bio-miga/miga

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

          left_time > 60   ? ('%.1fh left' % (left_time / 60))   :
          ('%.1fm left' % left_time)
Severity: Minor
Found in lib/miga/common.rb by rubocop

Use snake_case for variable names.
Open

  @@KNOWN_TYPES = {
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

Do not suppress exceptions.
Open

rescue LoadError
Severity: Minor
Found in lib/miga/json.rb by rubocop

This cop checks for rescue blocks with no body.

Example:

# bad

def some_method
  do_something
rescue
  # do nothing
end

Example:

# bad

begin
  do_something
rescue
  # do nothing
end

Example:

# good

def some_method
  do_something
rescue
  handle_exception
end

Example:

# good

begin
  do_something
rescue
  handle_exception
end

Use snake_case for variable names.
Open

  @@INCLADE_TASKS = %i[subclades ogs]
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

Put empty method definitions on a single line.
Open

  def inactivate!(reason = nil)
  end
Severity: Minor
Found in lib/miga/project/result.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

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

    $stderr.print("[%s] %s %s %-12s   \r" % [Time.now, step, adv, left])
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>

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/project/dataset.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

%w-literals should be delimited by [ and ].
Open

      %w(json start done).each do |suffix|
Severity: Minor
Found in lib/miga/project/dataset.rb by rubocop

This cop enforces the consistent usage of %-literal delimiters.

Specify the 'default' key to set all preferred delimiters at once. You can continue to specify individual preferred delimiters to override the default.

Example:

# Style/PercentLiteralDelimiters:
#   PreferredDelimiters:
#     default: '[]'
#     '%i':    '()'

# good
%w[alpha beta] + %i(gamma delta)

# bad
%W(alpha #{beta})

# bad
%I(alpha beta)

Redundant self detected.
Open

    self.metadata[:datasets].delete(name)
Severity: Minor
Found in lib/miga/project/dataset.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

Use // around regular expression.
Open

          file =~ %r{
            \.(fa(a|sta|stqc?)?|fna|solexaqa|gff[23]?|done|ess)(\.gz)?$
          }x
Severity: Minor
Found in lib/miga/project/dataset.rb by rubocop

This cop enforces using // or %r around regular expressions.

Example: EnforcedStyle: slashes (default)

# bad
snake_case = %r{^[\dA-Z_]+$}

# bad
regex = %r{
  foo
  (bar)
  (baz)
}x

# good
snake_case = /^[\dA-Z_]+$/

# good
regex = /
  foo
  (bar)
  (baz)
/x

Example: EnforcedStyle: percent_r

# bad
snake_case = /^[\dA-Z_]+$/

# bad
regex = /
  foo
  (bar)
  (baz)
/x

# good
snake_case = %r{^[\dA-Z_]+$}

# good
regex = %r{
  foo
  (bar)
  (baz)
}x

Example: EnforcedStyle: mixed

# bad
snake_case = %r{^[\dA-Z_]+$}

# bad
regex = /
  foo
  (bar)
  (baz)
/x

# good
snake_case = /^[\dA-Z_]+$/

# good
regex = %r{
  foo
  (bar)
  (baz)
}x

Example: AllowInnerSlashes: false (default)

# If `false`, the cop will always recommend using `%r` if one or more
# slashes are found in the regexp string.

# bad
x =~ /home\//

# good
x =~ %r{home/}

Example: AllowInnerSlashes: true

# good
x =~ /home\//

Use snake_case for method names.
Open

  def self.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

Use snake_case for method names.
Open

  def self.VERSION_DATE
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

Freeze mutable objects assigned to constants.
Open

  CITATION = []
Severity: Minor
Found in lib/miga/version.rb by rubocop

This cop checks whether some constant value isn't a mutable literal (e.g. array or hash).

Example:

# bad
CONST = [1, 2, 3]

# good
CONST = [1, 2, 3].freeze

Line is too long. [81/80]
Open

      " #{str} ".scan(/(?<= )([A-Za-z]+):([^:]*) /) { |r, n| self << { r => n } }
Severity: Minor
Found in lib/miga/taxonomy.rb by rubocop

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

        v = !!v
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.

Missing top-level module documentation comment.
Open

module MiGA::Result::Base
Severity: Minor
Found in lib/miga/result/base.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

Operator = should be surrounded by a single space.
Open

      @_advance_time[:avg]  = nil
Severity: Minor
Found in lib/miga/common.rb by rubocop

Checks that operators have space around them, except for ** which should not have surrounding space.

Example:

# bad
total = 3*4
"apple"+"juice"
my_number = 38/4
a ** b

# good
total = 3 * 4
"apple" + "juice"
my_number = 38 / 4
a**b

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>

Missing magic comment # frozen_string_literal: true.
Open

require 'miga/common/hooks'
Severity: Minor
Found in lib/miga/project/hooks.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

Redundant self detected.
Open

      File.join(self.path, 'metadata', "#{ds.name}.json"),
Severity: Minor
Found in lib/miga/project/dataset.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
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