def setup_formatter(snake: str, line_length: int = DEFAULT_LINE_LENGTH):
stream = StringIO(snake)
smk = Snakefile(stream)
return Formatter(smk, line_length=line_length)
def main(
ctx: click.Context,
line_length: int,
check: bool,
diff: bool,
compact_diff: bool,
include: str,
exclude: str,
src: List[PathLike],
config: Optional[PathLike],
verbose: bool,
):
"""The uncompromising Snakemake code formatter.
SRC specifies directories and files to format. Directories will be searched for
file names that conform to the include/exclude patterns provided.
Files are modified in-place by default; use diff, check, or
`snakefmt - < Snakefile` to avoid this.
"""
log_level = logging.DEBUG if verbose else logging.INFO
logging.basicConfig(format="[%(levelname)s] %(message)s", level=log_level)
if not src:
click.echo(
"No path provided. Nothing to do 😴. Call with -h for help.", err=True
)
ctx.exit(0)
if "-" in src and len(src) > 1:
raise click.BadArgumentUsage("Cannot mix stdin (-) with other files")
if diff and compact_diff:
logging.warning(
"Both --diff and --compact-diff given. Returning compact diff..."
)
try:
include_regex = construct_regex(include)
except re.error:
raise InvalidRegularExpression(
f"Invalid regular expression for --include given: {include!r}"
)
try:
exclude_regex = construct_regex(exclude)
except re.error:
raise InvalidRegularExpression(
f"Invalid regular expression for --exclude given: {exclude!r}"
)
files_to_format: Set[PathLike] = set()
gitignore = get_gitignore(Path())
for path in src:
path = Path(path)
if path.name == "-" or path.is_file():
# if a file was explicitly given, we don't care about its extension
files_to_format.add(path)
elif path.is_dir():
files_to_format.update(
get_snakefiles_in_dir(path, include_regex, exclude_regex, gitignore)
)
else:
logging.warning(f"ignoring invalid path: {path}")
differ = Diff(compact=compact_diff)
files_changed, files_unchanged = 0, 0
files_with_errors = 0
for path in files_to_format:
path_is_stdin = path.name == "-"
if path_is_stdin:
logging.debug("Formatting from stdin")
path = sys.stdin
else:
logging.debug(f"Formatting {path}")
try:
original_content = path.read_text()
except AttributeError:
original_content = path.read()
try:
snakefile = Snakefile(StringIO(original_content))
formatter = Formatter(
snakefile, line_length=line_length, black_config_file=config
)
formatted_content = formatter.get_formatted()
except Exception as error:
if check:
logging.error(f"'{error.__class__.__name__}: {error}' in file {path}")
files_with_errors += 1
continue
else:
raise error
if check:
is_changed = differ.is_changed(original_content, formatted_content)
if is_changed:
logging.debug("Formatted content is different from original")
files_changed += 1
else:
files_unchanged += 1
if diff or compact_diff:
filename = "stdin" if path_is_stdin else str(path)
click.echo(f"{'=' * 5}> Diff for {filename} <{'=' * 5}\n")
difference = differ.compare(original_content, formatted_content)
click.echo(difference)
elif not any([check, diff, compact_diff]):
if path_is_stdin:
sys.stdout.write(formatted_content)
else:
write_file_back = differ.is_changed(original_content, formatted_content)
if write_file_back:
logging.info(f"Writing formatted content to {path}")
with path.open("w") as out_handle:
out_handle.write(formatted_content)
if check:
if files_unchanged == len(files_to_format):
logging.info(
f"All {len(files_to_format)} file(s) would be left unchanged 🎉"
)
ctx.exit(ExitCode.NO_CHANGE.value)
elif files_with_errors > 0:
exit_value = ExitCode.ERROR.value
elif files_changed > 0:
exit_value = ExitCode.WOULD_CHANGE.value
if files_with_errors > 0:
logging.info(f"{files_with_errors} file(s) raised parsing errors 🤕")
if files_changed > 0:
logging.info(f"{files_changed} file(s) would be changed 😬")
if files_unchanged > 0:
logging.info(f"{files_unchanged} file(s) would be left unchanged 🎉")
ctx.exit(exit_value)
logging.info("All done 🎉")
def setup_formatter(snake: str, line_length: int = None, black_config_file=None):
stream = StringIO(snake)
smk = Snakefile(stream)
return Formatter(smk, line_length=line_length, black_config_file=black_config_file)