bio-miga/miga

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

      cli.opt_object(opt, [:project, :dataset_type])
Severity: Minor
Found in lib/miga/cli/action/find.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]

Favor a normal unless-statement over a modifier clause in a multiline statement.
Open

    call_cli(
      ['new', '-P', cli[:outdir], '-t', cli[:project_type]]
    ) unless MiGA::Project.exist? cli[:outdir]
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

Checks for uses of if/unless modifiers with multiple-lines bodies.

Example:

# bad
{
  result: 'this should not happen'
} unless cond

# good
{ result: 'ok' } if cond

Avoid multi-line ternary operators, use if or unless instead.
Open

      what = cli[:ncbi_ref] ? '--reference' :
             cli[:ncbi_draft] ? '--all' : '--complete'
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

This cop checks for multi-line ternary op expressions.

Example:

# bad
a = cond ?
  b : c
a = cond ? b :
    c
a = cond ?
    b :
    c

# good
a = cond ? b : c
a =
  if cond
    b
  else
    c
  end

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::Date < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/date.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 a guard clause instead of wrapping the code inside a conditional expression.
Open

    if cli[:collection]
Severity: Minor
Found in lib/miga/cli/action/derep_wf.rb by rubocop

Use a guard clause instead of wrapping the code inside a conditional expression

Example:

# bad
def test
  if something
    work
  end
end

# good
def test
  return unless something
  work
end

# also good
def test
  work if something
end

# bad
if something
  raise 'exception'
else
  ok
end

# good
raise 'exception' if something
ok

Do not prefix reader method names with get_.
Open

  def get_files_and_type
Severity: Minor
Found in lib/miga/cli/action/add.rb by rubocop

This cop makes sure that accessor methods are named properly.

Example:

# bad
def set_attribute(value)
end

# good
def attribute=(value)
end

# bad
def get_attribute
end

# good
def attribute
end

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

  @@INPUT_TYPES = {
Severity: Minor
Found in lib/miga/cli/action/add.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.

Unused block argument - v. If it's necessary, use _ or _v as an argument name to indicate that it won't be used.
Open

    obj.metadata.each do |k, v|
Severity: Minor
Found in lib/miga/cli/action/wf.rb by rubocop

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

Example:

#good

do_something do |used, _unused|
  puts used
end

do_something do
  puts :foo
end

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

Missing top-level class documentation comment.
Open

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

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/date.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 snake_case for variable names.
Open

  @@INPUT_TYPES = {
Severity: Minor
Found in lib/miga/cli/action/add.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

Use snake_case for variable names.
Open

  @@OPERATIONS = {
Severity: Minor
Found in lib/miga/cli/action/doctor.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

Use next to skip iteration.
Open

      if cli[:add]
Severity: Minor
Found in lib/miga/cli/action/find.rb by rubocop

Use next to skip iteration instead of a condition at the end.

Example: EnforcedStyle: skipmodifierifs (default)

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

# good
[1, 2].each do |o|
  puts o unless o == 1
end

Example: EnforcedStyle: always

# With `always` all conditions at the end of an iteration needs to be
# replaced by next - with `skip_modifier_ifs` the modifier if like
# this one are ignored: `[1, 2].each { |a| return 'yes' if a == 1 }`

# bad
[1, 2].each do |o|
  puts o unless o == 1
end

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

Missing top-level class documentation comment.
Open

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

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/stats.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 %i or %I for an array of symbols.
Open

      cli.puts MiGA.tabulate([:key, :value], p.metadata.data.keys.map do |k|
Severity: Minor
Found in lib/miga/cli/action/about.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

      cli.opt_object(opt, [:project, :dataset_opt])
Severity: Minor
Found in lib/miga/cli/action/ln.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]

Unnecessary splat expansion.
Open

            when *%w[project file verbose help debug]
Severity: Minor
Found in lib/miga/cli/action/get.rb by rubocop

This cop checks for unneeded usages of splat expansion

Example:

# bad

a = *[1, 2, 3]
a = *'a'
a = *1

begin
  foo
rescue *[StandardError, ApplicationError]
  bar
end

case foo
when *[1, 2, 3]
  bar
else
  baz
end

Example:

# good

c = [1, 2, 3]
a = *c
a, b = *c
a, *b = *c
a = *1..10
a = ['a']

begin
  foo
rescue StandardError, ApplicationError
  bar
end

case foo
when *[1, 2, 3]
  bar
else
  baz
end

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/get.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 each_key instead of keys.each.
Open

    @@OPERATIONS.keys.each do |k|
Severity: Minor
Found in lib/miga/cli/action/doctor.rb by rubocop

This cop checks for uses of each_key and each_value Hash methods.

Note: If you have an array of two-element arrays, you can put parentheses around the block arguments to indicate that you're not working with a hash, and suppress RuboCop offenses.

Example:

# bad
hash.keys.each { |k| p k }
hash.values.each { |v| p v }
hash.each { |k, _v| p k }
hash.each { |_k, v| p v }

# good
hash.each_key { |k| p k }
hash.each_value { |v| p v }
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