bio-miga/miga

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Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/wf.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

Use a guard clause instead of wrapping the code inside a conditional expression.
Open

    if cli[:seqcode_type]
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

Use a guard clause instead of wrapping the code inside a conditional expression

Example:

# bad
def test
  if something
    work
  end
end

# good
def test
  return unless something
  work
end

# also good
def test
  work if something
end

# bad
if something
  raise 'exception'
else
  ok
end

# good
raise 'exception' if something
ok

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

      cli.opt_object(opt, [:project, :dataset_opt, :result])
Severity: Minor
Found in lib/miga/cli/action/stats.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 top-level class documentation comment.
Open

class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/derep_wf.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

Non-local exit from iterator, without return value. next, break, Array#find, Array#any?, etc. is preferred.
Open

    %i[mytaxa rdp reads].each { |i| return if r[0] =~ /\(#{i}\)$/ && !cli[i] }
Severity: Minor
Found in lib/miga/cli/action/init.rb by rubocop

This cop checks for non-local exits from iterators without a return value. It registers an offense under these conditions:

  • No value is returned,
  • the block is preceded by a method chain,
  • the block has arguments,
  • the method which receives the block is not define_method or define_singleton_method,
  • the return is not contained in an inner scope, e.g. a lambda or a method definition.

Example:

class ItemApi
  rescue_from ValidationError do |e| # non-iteration block with arg
    return { message: 'validation error' } unless e.errors # allowed
    error_array = e.errors.map do |error| # block with method chain
      return if error.suppress? # warned
      return "#{error.param}: invalid" unless error.message # allowed
      "#{error.param}: #{error.message}"
    end
    { message: 'validation error', errors: error_array }
  end

  def update_items
    transaction do # block without arguments
      return unless update_necessary? # allowed
      find_each do |item| # block without method chain
        return if item.stock == 0 # false-negative...
        item.update!(foobar: true)
      end
    end
  end
end

Use snake_case for variable names.
Open

  @@INPUT_TYPES = {
Severity: Minor
Found in lib/miga/cli/action/add.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

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

  @@INPUT_TYPES = {
Severity: Minor
Found in lib/miga/cli/action/add.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 snake_case for method names.
Open

    def OPERATIONS
Severity: Minor
Found in lib/miga/cli/action/doctor.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 variable names.
Open

  @@OPERATIONS = {
Severity: Minor
Found in lib/miga/cli/action/doctor.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 each_key instead of keys.each.
Open

    @@OPERATIONS.keys.each do |k|
Severity: Minor
Found in lib/miga/cli/action/doctor.rb by rubocop

This cop checks for uses of each_key and each_value Hash methods.

Note: If you have an array of two-element arrays, you can put parentheses around the block arguments to indicate that you're not working with a hash, and suppress RuboCop offenses.

Example:

# bad
hash.keys.each { |k| p k }
hash.values.each { |v| p v }
hash.each { |k, _v| p k }
hash.each { |_k, v| p v }

# good
hash.each_key { |k| p k }
hash.each_value { |v| p v }

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

      cli.opt_object(opt, [:project, :dataset_type])
Severity: Minor
Found in lib/miga/cli/action/find.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 top-level class documentation comment.
Open

class MiGA::Cli::Action::Run < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/run.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

Unused block argument - v. You can omit the argument if you don't care about it.
Open

      ) { |v| cli[:criterion] = :quality }
Severity: Minor
Found in lib/miga/cli/action/derep_wf.rb by rubocop

This cop checks for unused block arguments.

Example:

# bad

do_something do |used, unused|
  puts used
end

do_something do |bar|
  puts :foo
end

define_method(:foo) do |bar|
  puts :baz
end

Example:

#good

do_something do |used, _unused|
  puts used
end

do_something do
  puts :foo
end

define_method(:foo) do |_bar|
  puts :baz
end

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/add.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

Useless assignment to variable - p.
Open

    p = cli.load_project
Severity: Minor
Found in lib/miga/cli/action/doctor.rb by rubocop

This cop checks for every useless assignment to local variable in every scope. The basic idea for this cop was from the warning of ruby -cw:

assigned but unused variable - foo

Currently this cop has advanced logic that detects unreferenced reassignments and properly handles varied cases such as branch, loop, rescue, ensure, etc.

Example:

# bad

def some_method
  some_var = 1
  do_something
end

Example:

# good

def some_method
  some_var = 1
  do_something(some_var)
end

Favor a normal unless-statement over a modifier clause in a multiline statement.
Open

    call_cli(
      ['new', '-P', cli[:outdir], '-t', cli[:project_type]]
    ) unless MiGA::Project.exist? cli[:outdir]
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

Checks for uses of if/unless modifiers with multiple-lines bodies.

Example:

# bad
{
  result: 'this should not happen'
} unless cond

# good
{ result: 'ok' } if cond

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/run.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

Unused block argument - v. You can omit the argument if you don't care about it.
Open

      ) { |v| cli[:criterion] = :medoids }
Severity: Minor
Found in lib/miga/cli/action/derep_wf.rb by rubocop

This cop checks for unused block arguments.

Example:

# bad

do_something do |used, unused|
  puts used
end

do_something do |bar|
  puts :foo
end

define_method(:foo) do |bar|
  puts :baz
end

Example:

#good

do_something do |used, _unused|
  puts used
end

do_something do
  puts :foo
end

define_method(:foo) do |_bar|
  puts :baz
end

Useless assignment to variable - p.
Open

    p = create_project(cli[:input_type], p_metadata, d_metadata)
Severity: Minor
Found in lib/miga/cli/action/preproc_wf.rb by rubocop

This cop checks for every useless assignment to local variable in every scope. The basic idea for this cop was from the warning of ruby -cw:

assigned but unused variable - foo

Currently this cop has advanced logic that detects unreferenced reassignments and properly handles varied cases such as branch, loop, rescue, ensure, etc.

Example:

# bad

def some_method
  some_var = 1
  do_something
end

Example:

# good

def some_method
  some_var = 1
  do_something(some_var)
end

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::Add < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/add.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
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