bio-miga/miga

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Use snake_case for method names.
Open

    def RESULT_DIRS
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

Favor modifier until usage when having a single-line body.
Open

      until fh.eof?
Severity: Minor
Found in lib/miga/cli/action/db.rb by rubocop

Checks for while and until statements that would fit on one line if written as a modifier while/until. The maximum line length is configured in the Metrics/LineLength cop.

Example:

# bad
while x < 10
  x += 1
end

# good
x += 1 while x < 10

Example:

# bad
until x > 10
  x += 1
end

# good
x += 1 until x > 10

Missing top-level class documentation comment.
Open

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

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

      'no', %w(yes no)
Severity: Minor
Found in lib/miga/cli/action/init.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)

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

    raise "Local manifest not found." unless local_manif
Severity: Minor
Found in lib/miga/cli/action/db.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"

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/classify_wf.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| cli[:activate] = false ; cli[:reason] = v }
Severity: Minor
Found in lib/miga/cli/action/edit.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

Extra empty line detected at module body end.
Open


end
Severity: Minor
Found in lib/miga/dataset/type.rb by rubocop

This cops checks if empty lines around the bodies of modules match the configuration.

Example: EnforcedStyle: empty_lines

# good

module Foo

  def bar
    # ...
  end

end

Example: EnforcedStyle: emptylinesexcept_namespace

# good

module Foo
  module Bar

    # ...

  end
end

Example: EnforcedStyle: emptylinesspecial

# good
module Foo

  def bar; end

end

Example: EnforcedStyle: noemptylines (default)

# good

module Foo
  def bar
    # ...
  end
end

Use snake_case for method names.
Open

    def PREPROCESSING_TASKS
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

    if cli[:result] && r = cli.load_result
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

Missing top-level class documentation comment.
Open

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

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/next_step.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]

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

    [:recommended, :test].each do |n|
Severity: Minor
Found in lib/miga/cli/action/db.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]

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/console.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 module documentation comment.
Open

module MiGA::Dataset::Result::Add
Severity: Minor
Found in lib/miga/dataset/result/add.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

Avoid comma after the last item of a hash.
Open

      on_preprocessing_ready: [[:clear_run_counts], [:recalculate_status]],
Severity: Minor
Found in lib/miga/dataset/hooks.rb by rubocop

This cop checks for trailing comma in array and hash literals.

Example: EnforcedStyleForMultiline: consistent_comma

# bad
a = [1, 2,]

# good
a = [
  1, 2,
  3,
]

# good
a = [
  1,
  2,
]

Example: EnforcedStyleForMultiline: comma

# bad
a = [1, 2,]

# good
a = [
  1,
  2,
]

Example: EnforcedStyleForMultiline: no_comma (default)

# bad
a = [1, 2,]

# good
a = [
  1,
  2
]

Space found before semicolon.
Open

      ) { |v| cli[:activate] = false ; cli[:reason] = v }
Severity: Minor
Found in lib/miga/cli/action/edit.rb by rubocop

Checks for semicolon (;) preceded by space.

Example:

# bad
x = 1 ; y = 2

# good
x = 1; y = 2

Do not use semicolons to terminate expressions.
Open

      ) { puts MiGA::MiGA.FULL_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

Do not use semicolons to terminate expressions.
Open

      ) { |v| puts MiGA::MiGA.CITATION; 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

Provide an exception class and message as arguments to raise.
Open

    raise MiGA::Error.new('Undefined dataset type') unless type
Severity: Minor
Found in lib/miga/dataset/type.rb by rubocop

This cop checks the args passed to fail and raise. For exploded style (default), it recommends passing the exception class and message to raise, rather than construct an instance of the error. It will still allow passing just a message, or the construction of an error with more than one argument.

The exploded style works identically, but with the addition that it will also suggest constructing error objects when the exception is passed multiple arguments.

Example: EnforcedStyle: exploded (default)

# bad
raise StandardError.new("message")

# good
raise StandardError, "message"
fail "message"
raise MyCustomError.new(arg1, arg2, arg3)
raise MyKwArgError.new(key1: val1, key2: val2)

Example: EnforcedStyle: compact

# bad
raise StandardError, "message"
raise RuntimeError, arg1, arg2, arg3

# good
raise StandardError.new("message")
raise MyCustomError.new(arg1, arg2, arg3)
fail "message"
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