fooBar; end

# good
def foo_bar; end

Example: EnforcedStyle: camelCase

# bad
def foo_bar; end

# good
def fooBar; end

Missing top-level class documentation comment.
Open

class MiGA::MiGA
Severity: Minor
Found in lib/miga/version.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

Avoid the use of double negation (!!).
Open

    !!self[:clean]
Severity: Minor
Found in lib/miga/result.rb by rubocop

This cop checks for uses of double negation (!!) to convert something to a boolean value. As this is both cryptic and usually redundant, it should be avoided.

Example:

# bad
!!something

# good
!something.nil?

Please, note that when something is a boolean value !!something and !something.nil? are not the same thing. As you're unlikely to write code that can accept values of any type this is rarely a problem in practice.

Use snake_case for method names.
Open

    def INCLADE_TASKS
Severity: Minor
Found in lib/miga/project/base.rb by rubocop

This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.

Example: EnforcedStyle: snake_case (default)

# bad
def fooBar; end

# good
def foo_bar; end

Example: EnforcedStyle: camelCase

# bad
def foo_bar; end

# good
def fooBar; end

Use snake_case for method names.
Open

    def KNOWN_TYPES
Severity: Minor
Found in lib/miga/project/base.rb by rubocop

This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.

Example: EnforcedStyle: snake_case (default)

# bad
def fooBar; end

# good
def foo_bar; end

Example: EnforcedStyle: camelCase

# bad
def foo_bar; end

# good
def fooBar; end

Replace class var @@OPTIONS with a class instance var.
Open

  @@OPTIONS = {
Severity: Minor
Found in lib/miga/project/base.rb by rubocop

This cop checks for uses of class variables. Offenses are signaled only on assignment to class variables to reduce the number of offenses that would be reported.

Use yield instead of blk.call.
Open

        when 1 then blk.call(file)
Severity: Minor
Found in lib/miga/result.rb by rubocop

This cop identifies the use of a &block parameter and block.call where yield would do just as well.

Example:

# bad
def method(&block)
  block.call
end
def another(&func)
  func.call 1, 2, 3
end

# good
def method
  yield
end
def another
  yield 1, 2, 3
end

Use yield instead of blk.call.
Open

        when 3 then blk.call(k, file, File.expand_path(file, dir))
Severity: Minor
Found in lib/miga/result.rb by rubocop

This cop identifies the use of a &block parameter and block.call where yield would do just as well.

Example:

# bad
def method(&block)
  block.call
end
def another(&func)
  func.call 1, 2, 3
end

# good
def method
  yield
end
def another
  yield 1, 2, 3
end

Avoid the use of double negation (!!).
Open

    !!runopts(:bypass_maintenance)
Severity: Minor
Found in lib/miga/daemon/base.rb by rubocop

This cop checks for uses of double negation (!!) to convert something to a boolean value. As this is both cryptic and usually redundant, it should be avoided.

Example:

# bad
!!something

# good
!something.nil?

Please, note that when something is a boolean value !!something and !something.nil? are not the same thing. As you're unlikely to write code that can accept values of any type this is rarely a problem in practice.

Avoid the use of Perl-style backrefs.
Open

      stats[:closest_relative] = $1
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid the use of Perl-style backrefs.
Open

        stats[:"#{$1}_pvalue"] = $3.to_f unless $1 == 'root'
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Missing magic comment # frozen_string_literal: true.
Open

class MiGA::Result < MiGA::MiGA
Severity: Minor
Found in lib/miga/result/base.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

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

Avoid the use of double negation (!!).
Open

    !!runopts(:shutdown_when_done)
Severity: Minor
Found in lib/miga/daemon/base.rb by rubocop

This cop checks for uses of double negation (!!) to convert something to a boolean value. As this is both cryptic and usually redundant, it should be avoided.

Example:

# bad
!!something

# good
!something.nil?

Please, note that when something is a boolean value !!something and !something.nil? are not the same thing. As you're unlikely to write code that can accept values of any type this is rarely a problem in practice.

Do not use parallel assignment.
Open

          id, df = $1, $2
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

Checks for simple usages of parallel assignment. This will only complain when the number of variables being assigned matched the number of assigning variables.

Example:

# bad
a, b, c = 1, 2, 3
a, b, c = [1, 2, 3]

# good
one, two = *foo
a, b = foo()
a, b = b, a

a = 1
b = 2
c = 3

Avoid rescuing without specifying an error class.
Open

      rescue
Severity: Minor
Found in lib/miga/common/format.rb by rubocop

This cop checks for rescuing StandardError. There are two supported styles implicit and explicit. This cop will not register an offense if any error other than StandardError is specified.

Example: EnforcedStyle: implicit

# `implicit` will enforce using `rescue` instead of
# `rescue StandardError`.

# bad
begin
  foo
rescue StandardError
  bar
end

# good
begin
  foo
rescue
  bar
end

# good
begin
  foo
rescue OtherError
  bar
end

# good
begin
  foo
rescue StandardError, SecurityError
  bar
end

Example: EnforcedStyle: explicit (default)

# `explicit` will enforce using `rescue StandardError`
# instead of `rescue`.

# bad
begin
  foo
rescue
  bar
end

# good
begin
  foo
rescue StandardError
  bar
end

# good
begin
  foo
rescue OtherError
  bar
end

# good
begin
  foo
rescue StandardError, SecurityError
  bar
end
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