Method has too many lines. [38/10] Open
def parse_cli
default_opts_for_wf
cli.defaults = {
metric: :ani, threshold: 95.0, criterion: :quality,
summaries: true, collection: true
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This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.
Assignment Branch Condition size for dereplicate is too high. [35.74/15] Open
def dereplicate(p)
return if cli[:prepare_and_exit]
cli.say 'Extracting genomospecies clades'
r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
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This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric
Method has too many lines. [20/10] Open
def dereplicate(p)
return if cli[:prepare_and_exit]
cli.say 'Extracting genomospecies clades'
r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
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This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.
Assignment Branch Condition size for parse_cli is too high. [23.41/15] Open
def parse_cli
default_opts_for_wf
cli.defaults = {
metric: :ani, threshold: 95.0, criterion: :quality,
summaries: true, collection: true
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This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric
Assignment Branch Condition size for representatives is too high. [17.15/15] Open
def representatives(p)
cli.say 'Identifying representatives'
f = File.join(cli[:outdir], 'representatives.txt')
if cli[:criterion] == :medoids
FileUtils.cp(p.result(:clade_finding).file_path(:medoids_gsp), f)
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This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric
Assignment Branch Condition size for perform is too high. [16.06/15] Open
def perform
# Input data
p = create_project(
:assembly,
{ run_clades: false },
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This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric
Method has too many lines. [11/10] Open
def perform
# Input data
p = create_project(
:assembly,
{ run_clades: false },
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This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.
Method parse_cli
has 38 lines of code (exceeds 25 allowed). Consider refactoring. Open
def parse_cli
default_opts_for_wf
cli.defaults = {
metric: :ani, threshold: 95.0, criterion: :quality,
summaries: true, collection: true
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Block has too many lines. [31/25] Open
cli.parse do |opt|
opt.on(
'--aai',
'Use Average Amino Acid Identity (AAI) as genome similarity metric',
'By default: Use Average Nucleotide Identity (ANI)'
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This cop checks if the length of a block exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable. The cop can be configured to ignore blocks passed to certain methods.
Missing top-level class documentation comment. Open
class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
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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
Unused block argument - v
. You can omit the argument if you don't care about it. Open
) { |v| cli[:criterion] = :medoids }
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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
Use a guard clause instead of wrapping the code inside a conditional expression. Open
if cli[:collection]
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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
Unused block argument - v
. You can omit the argument if you don't care about it. Open
) { |v| cli[:criterion] = :quality }
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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 magic comment # frozen_string_literal: true
. Open
# @package MiGA
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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
{ run_mytaxa_scan: false, run_ssu: false }
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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})