Showing 1,637 of 1,651 total issues
Use snake_case for variable names. Open
@@PREPROCESSING_TASKS = %i[
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This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for method names. Open
def INFO_FIELDS
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This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Missing magic comment # frozen_string_literal: true
. Open
require 'miga/remote_dataset/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
Use snake_case for variable names. Open
@@UNIVERSE = {
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This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@EXCLUDE_NOREF_TASKS = %i[mytaxa_scan taxonomy]
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This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Missing top-level class documentation comment. Open
class MiGA::Dataset < MiGA::MiGA
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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
Indent the first line of the right-hand-side of a multi-line assignment. Open
{
universe: universe, db: db, ids: ids.is_a?(Array) ? ids : [ids],
format: format, file: file, obj: obj,
extra: (database_hash[:extra] || {}).merge(extra),
_fun: :"#{getter}_#{action}"
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This cop checks the indentation of the first line of the right-hand-side of a multi-line assignment.
Example:
# bad
value =
if foo
'bar'
end
# good
value =
if foo
'bar'
end
The indentation of the remaining lines can be corrected with
other cops such as IndentationConsistency
and EndAlignment
.
Replace class var @@UNIVERSE with a class instance var. Open
@@UNIVERSE = {
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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.
Use ./*glob* or -- *glob* so names with dashes won't become options. Open
&& tar -zcf proteins.tar.gz *.faa \
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Use ./*glob* or -- *glob* so names with dashes won't become options.
Problematic code:
rm *
Correct code:
rm ./*
or
rm -- *
Rationale
Since files and arguments are strings passed the same way, programs can't properly determine which is which, and rely on dashes to determine what's what.
A file named -f
(touch -- -f
) will not be deleted by the problematic code. It will instead be interpreted as a command line option, and rm
will even report success.
Using ./*
will instead cause the glob to be expanded into ./-f
, which no program will treat as an option.
Similarly, --
by convention indicates the end of options, and nothing after it will be treated like flags (except for some programs possibly still special casing -
as e.g. stdin).
Note that changing *
to ./*
in GNU Tar parameters will add ./
prefix to path names in the created archive. This may cause subtle problems (eg. to search for a specific file in archive, the ./
prefix must be specified as well). So using -- *
is a safer fix for GNU Tar commands.
For more information, see "Filenames and Pathnames in Shell: How to do it Correctly".
Notice
Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.
Provide an exception class and message as arguments to raise
. Open
raise MiGA::Error.new("Unknown dataset type: #{type}")
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This cop checks the args passed to fail
and raise
. For exploded
style (default), it recommends passing the exception class and message
to raise
, rather than construct an instance of the error. It will
still allow passing just a message, or the construction of an error
with more than one argument.
The exploded style works identically, but with the addition that it will also suggest constructing error objects when the exception is passed multiple arguments.
Example: EnforcedStyle: exploded (default)
# bad
raise StandardError.new("message")
# good
raise StandardError, "message"
fail "message"
raise MyCustomError.new(arg1, arg2, arg3)
raise MyKwArgError.new(key1: val1, key2: val2)
Example: EnforcedStyle: compact
# bad
raise StandardError, "message"
raise RuntimeError, arg1, arg2, arg3
# good
raise StandardError.new("message")
raise MyCustomError.new(arg1, arg2, arg3)
fail "message"
Provide an exception class and message as arguments to raise
. Open
raise MiGA::Error.new(
"Dataset type (#{type}) incompatible with project (#{project.type})"
)
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This cop checks the args passed to fail
and raise
. For exploded
style (default), it recommends passing the exception class and message
to raise
, rather than construct an instance of the error. It will
still allow passing just a message, or the construction of an error
with more than one argument.
The exploded style works identically, but with the addition that it will also suggest constructing error objects when the exception is passed multiple arguments.
Example: EnforcedStyle: exploded (default)
# bad
raise StandardError.new("message")
# good
raise StandardError, "message"
fail "message"
raise MyCustomError.new(arg1, arg2, arg3)
raise MyKwArgError.new(key1: val1, key2: val2)
Example: EnforcedStyle: compact
# bad
raise StandardError, "message"
raise RuntimeError, arg1, arg2, arg3
# good
raise StandardError.new("message")
raise MyCustomError.new(arg1, arg2, arg3)
fail "message"
Add parentheses to nested method call spawn hook_args.first.miga_variables(
dataset: name, project: project.path, project_name: project.name,
miga: MiGA::MiGA.root_path, object: event_args.first
)
. Open
spawn hook_args.first.miga_variables(
dataset: name, project: project.path, project_name: project.name,
miga: MiGA::MiGA.root_path, object: event_args.first
)
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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)
Use snake_case for variable names. Open
@@KNOWN_TYPES = {
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This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Replace class var @@_EXCLUDE_NOREF_TASKS_H with a class instance var. Open
@@_EXCLUDE_NOREF_TASKS_H = Hash[@@EXCLUDE_NOREF_TASKS.map { |i| [i, true] }]
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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 @@_EXCLUDE_NOMARKER_TASKS_H with a class instance var. Open
@@_EXCLUDE_NOMARKER_TASKS_H =
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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.
Use snake_case for method names. Open
def UNIVERSE
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This cop makes sure that all methods use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
def fooBar; end
# good
def foo_bar; end
Example: EnforcedStyle: camelCase
# bad
def foo_bar; end
# good
def fooBar; end
Use snake_case for variable names. Open
@@_EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
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This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@_GTDB_API = 'https://gtdb-api.ecogenomic.org/'
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This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1
Use snake_case for variable names. Open
@@_SEQCODE_API = 'https://api.seqco.de/v1/'
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This cop makes sure that all variables use the configured style, snake_case or camelCase, for their names.
Example: EnforcedStyle: snake_case (default)
# bad
fooBar = 1
# good
foo_bar = 1
Example: EnforcedStyle: camelCase
# bad
foo_bar = 1
# good
fooBar = 1