wurmlab/sequenceserver

    merge(other) do |key, oldval, newval|

Close

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

# good
do_something do |used, _unused|
  puts used
end

do_something do
  puts :foo
end

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

Example: IgnoreEmptyBlocks: true (default)

# good
do_something { |unused| }

Example: IgnoreEmptyBlocks: false

# bad
do_something { |unused| }

Example: AllowUnusedKeywordArguments: false (default)

# bad
do_something do |unused: 42|
  foo
end

Example: AllowUnusedKeywordArguments: true

# good
do_something do |unused: 42|
  foo
end

      'std_tsv'         => [7, :tsv, STDREP],

Close

Check that the keys, separators, and values of a multi-line hash literal are aligned according to configuration. The configuration options are:

• key (left align keys, one space before hash rockets and values)
• separator (align hash rockets and colons, right align keys)
• table (left align keys, hash rockets, and values)

The treatment of hashes passed as the last argument to a method call can also be configured. The options are:

• always_inspect
• always_ignore
• ignore_implicit (without curly braces)

Alternatively you can specify multiple allowed styles. That's done by passing a list of styles to EnforcedStyles.

Example: EnforcedHashRocketStyle: key (default)

# bad
{
  :foo => bar,
   :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
  :ba => baz
}

Example: EnforcedHashRocketStyle: separator

# bad
{
  :foo => bar,
  :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
   :ba => baz
}

Example: EnforcedHashRocketStyle: table

# bad
{
  :foo => bar,
   :ba => baz
}

# good
{
  :foo => bar,
  :ba  => baz
}

Example: EnforcedColonStyle: key (default)

# bad
{
  foo: bar,
   ba: baz
}
{
  foo: bar,
  ba:  baz
}

# good
{
  foo: bar,
  ba: baz
}

Example: EnforcedColonStyle: separator

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
   ba: baz
}

Example: EnforcedColonStyle: table

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
  ba:  baz
}

Example: EnforcedLastArgumentHashStyle: always_inspect (default)

# Inspect both implicit and explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
             bar: 2)

# good
do_something(
  foo: 1,
  bar: 2
)

# good
do_something({foo: 1,
              bar: 2})

# good
do_something({
  foo: 1,
  bar: 2
})

Example: EnforcedLastArgumentHashStyle: always_ignore

# Ignore both implicit and explicit hashes.

# good
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

Example: EnforcedLastArgumentHashStyle: ignore_implicit

# Ignore only implicit hashes.

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
  bar: 2)

Example: EnforcedLastArgumentHashStyle: ignore_explicit

# Ignore only explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

      FLOAT_ARGS   = [2, 4].freeze

Close

Do not define constants within a block, since the block's scope does not isolate or namespace the constant in any way.

If you are trying to define that constant once, define it outside of the block instead, or use a variable or method if defining the constant in the outer scope would be problematic.

For meta-programming, use const_set.

Example:

# bad
task :lint do
  FILES_TO_LINT = Dir['lib/*.rb']
end

# bad
describe 'making a request' do
  class TestRequest; end
end

# bad
module M
  extend ActiveSupport::Concern
  included do
    LIST = []
  end
end

# good
task :lint do
  files_to_lint = Dir['lib/*.rb']
end

# good
describe 'making a request' do
  let(:test_request) { Class.new }
  # see also `stub_const` for RSpec
end

# good
module M
  extend ActiveSupport::Concern
  included do
    const_set(:LIST, [])
  end
end

Example: AllowedMethods: ['enums'] (default)

# good

# `enums` for Typed Enums via `T::Enum` in Sorbet.
# https://sorbet.org/docs/tenum
class TestEnum < T::Enum
  enums do
    Foo = new("foo")
  end
end

    def initialize(database_dir)
      @database_dir = database_dir
    end

Close

This cop checks for the presence of constructors and lifecycle callbacks without calls to super.

This cop does not consider method_missing (and respond_to_missing?) because in some cases it makes sense to overtake what is considered a missing method. In other cases, the theoretical ideal handling could be challenging or verbose for no actual gain.

