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Use next
to skip iteration. Open
if entry.file? && entry.name =~ /_genomic\.fna$/
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Use next
to skip iteration instead of a condition at the end.
Example: EnforcedStyle: skipmodifierifs (default)
# bad
[1, 2].each do |a|
if a == 1
puts a
end
end
# good
[1, 2].each do |a|
next unless a == 1
puts a
end
# good
[1, 2].each do |o|
puts o unless o == 1
end
Example: EnforcedStyle: always
# With `always` all conditions at the end of an iteration needs to be
# replaced by next - with `skip_modifier_ifs` the modifier if like
# this one are ignored: `[1, 2].each { |a| return 'yes' if a == 1 }`
# bad
[1, 2].each do |o|
puts o unless o == 1
end
# bad
[1, 2].each do |a|
if a == 1
puts a
end
end
# good
[1, 2].each do |a|
next unless a == 1
puts a
end
Align the parameters of a method call if they span more than one line. Open
db: opts[:db], id: opts[:ids], rettype: opts[:format], retmode: :text
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Here we check if the parameters on a multi-line method call or definition are aligned.
Example: EnforcedStyle: withfirstparameter (default)
# good
foo :bar,
:baz
# bad
foo :bar,
:baz
Example: EnforcedStyle: withfixedindentation
# good
foo :bar,
:baz
# bad
foo :bar,
:baz
Replace class var @@_GTDB_API with a class instance var. Open
@@_GTDB_API = 'https://gtdb-api.ecogenomic.org/'
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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 the new Ruby 1.9 hash syntax. Open
:'type-genomes' => { stage: :metadata, format: :json }
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This cop checks hash literal syntax.
It can enforce either the use of the class hash rocket syntax or the use of the newer Ruby 1.9 syntax (when applicable).
A separate offense is registered for each problematic pair.
The supported styles are:
- ruby19 - forces use of the 1.9 syntax (e.g.
{a: 1}
) when hashes have all symbols for keys - hash_rockets - forces use of hash rockets for all hashes
- nomixedkeys - simply checks for hashes with mixed syntaxes
- ruby19nomixed_keys - forces use of ruby 1.9 syntax and forbids mixed syntax hashes
Example: EnforcedStyle: ruby19 (default)
# bad
{:a => 2}
{b: 1, :c => 2}
# good
{a: 2, b: 1}
{:c => 2, 'd' => 2} # acceptable since 'd' isn't a symbol
{d: 1, 'e' => 2} # technically not forbidden
Example: EnforcedStyle: hash_rockets
# bad
{a: 1, b: 2}
{c: 1, 'd' => 5}
# good
{:a => 1, :b => 2}
Example: EnforcedStyle: nomixedkeys
# bad
{:a => 1, b: 2}
{c: 1, 'd' => 2}
# good
{:a => 1, :b => 2}
{c: 1, d: 2}
Example: EnforcedStyle: ruby19nomixed_keys
# bad
{:a => 1, :b => 2}
{c: 2, 'd' => 3} # should just use hash rockets
# good
{a: 1, b: 2}
{:c => 3, 'd' => 4}
Use snake_case for method names. Open
def ONLY_MULTI_TASKS
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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
@@_EXCLUDE_NOREF_TASKS_H = Hash[@@EXCLUDE_NOREF_TASKS.map { |i| [i, true] }]
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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
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
.
Prefer annotated tokens (like %<foo>s</foo>
) over unannotated tokens (like %s
). Open
ids = rang.map { |k| "%s%0#{a.size - pref.size}i" % [pref, k] }
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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>
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
To read lines rather than words, pipe/redirect to a 'while read' loop. Open
for win in $(cat "$DATASET.wintax.regions") ; do
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To read lines rather than words, pipe/redirect to a 'while read' loop.
Problematic code:
for line in $(cat file | grep -v '^ *#')
do
echo "Line: $line"
done
Correct code:
grep -v '^ *#' < file | while IFS= read -r line
do
echo "Line: $line"
done
or without a subshell (bash, zsh, ksh):
while IFS= read -r line
do
echo "Line: $line"
done < <(grep -v '^ *#' < file)
or without a subshell, with a pipe (more portable, but write a file on the filesystem):
mkfifo mypipe
grep -v '^ *#' < file > mypipe &
while IFS= read -r line
do
echo "Line: $line"
done < mypipe
rm mypipe
Rationale:
For loops by default (subject to $IFS
) read word by word. Additionally, glob expansion will occur.
Given this text file:
foo *
bar
The for loop will print:
Line: foo
Line: aardwark.jpg
Line: bullfrog.jpg
...
The while loop will print:
Line: foo *
Line: bar
Exceptions
If you want to read word by word, you should still use a while read loop (e.g. with read -a
to read words into an array).
Rare reasons for ignoring this message is if you don't care because your file only contains numbers and you're not interested in good practices, or if you've set $IFS
appropriately and also disabled globbing.
Notice
Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.
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
Use snake_case for variable names. Open
@@EXCLUDE_NOMARKER_TASKS = %i[essential_genes ssu]
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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 with a class instance var. Open
@@EXCLUDE_NOREF_TASKS = %i[mytaxa_scan taxonomy]
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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.
Useless assignment to variable - ids
. Open
ids =
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This cop checks for every useless assignment to local variable in every
scope.
