Showing 1,637 of 1,651 total issues
Missing magic comment # frozen_string_literal: true
. Open
require 'miga/result/base'
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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
Incorrect indentation detected (column 8 instead of 6). Open
# * Bowers et al 2017, DOI: 10.1038/nbt.3893
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This cops checks the indentation of comments.
Example:
# bad
# comment here
def method_name
end
# comment here
a = 'hello'
# yet another comment
if true
true
end
# good
# comment here
def method_name
end
# comment here
a = 'hello'
# yet another comment
if true
true
end
Use k.zero?
instead of k == 0
. Open
miga_say if k == 0
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This cop checks for usage of comparison operators (==
,
>
, <
) to test numbers as zero, positive, or negative.
These can be replaced by their respective predicate methods.
The cop can also be configured to do the reverse.
The cop disregards #nonzero?
as it its value is truthy or falsey,
but not true
and false
, and thus not always interchangeable with
!= 0
.
The cop ignores comparisons to global variables, since they are often
populated with objects which can be compared with integers, but are
not themselves Interger
polymorphic.
Example: EnforcedStyle: predicate (default)
# bad
foo == 0
0 > foo
bar.baz > 0
# good
foo.zero?
foo.negative?
bar.baz.positive?
Example: EnforcedStyle: comparison
# bad
foo.zero?
foo.negative?
bar.baz.positive?
# good
foo == 0
0 > foo
bar.baz > 0
Use ||
instead of or
. Open
unless asm.nil? or asm[:stats][:total_length].nil?
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This cop checks for uses of and
and or
, and suggests using &&
and
|| instead
. It can be configured to check only in conditions, or in
all contexts.
Example: EnforcedStyle: always (default)
# bad
foo.save and return
# bad
if foo and bar
end
# good
foo.save && return
# good
if foo && bar
end
Example: EnforcedStyle: conditionals
# bad
if foo and bar
end
# good
foo.save && return
# good
foo.save and return
# good
if foo && bar
end
Align the operands of a condition in an if
statement spanning multiple lines. Open
metadata[:ncbi_nuccore] && !metadata[:ncbi_wgs]
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This cop checks the indentation of the right hand side operand in binary operations that span more than one line.
Example:
# bad
if a +
b
something
end
# good
if a +
b
something
end
Use ||
instead of or
. Open
if unknown or not datasets.empty? or not name.nil?
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This cop checks for uses of and
and or
, and suggests using &&
and
|| instead
. It can be configured to check only in conditions, or in
all contexts.
Example: EnforcedStyle: always (default)
# bad
foo.save and return
# bad
if foo and bar
end
# good
foo.save && return
# good
if foo && bar
end
Example: EnforcedStyle: conditionals
# bad
if foo and bar
end
# good
foo.save && return
# good
foo.save and return
# good
if foo && bar
end
Do not prefix reader method names with get_
. Open
def get_ncbi_taxid_from_web
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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
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
Prefer annotated tokens (like %<foo>s</foo>
) over unannotated tokens (like %s
). Open
'%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
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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>
Favor a normal if-statement over a modifier clause in a multiline statement. Open
Zlib::GzipReader.open(file_path(:trna_list)) do |fh|
no = 0
stats[:trna_count] = 0
aa = {}
fh.each_line do |ln|
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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
Omit parentheses for ternary conditions. Open
(@ncbi_taxonomy_names ||= nil) ? true : false
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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
Avoid the use of Perl-style backrefs. Open
stats[:codon_table] = $1
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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)
Unused block argument - k
. If it's necessary, use _
or _k
as an argument name to indicate that it won't be used. Open
MiGA::Result.RESULT_DIRS.find do |k, v|
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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
require 'miga/result/base'
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- Exclude checks
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
# @package MiGA
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- Exclude checks
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 !
instead of not
. Open
if unknown or not datasets.empty? or not name.nil?
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This cop checks for uses of the keyword not
instead of !
.
Example:
# bad - parentheses are required because of op precedence
x = (not something)
# good
x = !something
Avoid when
branches without a body. Open
when nil
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This cop checks for the presence of when
branches without a body.
Example:
# bad
case foo
when bar then 1
when baz then # nothing
end
Example:
# good
case foo
when bar then 1
when baz then 2
end
Do not prefix reader method names with get_
. Open
def get_ncbi_taxid_from_ebi
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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
Missing magic comment # frozen_string_literal: true
. Open
# @package MiGA
- Read upRead up
- Create a ticketCreate a ticket
- Exclude checks
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 alias get_ncbi_taxid_from_seqcode get_ncbi_taxid_from_ncbi
instead of alias :get_ncbi_taxid_from_seqcode :get_ncbi_taxid_from_ncbi
. Open
alias :get_ncbi_taxid_from_seqcode :get_ncbi_taxid_from_ncbi
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This cop enforces the use of either #alias
or #alias_method
depending on configuration.
It also flags uses of alias :symbol
rather than alias bareword
.
Example: EnforcedStyle: prefer_alias (default)
# bad
alias_method :bar, :foo
alias :bar :foo
# good
alias bar foo
Example: EnforcedStyle: preferaliasmethod
# bad
alias :bar :foo
alias bar foo
# good
alias_method :bar, :foo