Example:

# bad
class Employee < Person
  def initialize(name, salary)
    @salary = salary
  end
end

# good
class Employee < Person
  def initialize(name, salary)
    super(name)
    @salary = salary
  end
end

# bad
class Parent
  def self.inherited(base)
    do_something
  end
end

# good
class Parent
  def self.inherited(base)
    super
    do_something
  end
end

  class INCOMPATIBLE_BLAST_DATABASES < StandardError

Close

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, constant definitions or constant visibility declarations.

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

module Math
end

# good
# Description/Explanation of Person class
class Person
  # ...
end

# allowed
  # Class without body
  class Person
  end

  # Namespace - A namespace can be a class or a module
  # Containing a class
  module Namespace
    # Description/Explanation of Person class
    class Person
      # ...
    end
  end

  # Containing constant visibility declaration
  module Namespace
    class Private
    end

    private_constant :Private
  end

  # Containing constant definition
  module Namespace
    Public = Class.new
  end

  # Macro calls
  module Namespace
    extend Foo
  end

Example: AllowedConstants: ['ClassMethods']

# good
 module A
   module ClassMethods
     # ...
   end
  end

    def make_blast_database(action, file, title, type, non_parse_seqids = false)

Close

This cop checks for places where keyword arguments can be used instead of boolean arguments when defining methods. respond_to_missing? method is allowed by default. These are customizable with AllowedMethods option.

Safety:

This cop is unsafe because changing a method signature will implicitly change behaviour.

Example:

# bad
def some_method(bar = false)
  puts bar
end

# bad - common hack before keyword args were introduced
def some_method(options = {})
  bar = options.fetch(:bar, false)
  puts bar
end

# good
def some_method(bar: false)
  puts bar
end

Example: AllowedMethods: ['some_method']

# good
def some_method(bar = false)
  puts bar
end

class Hash

Close

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, constant definitions or constant visibility declarations.

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

module Math
end

# good
# Description/Explanation of Person class
class Person
  # ...
end

# allowed
  # Class without body
  class Person
  end

  # Namespace - A namespace can be a class or a module
  # Containing a class
  module Namespace
    # Description/Explanation of Person class
    class Person
      # ...
    end
  end

  # Containing constant visibility declaration
  module Namespace
    class Private
    end

    private_constant :Private
  end

  # Containing constant definition
  module Namespace
    Public = Class.new
  end

  # Macro calls
  module Namespace
    extend Foo
  end

Example: AllowedConstants: ['ClassMethods']

# good
 module A
   module ClassMethods
     # ...
   end
  end

        end

Close

This cop enforces empty line after guard clause

Example:

# bad
def foo
  return if need_return?
  bar
end

# good
def foo
  return if need_return?

  bar
end

# good
def foo
  return if something?
  return if something_different?

  bar
end

# also good
def foo
  if something?
    do_something
    return if need_return?
  end
end

                    Logger.new(STDERR, Logger::WARN)

Close

This cop enforces the use of $stdout/$stderr/$stdin instead of STDOUT/STDERR/STDIN. STDOUT/STDERR/STDIN are constants, and while you can actually reassign (possibly to redirect some stream) constants in Ruby, you'll get an interpreter warning if you do so.

Safety:

Autocorrection is unsafe because STDOUT and $stdout may point to different objects, for example.

Example:

# bad
STDOUT.puts('hello')

hash = { out: STDOUT, key: value }

def m(out = STDOUT)
  out.puts('hello')
end

# good
$stdout.puts('hello')

hash = { out: $stdout, key: value }

def m(out = $stdout)
  out.puts('hello')
end

      'csv'             => [10, :csv],

Close

Check that the keys, separators, and values of a multi-line hash literal are aligned according to configuration. The configuration options are:

• key (left align keys, one space before hash rockets and values)
• separator (align hash rockets and colons, right align keys)
• table (left align keys, hash rockets, and values)

The treatment of hashes passed as the last argument to a method call can also be configured. The options are:

• always_inspect
• always_ignore
• ignore_implicit (without curly braces)

Alternatively you can specify multiple allowed styles. That's done by passing a list of styles to EnforcedStyles.

