bio-miga/miga

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Add parentheses to nested method call o.is_a? Errno::ENOENT.
Open

    assert(o.is_a? Errno::ENOENT)
Severity: Minor
Found in test/system_call_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Missing magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/tax_index_test.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

Dependencies should be sorted in an alphabetical order within their section of the gemspec. Dependency net-ftp should appear before net-http.
Open

  s.add_runtime_dependency 'net-ftp'
Severity: Minor
Found in miga-base.gemspec by rubocop

Dependencies in the gemspec should be alphabetically sorted.

Example:

# bad
spec.add_dependency 'rubocop'
spec.add_dependency 'rspec'

# good
spec.add_dependency 'rspec'
spec.add_dependency 'rubocop'

# good
spec.add_dependency 'rubocop'

spec.add_dependency 'rspec'

# bad
spec.add_development_dependency 'rubocop'
spec.add_development_dependency 'rspec'

# good
spec.add_development_dependency 'rspec'
spec.add_development_dependency 'rubocop'

# good
spec.add_development_dependency 'rubocop'

spec.add_development_dependency 'rspec'

# bad
spec.add_runtime_dependency 'rubocop'
spec.add_runtime_dependency 'rspec'

# good
spec.add_runtime_dependency 'rspec'
spec.add_runtime_dependency 'rubocop'

# good
spec.add_runtime_dependency 'rubocop'

spec.add_runtime_dependency 'rspec'

# good only if TreatCommentsAsGroupSeparators is true
# For code quality
spec.add_dependency 'rubocop'
# For tests
spec.add_dependency 'rspec'

Add parentheses to nested method call u.is_a? URI.
Open

    assert(u.is_a? URI)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

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

  s.rdoc_options = %w(lib README.md --main README.md)
Severity: Minor
Found in miga-base.gemspec 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)

end at 171, 17 is not aligned with %w[ess.faa ess/log done] at 168, 23 or .map do |x| at 169, 12.
Open

                 end,
Severity: Minor
Found in test/dataset_test.rb by rubocop

This cop checks whether the end keywords are aligned properly for do end blocks.

Three modes are supported through the EnforcedStyleAlignWith configuration parameter:

start_of_block : the end shall be aligned with the start of the line where the do appeared.

start_of_line : the end shall be aligned with the start of the line where the expression started.

either (which is the default) : the end is allowed to be in either location. The autofixer will default to start_of_line.

Example: EnforcedStyleAlignWith: either (default)

# bad

foo.bar
   .each do
     baz
       end

# good

variable = lambda do |i|
  i
end

Example: EnforcedStyleAlignWith: startofblock

# bad

foo.bar
   .each do
     baz
       end

# good

foo.bar
  .each do
     baz
   end

Example: EnforcedStyleAlignWith: startofline

# bad

foo.bar
   .each do
     baz
       end

# good

foo.bar
  .each do
     baz
end

Add parentheses to nested method call o.is_a? Process::Status.
Open

    assert(o.is_a? Process::Status)
Severity: Minor
Found in test/system_call_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call p.is_a? String.
Open

    assert(p.is_a? String)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Prefer $LOAD_PATH over $:.
Open

$:.unshift File.expand_path('../lib', __FILE__)
Severity: Minor
Found in miga-base.gemspec by rubocop

Use the new Ruby 1.9 hash syntax.
Open

task :default => 'test:all'
Severity: Minor
Found in Rakefile by rubocop

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}

Align .map with { on line 154.
Open

            .map do |x|
Severity: Minor
Found in test/dataset_test.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

Add parentheses to nested method call u.is_a? URI.
Open

    assert(u.is_a? URI)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Space found before semicolon.
Open

    o = MiGA::Parallel.process(1) { |i| $stderr = StringIO.new ; 1 / i }
Severity: Minor
Found in test/parallel_test.rb by rubocop

Checks for semicolon (;) preceded by space.

Example:

# bad
x = 1 ; y = 2

# good
x = 1; y = 2

Missing magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/system_call_test.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 magic comment # frozen_string_literal: true.
Open

$:.unshift File.expand_path('../lib', __FILE__)
Severity: Minor
Found in miga-base.gemspec 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 magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/json_test.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

Add parentheses to nested method call md[:tax].alternative(1).is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].alternative(1).is_a? MiGA::Taxonomy)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Add parentheses to nested method call u.is_a? URI.
Open

    assert(u.is_a? URI)
Severity: Minor
Found in test/remote_dataset_test.rb by rubocop

This cop checks for unparenthesized method calls in the argument list of a parenthesized method call.

Example:

# good
method1(method2(arg), method3(arg))

# bad
method1(method2 arg, method3, arg)

Missing magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/result_stats_test.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 curly braces around a hash parameter.
Open

      MiGA::Json.generate({ a: 1, b: 2 })
Severity: Minor
Found in test/json_test.rb by rubocop

This cop checks for braces around the last parameter in a method call if the last parameter is a hash. It supports braces, no_braces and context_dependent styles.

Example: EnforcedStyle: braces

# The `braces` style enforces braces around all method
# parameters that are hashes.

# bad
some_method(x, y, a: 1, b: 2)

# good
some_method(x, y, {a: 1, b: 2})

Example: EnforcedStyle: no_braces (default)

# The `no_braces` style checks that the last parameter doesn't
# have braces around it.

# bad
some_method(x, y, {a: 1, b: 2})

# good
some_method(x, y, a: 1, b: 2)

Example: EnforcedStyle: context_dependent

# The `context_dependent` style checks that the last parameter
# doesn't have braces around it, but requires braces if the
# second to last parameter is also a hash literal.

# bad
some_method(x, y, {a: 1, b: 2})
some_method(x, y, {a: 1, b: 2}, a: 1, b: 2)

# good
some_method(x, y, a: 1, b: 2)
some_method(x, y, {a: 1, b: 2}, {a: 1, b: 2})
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