The basic idea for this cop was from the warning of ruby -cw
:
assigned but unused variable - foo
Currently this cop has advanced logic that detects unreferenced reassignments and properly handles varied cases such as branch, loop, rescue, ensure, etc.
Example:
# bad
def some_method
some_var = 1
do_something
end
Example:
# good
def some_method
some_var = 1
do_something(some_var)
end
Align the parameters of a method call if they span more than one line. Open
db: opts[:db], id: opts[:ids], retmode: opts[:format]
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Here we check if the parameters on a multi-line method call or definition are aligned.
Example: EnforcedStyle: withfirstparameter (default)
# good
foo :bar,
:baz
# bad
foo :bar,
:baz
Example: EnforcedStyle: withfixedindentation
# good
foo :bar,
:baz
# bad
foo :bar,
:baz
Use snake_case for variable names. Open
@@_EBI_API = 'https://www.ebi.ac.uk/Tools/'
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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 @@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.
Double quote to prevent globbing and word splitting. Open
echo O | tRNAscan-SE $dom_opt -o "${DATASET}.trna.txt" -q "$fa" || true
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Double quote to prevent globbing and word splitting.
Problematic code:
echo $1
for i in $*; do :; done # this done and the next one also applies to expanding arrays.
for i in $@; do :; done
Correct code:
echo "$1"
for i in "$@"; do :; done # or, 'for i; do'
Rationale
The first code looks like "print the first argument". It's actually "Split the first argument by IFS (spaces, tabs and line feeds). Expand each of them as if it was a glob. Join all the resulting strings and filenames with spaces. Print the result."
The second one looks like "iterate through all arguments". It's actually "join all the arguments by the first character of IFS (space), split them by IFS and expand each of them as globs, and iterate on the resulting list". The third one skips the joining part.
Quoting variables prevents word splitting and glob expansion, and prevents the script from breaking when input contains spaces, line feeds, glob characters and such.
Strictly speaking, only expansions themselves need to be quoted, but for stylistic reasons, entire arguments with multiple variable and literal parts are often quoted as one:
$HOME/$dir/dist/bin/$file # Unquoted (bad)
"$HOME"/"$dir"/dist/bin/"$file" # Minimal quoting (good)
"$HOME/$dir/dist/bin/$file" # Canonical quoting (good)
When quoting composite arguments, make sure to exclude globs and brace expansions, which lose their special meaning in double quotes: "$HOME/$dir/src/*.c"
will not expand, but "$HOME/$dir/src"/*.c
will.
Note that $( )
starts a new context, and variables in it have to be quoted independently:
echo "This $variable is quoted $(but this $variable is not)"
echo "This $variable is quoted $(and now this "$variable" is too)"
Exceptions
Sometimes you want to split on spaces, like when building a command line:
options="-j 5 -B"
make $options file
Just quoting this doesn't work. Instead, you should have used an array (bash, ksh, zsh):
options=(-j 5 -B) # ksh: set -A options -- -j 5 -B
make "${options[@]}" file
or a function (POSIX):
make_with_flags() { make -j 5 -B "$@"; }
make_with_flags file
To split on spaces but not perform glob expansion, Posix has a set -f
to disable globbing. You can disable word splitting by setting IFS=''
.
Similarly, you might want an optional argument:
debug=""
[[ $1 == "--trace-commands" ]] && debug="-x"
bash $debug script
Quoting this doesn't work, since in the default case, "$debug"
would expand to one empty argument while $debug
would expand into zero arguments. In this case, you can use an array with zero or one elements as outlined above, or you can use an unquoted expansion with an alternate value:
debug=""
[[ $1 == "--trace-commands" ]] && debug="yes"
bash ${debug:+"-x"} script
This is better than an unquoted value because the alternative value can be properly quoted, e.g. wget ${output:+ -o "$output"}
.
As always, this warning can be [[ignore]]d on a case-by-case basis.
this is especially relevant when BASH many not be available for the array work around. For example, use in eval or in command options where script has total control of the variables...
FLAGS="-av -e 'ssh -x' --delete --delete-excluded"
...
# shellcheck disable=SC2086
eval rsync $FLAGS ~/dir remote_host:dir
Notice
Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.
Closing method definition brace must be on the line after the last parameter when opening brace is on a separate line from the first parameter. Open
universe, db, ids, format, file = nil, extra = {}, obj = nil)
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This cop checks that the closing brace in a method definition is either on the same line as the last method parameter, or a new line.
When using the symmetrical
(default) style:
If a method definition's opening brace is on the same line as the first parameter of the definition, then the closing brace should be on the same line as the last parameter of the definition.
If an method definition's opening brace is on the line above the first parameter of the definition, then the closing brace should be on the line below the last parameter of the definition.
When using the new_line
style:
The closing brace of a multi-line method definition must be on the line after the last parameter of the definition.
When using the same_line
style:
The closing brace of a multi-line method definition must be on the same line as the last parameter of the definition.
Example:
# symmetrical: bad
# new_line: good
# same_line: bad
def foo(a,
b
)
end
# symmetrical: bad
# new_line: bad
# same_line: good
def foo(
a,
b)
end
# symmetrical: good
# new_line: bad
# same_line: good
def foo(a,
b)
end
# symmetrical: good
# new_line: good
# same_line: bad
def foo(
a,
b
)
end
Missing top-level module documentation comment. Open
module MiGA::RemoteDataset::Download
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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