Example: EnforcedHashRocketStyle: key (default)

# bad
{
  :foo => bar,
   :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
  :ba => baz
}

Example: EnforcedHashRocketStyle: separator

# bad
{
  :foo => bar,
  :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
   :ba => baz
}

Example: EnforcedHashRocketStyle: table

# bad
{
  :foo => bar,
   :ba => baz
}

# good
{
  :foo => bar,
  :ba  => baz
}

Example: EnforcedColonStyle: key (default)

# bad
{
  foo: bar,
   ba: baz
}
{
  foo: bar,
  ba:  baz
}

# good
{
  foo: bar,
  ba: baz
}

Example: EnforcedColonStyle: separator

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
   ba: baz
}

Example: EnforcedColonStyle: table

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
  ba:  baz
}

Example: EnforcedLastArgumentHashStyle: always_inspect (default)

# Inspect both implicit and explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
             bar: 2)

# good
do_something(
  foo: 1,
  bar: 2
)

# good
do_something({foo: 1,
              bar: 2})

# good
do_something({
  foo: 1,
  bar: 2
})

Example: EnforcedLastArgumentHashStyle: always_ignore

# Ignore both implicit and explicit hashes.

# good
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

Example: EnforcedLastArgumentHashStyle: ignore_implicit

# Ignore only implicit hashes.

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
  bar: 2)

Example: EnforcedLastArgumentHashStyle: ignore_explicit

# Ignore only explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

                     :sstart, :send, :qframe, :sframe, :identity, :positives,

Close

This cop checks unexpected overrides of the Struct built-in methods via Struct.new.

Example:

# bad
Bad = Struct.new(:members, :clone, :count)
b = Bad.new([], true, 1)
b.members #=> [] (overriding `Struct#members`)
b.clone #=> true (overriding `Object#clone`)
b.count #=> 1 (overriding `Enumerable#count`)

# good
Good = Struct.new(:id, :name)
g = Good.new(1, "foo")
g.members #=> [:id, :name]
g.clone #=> #<struct good id="1," name="foo">
g.count #=&gt; 2</struct>

    def initialize(database_dir)
      @database_dir = database_dir
    end

Close

This cop checks for the presence of constructors and lifecycle callbacks without calls to super.

This cop does not consider method_missing (and respond_to_missing?) because in some cases it makes sense to overtake what is considered a missing method. In other cases, the theoretical ideal handling could be challenging or verbose for no actual gain.

Example:

# bad
class Employee < Person
  def initialize(name, salary)
    @salary = salary
  end
end

# good
class Employee < Person
  def initialize(name, salary)
    super(name)
    @salary = salary
  end
end

# bad
class Parent
  def self.inherited(base)
    do_something
  end
end

# good
class Parent
  def self.inherited(base)
    super
    do_something
  end
end

    def initialize(cmd, out)
      @cmd = cmd
      @out = out
    end

Close

This cop checks for the presence of constructors and lifecycle callbacks without calls to super.

This cop does not consider method_missing (and respond_to_missing?) because in some cases it makes sense to overtake what is considered a missing method. In other cases, the theoretical ideal handling could be challenging or verbose for no actual gain.

Example:

# bad
class Employee < Person
  def initialize(name, salary)
    @salary = salary
  end
end

# good
class Employee < Person
  def initialize(name, salary)
    super(name)
    @salary = salary
  end
end

# bad
class Parent
  def self.inherited(base)
    do_something
  end
end

# good
class Parent
  def self.inherited(base)
    super
    do_something
  end
end

    def initialize(exitstatus, stdout: nil, stderr: nil)
      @exitstatus = exitstatus
      @stdout = stdout
      @stderr = stderr
    end

Close

This cop checks for the presence of constructors and lifecycle callbacks without calls to super.

This cop does not consider method_missing (and respond_to_missing?) because in some cases it makes sense to overtake what is considered a missing method. In other cases, the theoretical ideal handling could be challenging or verbose for no actual gain.

