wurmlab/sequenceserver

    extend Forwardable

Close

This cop checks if empty lines around the bodies of blocks match the configuration.

Example: EnforcedStyle: empty_lines

# good

foo do |bar|

  # ...

end

Example: EnforcedStyle: noemptylines (default)

# good

foo do |bar|
  # ...
end

        url:   url,

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})

        url:   url,

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})

Close

This cop looks for trailing whitespace in the source code.

Example:

# The line in this example contains spaces after the 0.
# bad
x = 0

# The line in this example ends directly after the 0.
# good
x = 0

Example: AllowInHeredoc: false (default)

# The line in this example contains spaces after the 0.
# bad
code = <<~RUBY
  x = 0
RUBY

# ok
code = <<~RUBY
  x = 0 #{}
RUBY

# good
trailing_whitespace = ' '
code = <<~RUBY
  x = 0#{trailing_whitespace}
RUBY

Example: AllowInHeredoc: true

# The line in this example contains spaces after the 0.
# good
code = <<~RUBY
  x = 0
RUBY

        params = {:xml => xml_file_path}

Close

Checks that braces used for hash literals have or don't have surrounding space depending on configuration.

Example: EnforcedStyle: space (default)

# The `space` style enforces that hash literals have
# surrounding space.

# bad
h = {a: 1, b: 2}

# good
h = { a: 1, b: 2 }

Example: EnforcedStyle: no_space

# The `no_space` style enforces that hash literals have
# no surrounding space.

# bad
h = { a: 1, b: 2 }

# good
h = {a: 1, b: 2}

Example: EnforcedStyle: compact

# The `compact` style normally requires a space inside
# hash braces, with the exception that successive left
# braces or right braces are collapsed together in nested hashes.

# bad
h = { a: { b: 2 } }
foo = { { a: 1 } => { b: { c: 2 } } }

# good
h = { a: { b: 2 }}
foo = {{ a: 1 } => { b: { c: 2 }}}

Example: EnforcedStyleForEmptyBraces: no_space (default)

# The `no_space` EnforcedStyleForEmptyBraces style enforces that
# empty hash braces do not contain spaces.

# bad
foo = { }
bar = {    }

# good
foo = {}
bar = {}

Example: EnforcedStyleForEmptyBraces: space

# The `space` EnforcedStyleForEmptyBraces style enforces that
# empty hash braces contain space.

# bad
foo = {}

# good
foo = { }
foo = {  }
foo = {     }

          response = STDIN.gets.to_s.strip

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

          response = STDIN.gets.to_s.strip

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

      if num_threads > 256

Close

Checks for if and unless statements that would fit on one line if written as modifier if/unless. The cop also checks for modifier if/unless lines that exceed the maximum line length.

The maximum line length is configured in the Layout/LineLength cop. The tab size is configured in the IndentationWidth of the Layout/IndentationStyle cop.

Example:

# bad
if condition
  do_stuff(bar)
end

unless qux.empty?
  Foo.do_something
end

do_something_with_a_long_name(arg) if long_condition_that_prevents_code_fit_on_single_line

# good
do_stuff(bar) if condition
Foo.do_something unless qux.empty?

if long_condition_that_prevents_code_fit_on_single_line
  do_something_with_a_long_name(arg)
end

if short_condition # a long comment that makes it too long if it were just a single line
  do_something
end

      args[2].downcase!   # type

Close

This cop checks for extra/unnecessary whitespace.

Example:

# good if AllowForAlignment is true
name      = "RuboCop"
# Some comment and an empty line

website  += "/rubocop/rubocop" unless cond
puts        "rubocop"          if     debug

# bad for any configuration
set_app("RuboCop")
website  = "https://github.com/rubocop/rubocop"

# good only if AllowBeforeTrailingComments is true
object.method(arg)  # this is a comment

# good even if AllowBeforeTrailingComments is false or not set
object.method(arg) # this is a comment

# good with either AllowBeforeTrailingComments or AllowForAlignment
object.method(arg)         # this is a comment
another_object.method(arg) # this is another comment
some_object.method(arg)    # this is some comment

      sys(cmd, path: config[:bin]) rescue false

Close

This cop checks for uses of rescue in its modifier form.

