OpenJij/cimod

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Dollar signs used before commands without showing output
Open

```sh
Severity: Info
Found in docs/index.md by markdownlint

MD014 - Dollar signs used before commands without showing output

Tags: code

Aliases: commands-show-output

This rule is triggered when there are code blocks showing shell commands to be typed, and the shell commands are preceded by dollar signs ($):

$ ls
$ cat foo
$ less bar

The dollar signs are unnecessary in the above situation, and should not be included:

ls
cat foo
less bar

However, an exception is made when there is a need to distinguish between typed commands and command output, as in the following example:

$ ls
foo bar
$ cat foo
Hello world
$ cat bar
baz

Rationale: it is easier to copy and paste and less noisy if the dollar signs are omitted when they are not needed. See http://www.cirosantilli.com/markdown-styleguide/#dollar-signs-in-shell-code for more information.

Line too long (85 > 79 characters)
Open

                    val_condition = isinstance(kwargs["values"], list) or isinstance(
Severity: Minor
Found in cimod/model/binary_polynomial_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (80 > 79 characters)
Open

            indices (list): labels of each variables sorted by results variables

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Double quote array expansions to avoid re-splitting elements.
Open

exec $LLVM_COV_BIN gcov $@
Severity: Minor
Found in cmake/llvm-cov-wrapper by shellcheck

Double quote array expansions to avoid re-splitting elements.

Problematic code:

cp $@ ~/dir

Correct code:

cp "$@" ~/dir

Rationale:

Double quotes around $@ (and similarly, ${array[@]}) prevents globbing and word splitting of individual elements, while still expanding to multiple separate arguments.

Let's say you have three arguments: baz, foo bar and *

"$@" will expand into exactly that: baz, foo bar and *

$@ will expand into multiple other arguments: baz, foo, bar, file.txt and otherfile.jpg

Since the latter is rarely expected or desired, ShellCheck warns about it.

Exceptions

When you want globbing of individual elements.

Notice

Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.

Line too long (84 > 79 characters)
Open

                f"Offset or vartype is configured incorrectly. Vartype must be set."
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (81 > 79 characters)
Open

                offset, vartype = extract_offset_and_vartype(*args[2:], **kwargs)
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (83 > 79 characters)
Open

                sample = {self.variables[k]: elem for k, elem in enumerate(sample)}
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (110 > 79 characters)
Open

       Generate BinaryQuadraticModel class with the base class specified by the arguments linear and quadratic

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (88 > 79 characters)
Open

                numpy.ndarray: interactioin matrix H_{ij} or Q_{ij}, energy_bias (float)

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (85 > 79 characters)
Open

                        np.dot(sample, np.dot(int_mat, sample)) - np.sum(linear_term)

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Double quote to prevent globbing and word splitting.
Open

        exec $LLVM_COV_BIN $@
Severity: Minor
Found in cmake/llvm-cov-wrapper by shellcheck

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.

Double quote array expansions to avoid re-splitting elements.
Open

        exec $LLVM_COV_BIN $@
Severity: Minor
Found in cmake/llvm-cov-wrapper by shellcheck

Double quote array expansions to avoid re-splitting elements.

Problematic code:

cp $@ ~/dir

Correct code:

cp "$@" ~/dir

Rationale:

Double quotes around $@ (and similarly, ${array[@]}) prevents globbing and word splitting of individual elements, while still expanding to multiple separate arguments.

Let's say you have three arguments: baz, foo bar and *

"$@" will expand into exactly that: baz, foo bar and *

$@ will expand into multiple other arguments: baz, foo, bar, file.txt and otherfile.jpg

Since the latter is rarely expected or desired, ShellCheck warns about it.

Exceptions

When you want globbing of individual elements.

Notice

Original content from the ShellCheck https://github.com/koalaman/shellcheck/wiki.

Line too long (83 > 79 characters)
Open

            key_condition = isinstance(args[0], list) or isinstance(args[0], tuple)
Severity: Minor
Found in cimod/model/binary_polynomial_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (141 > 79 characters)
Open

           The dictionaries between indices and integers are self.ind_to_num (indices -> integers) and self.num_to_ind (integers -> indices).
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (88 > 79 characters)
Open

            """Determine the energy of the specified sample of a binary quadratic model.

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (113 > 79 characters)
Open

        sparse (bool): if true, the inner data will be a sparse matrix, otherwise the data will be a dense matrix
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (89 > 79 characters)
Open

            # if linear and quadratic are given. generate matrix and initialize as matrix
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (128 > 79 characters)
Open

            return f"BinaryQuadraticModel({self.linear}, {self.quadratic}, {self.offset}, {self.vartype}, sparse={self.sparse})"
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Line too long (83 > 79 characters)
Open

            mat, idx_to_label = cls._generate_mat(linear, quadratic, False, sparse)
Severity: Minor
Found in cimod/model/binary_quadratic_model.py by pep8

Limit all lines to a maximum of 79 characters.

There are still many devices around that are limited to 80 character
lines; plus, limiting windows to 80 characters makes it possible to
have several windows side-by-side.  The default wrapping on such
devices looks ugly.  Therefore, please limit all lines to a maximum
of 79 characters. For flowing long blocks of text (docstrings or
comments), limiting the length to 72 characters is recommended.

Reports error E501.

Double quote to prevent globbing and word splitting.
Open

                "gcda") exec $LLVM_COV_BIN --gcda="$1" ;;
Severity: Minor
Found in cmake/llvm-cov-wrapper by shellcheck

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.

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