Example:

# bad
class Employee < Person
  def initialize(name, salary)
    @salary = salary
  end
end

# good
class Employee < Person
  def initialize(name, salary)
    super(name)
    @salary = salary
  end
end

# bad
class Parent
  def self.inherited(base)
    do_something
  end
end

# good
class Parent
  def self.inherited(base)
    super
    do_something
  end
end

        icon:  'fa-external-link'

Close

Check that the keys, separators, and values of a multi-line hash literal are aligned according to configuration. The configuration options are:

• key (left align keys, one space before hash rockets and values)
• separator (align hash rockets and colons, right align keys)
• table (left align keys, hash rockets, and values)

The treatment of hashes passed as the last argument to a method call can also be configured. The options are:

• always_inspect
• always_ignore
• ignore_implicit (without curly braces)

Alternatively you can specify multiple allowed styles. That's done by passing a list of styles to EnforcedStyles.

Example: EnforcedHashRocketStyle: key (default)

# bad
{
  :foo => bar,
   :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
  :ba => baz
}

Example: EnforcedHashRocketStyle: separator

# bad
{
  :foo => bar,
  :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
   :ba => baz
}

Example: EnforcedHashRocketStyle: table

# bad
{
  :foo => bar,
   :ba => baz
}

# good
{
  :foo => bar,
  :ba  => baz
}

Example: EnforcedColonStyle: key (default)

# bad
{
  foo: bar,
   ba: baz
}
{
  foo: bar,
  ba:  baz
}

# good
{
  foo: bar,
  ba: baz
}

Example: EnforcedColonStyle: separator

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
   ba: baz
}

Example: EnforcedColonStyle: table

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
  ba:  baz
}

Example: EnforcedLastArgumentHashStyle: always_inspect (default)

# Inspect both implicit and explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
             bar: 2)

# good
do_something(
  foo: 1,
  bar: 2
)

# good
do_something({foo: 1,
              bar: 2})

# good
do_something({
  foo: 1,
  bar: 2
})

Example: EnforcedLastArgumentHashStyle: always_ignore

# Ignore both implicit and explicit hashes.

# good
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

Example: EnforcedLastArgumentHashStyle: ignore_implicit

# Ignore only implicit hashes.

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
  bar: 2)

Example: EnforcedLastArgumentHashStyle: ignore_explicit

# Ignore only explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

        icon:  'fa-external-link'

Close

Check that the keys, separators, and values of a multi-line hash literal are aligned according to configuration. The configuration options are:

• key (left align keys, one space before hash rockets and values)
• separator (align hash rockets and colons, right align keys)
• table (left align keys, hash rockets, and values)

The treatment of hashes passed as the last argument to a method call can also be configured. The options are:

• always_inspect
• always_ignore
• ignore_implicit (without curly braces)

Alternatively you can specify multiple allowed styles. That's done by passing a list of styles to EnforcedStyles.

Example: EnforcedHashRocketStyle: key (default)

# bad
{
  :foo => bar,
   :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
  :ba => baz
}

Example: EnforcedHashRocketStyle: separator

# bad
{
  :foo => bar,
  :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
   :ba => baz
}

Example: EnforcedHashRocketStyle: table

# bad
{
  :foo => bar,
   :ba => baz
}

# good
{
  :foo => bar,
  :ba  => baz
}

Example: EnforcedColonStyle: key (default)

# bad
{
  foo: bar,
   ba: baz
}
{
  foo: bar,
  ba:  baz
}

# good
{
  foo: bar,
  ba: baz
}

Example: EnforcedColonStyle: separator

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
   ba: baz
}

Example: EnforcedColonStyle: table

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
  ba:  baz
}

Example: EnforcedLastArgumentHashStyle: always_inspect (default)

# Inspect both implicit and explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
             bar: 2)

# good
do_something(
  foo: 1,
  bar: 2
)

# good
do_something({foo: 1,
              bar: 2})

# good
do_something({
  foo: 1,
  bar: 2
})

Example: EnforcedLastArgumentHashStyle: always_ignore

# Ignore both implicit and explicit hashes.

# good
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

Example: EnforcedLastArgumentHashStyle: ignore_implicit

# Ignore only implicit hashes.

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
  bar: 2)

Example: EnforcedLastArgumentHashStyle: ignore_explicit

# Ignore only explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

        SequenceServer::NUM_THREADS_INCORRECT => e

Close

Here we check if the elements of a multi-line array literal are aligned.

