bio-miga/miga

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Use snake_case for method names.
Open

    def KNOWN_TYPES
Severity: Minor
Found in lib/miga/dataset/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 == if you meant to do a comparison or wrap the expression in parentheses to indicate you meant to assign in a condition.
Open

    elsif d = cli.load_dataset
Severity: Minor
Found in lib/miga/cli/action/rm.rb by rubocop

This cop checks for assignments in the conditions of if/while/until.

Example:

# bad

if some_var = true
  do_something
end

Example:

# good

if some_var == true
  do_something
end

Use safe navigation (&.) instead of checking if an object exists before calling the method.
Open

    @ftp.close unless @ftp.nil?
Severity: Minor
Found in lib/miga/cli/action/db.rb by rubocop

This cop transforms usages of a method call safeguarded by a non nil check for the variable whose method is being called to safe navigation (&.).

Configuration option: ConvertCodeThatCanStartToReturnNil The default for this is false. When configured to true, this will check for code in the format !foo.nil? && foo.bar. As it is written, the return of this code is limited to false and whatever the return of the method is. If this is converted to safe navigation, foo&.bar can start returning nil as well as what the method returns.

Example:

# bad
foo.bar if foo
foo.bar(param1, param2) if foo
foo.bar { |e| e.something } if foo
foo.bar(param) { |e| e.something } if foo

foo.bar if !foo.nil?
foo.bar unless !foo
foo.bar unless foo.nil?

foo && foo.bar
foo && foo.bar(param1, param2)
foo && foo.bar { |e| e.something }
foo && foo.bar(param) { |e| e.something }

# good
foo&.bar
foo&.bar(param1, param2)
foo&.bar { |e| e.something }
foo&.bar(param) { |e| e.something }

foo.nil? || foo.bar
!foo || foo.bar

# Methods that `nil` will `respond_to?` should not be converted to
# use safe navigation
foo.to_i if foo

Prefer single-quoted strings when you don't need string interpolation or special symbols.
Open

      cli.say "Summary: classification"
Severity: Minor
Found in lib/miga/cli/action/classify_wf.rb by rubocop

Checks if uses of quotes match the configured preference.

Example: EnforcedStyle: single_quotes (default)

# bad
"No special symbols"
"No string interpolation"
"Just text"

# good
'No special symbols'
'No string interpolation'
'Just text'
"Wait! What's #{this}!"

Example: EnforcedStyle: double_quotes

# bad
'Just some text'
'No special chars or interpolation'

# good
"Just some text"
"No special chars or interpolation"
"Every string in #{project} uses double_quotes"

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

      ) { |v| puts MiGA::MiGA.LONG_VERSION; exit }
Severity: Minor
Found in lib/miga/cli/action/generic.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

Put empty method definitions on a single line.
Open

  def perform
  end
Severity: Minor
Found in lib/miga/cli/action/generic.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/cli/action/generic.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 top-level class documentation comment.
Open

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

Put empty method definitions on a single line.
Open

  def empty_action
  end
Severity: Minor
Found in lib/miga/cli/action/console.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/cli/action.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

Parenthesize the param opt.to_a.select { |i| i !~ /\s::HIDE::\s/ } to make sure that the block will be associated with the opt.to_a.select method call.
Open

      puts opt.to_a.select { |i| i !~ /\s::HIDE::\s/ }
Severity: Minor
Found in lib/miga/cli/opt_helper.rb by rubocop

This cop checks for ambiguous block association with method when param passed without parentheses.

Example:

# bad
some_method a { |val| puts val }

Example:

# good
# With parentheses, there's no ambiguity.
some_method(a) { |val| puts val }

# good
# Operator methods require no disambiguation
foo == bar { |b| b.baz }

# good
# Lambda arguments require no disambiguation
foo = ->(bar) { bar.baz }

Avoid multi-line ternary operators, use if or unless instead.
Open

    keys = cli[:key_md].nil? ? stats.map(&:keys).flatten.uniq :
      [:dataset, cli[:key_md].downcase.miga_name.to_sym]
Severity: Minor
Found in lib/miga/cli/action/summary.rb by rubocop

This cop checks for multi-line ternary op expressions.

Example:

# bad
a = cond ?
  b : c
a = cond ? b :
    c
a = cond ?
    b :
    c

# good
a = cond ? b : c
a =
  if cond
    b
  else
    c
  end

Ternary operators must not be nested. Prefer if or else constructs instead.
Open

      stats.map { |s| keys.map { |k| s[k].is_a?(Array) ? s[k].first : s[k] } }
Severity: Minor
Found in lib/miga/cli/action/summary.rb by rubocop

Missing magic comment # frozen_string_literal: true.
Open

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

Do not use semicolons to terminate expressions.
Open

      ) { |v| puts MiGA::MiGA.LONG_VERSION; exit }
Severity: Minor
Found in lib/miga/cli/action/generic.rb by rubocop

This cop checks for multiple expressions placed on the same line. It also checks for lines terminated with a semicolon.

Example:

# bad
foo = 1; bar = 2;
baz = 3;

# good
foo = 1
bar = 2
baz = 3

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

        [:action, :description], descriptions
Severity: Minor
Found in lib/miga/cli/action/generic.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]

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

    !!metadata["run_#{task}"]
Severity: Minor
Found in lib/miga/dataset/result/ignore.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.

Add parentheses to nested method call spawn hook_args.first.miga_variables( dataset: name, project: project.path, project_name: project.name, miga: MiGA::MiGA.root_path, object: event_args.first ).
Open

      spawn hook_args.first.miga_variables(
        dataset: name, project: project.path, project_name: project.name,
        miga: MiGA::MiGA.root_path, object: event_args.first
      )
Severity: Minor
Found in lib/miga/dataset/hooks.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

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

      cli.opt_object(opt, [:project, :dataset_opt])
Severity: Minor
Found in lib/miga/cli/action/edit.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]

Unused block argument - v. If it's necessary, use _ or _v as an argument name to indicate that it won't be used.
Open

      descriptions = cli.class.TASK_DESC.keep_if { |k, v| k != :generic }
Severity: Minor
Found in lib/miga/cli/action/generic.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
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