bio-miga/miga

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Avoid comma after the last item of a hash.
Open

    tax_distributions: :tax_dist,
Severity: Minor
Found in lib/miga/cli/base.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
]

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::GtdbGet < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/gtdb_get.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/files.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

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

  @@EXECS = @@TASK_DESC.keys
Severity: Minor
Found in lib/miga/cli/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.

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

  @@FILE_REGEXP =
Severity: Minor
Found in lib/miga/cli/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/cli/action/add_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 %i or %I for an array of symbols.
Open

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

Extra blank line detected.
Open


  def finalize_tasks(d, downloaded)

This cops checks for two or more consecutive blank lines.

Example:

# bad - It has two empty lines.
some_method
# one empty line
# two empty lines
some_method

# good
some_method
# one empty line
some_method

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/archive.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

Omit parentheses for ternary conditions.
Open

      (@@TASK_DESC[task] =~ /\(alias: .*\)\./) ?
        @@TASK_DESC[task].sub(/\)\.$/, ", #{nick}).") :
        @@TASK_DESC[task].sub(/\.$/, " (alias: #{nick}).")
Severity: Minor
Found in lib/miga/cli/base.rb by rubocop

This cop checks for the presence of parentheses around ternary conditions. It is configurable to enforce inclusion or omission of parentheses using EnforcedStyle. Omission is only enforced when removing the parentheses won't cause a different behavior.

Example: EnforcedStyle: requirenoparentheses (default)

# bad
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = (bar && baz) ? a : b

# good
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = bar && baz ? a : b

Example: EnforcedStyle: require_parentheses

# bad
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = bar && baz ? a : b

# good
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = (bar && baz) ? a : b

Example: EnforcedStyle: requireparentheseswhen_complex

# bad
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = bar && baz ? a : b

# good
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = (bar && baz) ? a : b

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/tax_set.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 top-level class documentation comment.
Open

class MiGA::Cli::Action::TaxIndex < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/tax_index.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 each_key instead of keys.each.
Open

    dist.keys.each do |k|
Severity: Minor
Found in lib/miga/cli/action/tax_dist.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 }

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

      fh.puts('# %i' % list.size)

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

Prefer annotated tokens (like %<foo>s</foo>) over unannotated tokens (like %s).
Open

        MiGA::MiGA.run_cmd('cd "%s" && tar -zxf "%s"' % [dir, file])

Use a consistent style for named format string tokens.

Note: unannotated style cop only works for strings which are passed as arguments to those methods: sprintf, format, %. The reason is that unannotated format is very similar to encoded URLs or Date/Time formatting strings.

Example: EnforcedStyle: annotated (default)

# bad
format('%{greeting}', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%<greeting>s', greeting: 'Hello')</greeting>

Example: EnforcedStyle: template

# bad
format('%<greeting>s', greeting: 'Hello')
format('%s', 'Hello')

# good
format('%{greeting}', greeting: 'Hello')</greeting>

Example: EnforcedStyle: unannotated

# bad
format('%<greeting>s', greeting: 'Hello')
format('%{greeting}', 'Hello')

# good
format('%s', 'Hello')</greeting>

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

  @@PAIRED_FILE_REGEXP =
Severity: Minor
Found in lib/miga/cli/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/cli/action/index_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

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/tax_dist.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 the use of Perl-style backrefs.
Open

          sw = $1
Severity: Minor
Found in lib/miga/cli/action/add_result.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)

Prefer Date or Time over DateTime.
Open

    ) { |v| cli[:updated_before] = DateTime.parse(v) }

This cop checks for uses of DateTime that should be replaced by Date or Time.

Example:

# bad - uses `DateTime` for current time
DateTime.now

# good - uses `Time` for current time
Time.now

# bad - uses `DateTime` for modern date
DateTime.iso8601('2016-06-29')

# good - uses `Date` for modern date
Date.iso8601('2016-06-29')

# good - uses `DateTime` with start argument for historical date
DateTime.iso8601('1751-04-23', Date::ENGLAND)
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