bio-miga/miga

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Redundant self detected.
Open

    self.load if self.metadata.nil?
Severity: Minor
Found in lib/miga/project.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 snake_case for method names.
Open

    def DISTANCE_TASKS
Severity: Minor
Found in lib/miga/project/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

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/project/result.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 yield instead of blk.call.
Open

      metadata[:datasets].each { |name| blk.call(dataset(name)) }
Severity: Minor
Found in lib/miga/project/dataset.rb by rubocop

This cop identifies the use of a &block parameter and block.call where yield would do just as well.

Example:

# bad
def method(&block)
  block.call
end
def another(&func)
  func.call 1, 2, 3
end

# good
def method
  yield
end
def another
  yield 1, 2, 3
end

Align .map with .times on line 11.
Open

        .map { |pid| Process.waitpid2(pid) }
Severity: Minor
Found in lib/miga/parallel.rb by rubocop

This cop checks the indentation of the method name part in method calls that span more than one line.

Example: EnforcedStyle: aligned

# bad
while myvariable
.b
  # do something
end

# good
while myvariable
      .b
  # do something
end

# good
Thing.a
     .b
     .c

Example: EnforcedStyle: indented

# good
while myvariable
  .b

  # do something
end

Example: EnforcedStyle: indentedrelativeto_receiver

# good
while myvariable
        .a
        .b

  # do something
end

# good
myvariable = Thing
               .a
               .b
               .c

Avoid the use of Perl-style backrefs.
Open

            stats["#{$1.downcase}_copies".to_sym] = $2.to_f
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Use snake_case for method names.
Open

    def RESULT_DIRS
Severity: Minor
Found in lib/miga/result/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

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

  @@RESULT_DIRS = {
Severity: Minor
Found in lib/miga/project/base.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.

Trailing whitespace detected.
Open

    # JSON in +path+ if any, but it can rescue the versions 
Severity: Minor
Found in lib/miga/result.rb by rubocop

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

      @@RESULT_DIRS ||=
Severity: Minor
Found in lib/miga/result/base.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.

Missing magic comment # frozen_string_literal: true.
Open

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

    self.metadata[:type] = :mixed if type.nil?
Severity: Minor
Found in lib/miga/project.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

Space around operator ** detected.
Open

          cont += fh.read(2 ** 16) until fh.eof?
Severity: Minor
Found in lib/miga/json.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

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

  @@INCLADE_TASKS = %i[subclades ogs]
Severity: Minor
Found in lib/miga/project/base.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.

Redundant self detected.
Open

    self.add_dataset(ds.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 Array.new(threads) with a block instead of .times.map only if threads is always 0 or more.
Open

      threads.times
        .map { |i| Process.fork { yield(i) } }
Severity: Minor
Found in lib/miga/parallel.rb by rubocop

This cop checks for .times.map calls. In most cases such calls can be replaced with an explicit array creation.

Example:

# bad
9.times.map do |i|
  i.to_s
end

# good
Array.new(9) do |i|
  i.to_s
end

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

    !!self[:recalculate]
Severity: Minor
Found in lib/miga/result.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.

Avoid the use of Perl-style backrefs.
Open

            stats[$1.downcase.to_sym][0] = $2.to_f
Severity: Minor
Found in lib/miga/result/stats.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Avoid more than 3 levels of block nesting.
Open

          left_time > 1440 ? ('%.1fd left' % (left_time / 1440)) :
          left_time > 60   ? ('%.1fh left' % (left_time / 60))   :
          ('%.1fm left' % left_time)
Severity: Minor
Found in lib/miga/common.rb by rubocop

This cop checks for excessive nesting of conditional and looping constructs.

You can configure if blocks are considered using the CountBlocks option. When set to false (the default) blocks are not counted towards the nesting level. Set to true to count blocks as well.

The maximum level of nesting allowed is configurable.

Redundant self detected.
Open

    stats = self.respond_to?(method, true) ? send(method) : nil
Severity: Minor
Found in lib/miga/result/stats.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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