Example: EnforcedStyle: withfirstelement (default)

# good

array = [1, 2, 3,
         4, 5, 6]
array = ['run',
         'forrest',
         'run']

# bad

array = [1, 2, 3,
  4, 5, 6]
array = ['run',
     'forrest',
     'run']

Example: EnforcedStyle: withfixedindentation

# good

array = [1, 2, 3,
  4, 5, 6]

# bad

array = [1, 2, 3,
         4, 5, 6]

      'full_tsv'        => [7, :tsv, OUTFMT_SPECIFIERS],

Close

Check that the keys, separators, and values of a multi-line hash literal are aligned according to configuration. The configuration options are:

• key (left align keys, one space before hash rockets and values)
• separator (align hash rockets and colons, right align keys)
• table (left align keys, hash rockets, and values)

The treatment of hashes passed as the last argument to a method call can also be configured. The options are:

• always_inspect
• always_ignore
• ignore_implicit (without curly braces)

Alternatively you can specify multiple allowed styles. That's done by passing a list of styles to EnforcedStyles.

Example: EnforcedHashRocketStyle: key (default)

# bad
{
  :foo => bar,
   :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
  :ba => baz
}

Example: EnforcedHashRocketStyle: separator

# bad
{
  :foo => bar,
  :ba => baz
}
{
  :foo => bar,
  :ba  => baz
}

# good
{
  :foo => bar,
   :ba => baz
}

Example: EnforcedHashRocketStyle: table

# bad
{
  :foo => bar,
   :ba => baz
}

# good
{
  :foo => bar,
  :ba  => baz
}

Example: EnforcedColonStyle: key (default)

# bad
{
  foo: bar,
   ba: baz
}
{
  foo: bar,
  ba:  baz
}

# good
{
  foo: bar,
  ba: baz
}

Example: EnforcedColonStyle: separator

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
   ba: baz
}

Example: EnforcedColonStyle: table

# bad
{
  foo: bar,
  ba: baz
}

# good
{
  foo: bar,
  ba:  baz
}

Example: EnforcedLastArgumentHashStyle: always_inspect (default)

# Inspect both implicit and explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
             bar: 2)

# good
do_something(
  foo: 1,
  bar: 2
)

# good
do_something({foo: 1,
              bar: 2})

# good
do_something({
  foo: 1,
  bar: 2
})

Example: EnforcedLastArgumentHashStyle: always_ignore

# Ignore both implicit and explicit hashes.

# good
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

Example: EnforcedLastArgumentHashStyle: ignore_implicit

# Ignore only implicit hashes.

# bad
do_something({foo: 1,
  bar: 2})

# good
do_something(foo: 1,
  bar: 2)

Example: EnforcedLastArgumentHashStyle: ignore_explicit

# Ignore only explicit hashes.

# bad
do_something(foo: 1,
  bar: 2)

# good
do_something({foo: 1,
  bar: 2})

                     :length, :sciname, :qcovs, :hsps) do

Close

This cop checks unexpected overrides of the Struct built-in methods via Struct.new.

Example:

# bad
Bad = Struct.new(:members, :clone, :count)
b = Bad.new([], true, 1)
b.members #=> [] (overriding `Struct#members`)
b.clone #=> true (overriding `Object#clone`)
b.count #=> 1 (overriding `Enumerable#count`)

# good
Good = Struct.new(:id, :name)
g = Good.new(1, "foo")
g.members #=> [:id, :name]
g.clone #=> #<struct good id="1," name="foo">
g.count #=&gt; 2</struct>

    Query = Struct.new(:report, :number, :def, :length, :hits) do

Close

This cop checks unexpected overrides of the Struct built-in methods via Struct.new.

Example:

# bad
Bad = Struct.new(:members, :clone, :count)
b = Bad.new([], true, 1)
b.members #=> [] (overriding `Struct#members`)
b.clone #=> true (overriding `Object#clone`)
b.count #=> 1 (overriding `Enumerable#count`)

# good
Good = Struct.new(:id, :name)
g = Good.new(1, "foo")
g.members #=> [:id, :name]
g.clone #=> #<struct good id="1," name="foo">
g.count #=&gt; 2</struct>