bio-miga/miga

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Add parentheses to nested method call MiGA::Project.KNOWN_TYPES.is_a? Hash.
Open

    assert(MiGA::Project.KNOWN_TYPES.is_a? Hash)
Severity: Minor
Found in test/project_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 md[:tax].is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].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 md[:tax].alternative(:gtdb).is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].alternative(:gtdb).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 h.is_a? Hash.
Open

    assert(h.is_a? Hash)
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 h.is_a? Hash.
Open

    assert(h.is_a? Hash)
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)

Dependencies should be sorted in an alphabetical order within their section of the gemspec. Dependency net-http should appear before sqlite3.
Open

  s.add_runtime_dependency 'net-http'
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 md[:tax].is_a? MiGA::Taxonomy.
Open

    assert(md[:tax].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)

Dependencies should be sorted in an alphabetical order within their section of the gemspec. Dependency assertions should appear before test-unit.
Open

  s.add_development_dependency 'assertions', '~> 1'
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 MiGA::Project.INCLADE_TASKS.is_a? Array.
Open

    assert(MiGA::Project.INCLADE_TASKS.is_a? Array)
Severity: Minor
Found in test/project_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/remote_dataset_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

required_ruby_version (2.7, declared in miga-base.gemspec) and TargetRubyVersion (2.3, declared in .rubocop.yml) should be equal.
Open

  s.required_ruby_version = '>= 2.7'
Severity: Minor
Found in miga-base.gemspec by rubocop

Checks that required_ruby_version of gemspec and TargetRubyVersion of .rubocop.yml are equal. Thereby, RuboCop to perform static analysis working on the version required by gemspec.

Example:

# When `TargetRubyVersion` of .rubocop.yml is `2.3`.

# bad
Gem::Specification.new do |spec|
  spec.required_ruby_version = '>= 2.2.0'
end

# bad
Gem::Specification.new do |spec|
  spec.required_ruby_version = '>= 2.4.0'
end

# good
Gem::Specification.new do |spec|
  spec.required_ruby_version = '>= 2.3.0'
end

# good
Gem::Specification.new do |spec|
  spec.required_ruby_version = '>= 2.3'
end

# good
Gem::Specification.new do |spec|
  spec.required_ruby_version = ['>= 2.3.0', '< 2.5.0']
end

Missing space after #.
Open

    #o = m.http_request(:get, 'http://uibk.microbial-genomes.org/robots.txt')
Severity: Minor
Found in test/net_test.rb by rubocop

This cop checks whether comments have a leading space after the # denoting the start of the comment. The leading space is not required for some RDoc special syntax, like #++, #--, #:nodoc, =begin- and =end comments, "shebang" directives, or rackup options.

Example:

# bad
#Some comment

# good
# Some comment

Missing magic comment # frozen_string_literal: true.
Open

require 'test_helper'
Severity: Minor
Found in test/net_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

end at 179, 17 is not aligned with %w[pdf wintax mytaxa reg done] at 176, 19 or .map do |x| at 177, 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 MiGA::Project.DISTANCE_TASKS.is_a? Array.
Open

    assert(MiGA::Project.DISTANCE_TASKS.is_a? Array)
Severity: Minor
Found in test/project_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)

Do not introduce global variables.
Open

    $counter = 1
Severity: Minor
Found in test/hook_test.rb by rubocop

This cops looks for uses of global variables. It does not report offenses for built-in global variables. Built-in global variables are allowed by default. Additionally users can allow additional variables via the AllowedVariables option.

Note that backreferences like $1, $2, etc are not global variables.

Example:

# bad
$foo = 2
bar = $foo + 5

# good
FOO = 2
foo = 2
$stdin.read

Use proc instead of Proc.new.
Open

    dataset.add_hook(:on_result_ready, :run_lambda, Proc.new { |r| $res = r })
Severity: Minor
Found in test/hook_test.rb by rubocop

This cops checks for uses of Proc.new where Kernel#proc would be more appropriate.

Example:

# bad
p = Proc.new { |n| puts n }

# good
p = proc { |n| puts n }

Redundant curly braces around a hash parameter.
Open

    tx_js = JSON.parse(js, { symbolize_names: false, create_additions: true })
Severity: Minor
Found in test/taxonomy_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})

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/metadata.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 // around regular expression.
Open

    assert_match(%r{\] x *\r}, o)
Severity: Minor
Found in test/common_test.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\//
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