The cop to check rescue in its modifier form is added for following reasons:

• The syntax of modifier form rescue can be misleading because it might led us to believe that rescue handles the given exception but it actually rescue all exceptions to return the given rescue block. In this case, value returned by handle_error or SomeException.

• Modifier form rescue would rescue all the exceptions. It would silently skip all exception or errors and handle the error. Example: If NoMethodError is raised, modifier form rescue would handle the exception.

Example:

# bad
some_method rescue handle_error

# bad
some_method rescue SomeException

# good
begin
  some_method
rescue
  handle_error
end

# good
begin
  some_method
rescue SomeException
  handle_error
end

    def spawn_cleanup
      Thread.new do
        loop do
          now = Time.now
          finished_jobs = Job.all.select(&:done?)

Close

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 and https://en.wikipedia.org/wiki/ABC_Software_Metric.

Interpreting ABC size:

• <= 17 satisfactory
• 18..30 unsatisfactory
• > 30 dangerous

You can have repeated "attributes" calls count as a single "branch". For this purpose, attributes are any method with no argument; no attempt is meant to distinguish actual attr_reader from other methods.

Example: CountRepeatedAttributes: false (default is true)

# `model` and `current_user`, refenced 3 times each,
 # are each counted as only 1 branch each if
 # `CountRepeatedAttributes` is set to 'false'

 def search
   @posts = model.active.visible_by(current_user)
             .search(params[:q])
   @posts = model.some_process(@posts, current_user)
   @posts = model.another_process(@posts, current_user)

   render 'pages/search/page'
 end

This cop also takes into account IgnoredMethods (defaults to [])

        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})

      return nil unless id.match(RFAM_ID_PATTERN) or title.match(RFAM_ID_PATTERN)

Close

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions or in all contexts.

Safety:

Auto-correction is unsafe because there is a different operator precedence between logical operators (&& and ||) and semantic operators (and and or), and that might change the behaviour.

Example: EnforcedStyle: always

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals (default)

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

    rescue CommandFailed => e

Close

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

      from_user = STDIN.gets.to_s.strip

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

    Do you want to be notified of SequenceServer releases and any
    other important announcements (3-12 messages a year)? If yes,
    please provide your email address below or press enter to
    continue (you won't be prompted again).
    MSG

Close

This cop checks the indentation of the here document bodies. The bodies are indented one step.

Note: When Layout/LineLength's AllowHeredoc is false (not default), this cop does not add any offenses for long here documents to avoid Layout/LineLength's offenses.

Example:

# bad
<<-RUBY
something
RUBY

# good
<<~RUBY
  something
RUBY

        params = {:xml => xml_file_path}

Close

This cop checks hash literal syntax.

It can enforce either the use of the class hash rocket syntax or the use of the newer Ruby 1.9 syntax (when applicable).

A separate offense is registered for each problematic pair.

The supported styles are:

• ruby19 - forces use of the 1.9 syntax (e.g. {a: 1}) when hashes have all symbols for keys
• hash_rockets - forces use of hash rockets for all hashes
• nomixedkeys - simply checks for hashes with mixed syntaxes
• ruby19nomixed_keys - forces use of ruby 1.9 syntax and forbids mixed syntax hashes

Example: EnforcedStyle: ruby19 (default)

# bad
{:a => 2}
{b: 1, :c => 2}

# good
{a: 2, b: 1}
{:c => 2, 'd' => 2} # acceptable since 'd' isn't a symbol
{d: 1, 'e' => 2} # technically not forbidden

Example: EnforcedStyle: hash_rockets

# bad
{a: 1, b: 2}
{c: 1, 'd' => 5}

# good
{:a => 1, :b => 2}

Example: EnforcedStyle: nomixedkeys

# bad
{:a => 1, b: 2}
{c: 1, 'd' => 2}

# good
{:a => 1, :b => 2}
{c: 1, d: 2}

Example: EnforcedStyle: ruby19nomixed_keys

# bad
{:a => 1, :b => 2}
{c: 2, 'd' => 3} # should just use hash rockets

# good
{a: 1, b: 2}
{:c => 3, 'd' => 4}

      fail NUM_THREADS_INCORRECT unless num_threads.positive?

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

      'pairwise'        => [0, :txt],

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})

      'custom_tsv'      => [7, :tsv, 'qseqid sseqid sscinames qcovs qcovhsp'],

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})