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hash = "sha256:0210b2668f24c078307260bf88bdac9d6f1093635df5123789bfee4d8d7fc8e7"}, ] [[package]] @@ -1566,4 +1566,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8.1" -content-hash = "16e63c29e4b70cb2dd143525a98b52d7e479501c67c51b98fd801a591d9550a4" +content-hash = "ac1fe1e90680e0958321b8f8a91f2353585538d87d438df4b13144460105683c" diff --git a/pyproject.toml b/pyproject.toml index c1fe2c9..33140cc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ snakefmt = 'snakefmt.snakefmt:main' [tool.poetry.dependencies] python = "^3.8.1" click = "^8.0.0" -black = "^23.12.1" +black = "^24.1.1" toml = "^0.10.2" importlib_metadata = {version = ">=1.7.0,<5.0", python = "<3.8"} diff --git a/snakefmt/__init__.py b/snakefmt/__init__.py index bee1610..5781736 100644 --- a/snakefmt/__init__.py +++ b/snakefmt/__init__.py @@ -6,6 +6,8 @@ (in dist-info or egg-info dirs). From Python 3.8, importlib_metadata is in standard library as importlib.metadata. """ +from black import TargetVersion + if sys.version_info >= (3, 8): from importlib import metadata else: @@ -14,3 +16,10 @@ __version__ = metadata.version("snakefmt") DEFAULT_LINE_LENGTH = 88 +DEFAULT_TARGET_VERSIONS = { + TargetVersion.PY38, + TargetVersion.PY39, + TargetVersion.PY310, + TargetVersion.PY311, + TargetVersion.PY312, +} diff --git a/snakefmt/config.py b/snakefmt/config.py index 72bf2bf..7de751e 100644 --- a/snakefmt/config.py +++ b/snakefmt/config.py @@ -10,7 +10,7 @@ import toml from black import Mode, find_project_root -from snakefmt import DEFAULT_LINE_LENGTH +from snakefmt import DEFAULT_LINE_LENGTH, DEFAULT_TARGET_VERSIONS from snakefmt.exceptions import MalformattedToml PathLike = Union[Path, str] @@ -57,7 +57,9 @@ def inject_snakefmt_config( def read_black_config(path: Optional[PathLike]) -> Mode: """Parse Black configuration from provided toml.""" - black_mode = Mode(line_length=DEFAULT_LINE_LENGTH) + black_mode = Mode( + line_length=DEFAULT_LINE_LENGTH, target_versions=DEFAULT_TARGET_VERSIONS + ) if path is None: return black_mode if not Path(path).is_file(): diff --git a/snakefmt/formatter.py b/snakefmt/formatter.py index 275459e..7f4ecf7 100644 --- a/snakefmt/formatter.py +++ b/snakefmt/formatter.py @@ -26,6 +26,10 @@ full_string_matcher = re.compile( r"^\s*(\w?([\"']{3}.*?[\"']{3})|([\"']{1}.*?[\"']{1}))$", re.DOTALL | re.MULTILINE ) +# this regex matches any docstring; can span multiple lines +docstring_matcher = re.compile( + r"\s*([rR]?[\"']{3}.*?[\"']{3})", re.DOTALL | re.MULTILINE +) contextual_matcher = re.compile( r"(.*)^(if|elif|else|with|for|while)([^:]*)(:.*)", re.S | re.M ) @@ -41,6 +45,17 @@ def is_all_comments(string): ) +def index_of_first_docstring(s: str) -> Optional[int]: + """ + Returns the index (i.e., index of last quote character) of the first docstring in + a string, or None if there are no docstrings. + """ + match = docstring_matcher.search(s) + if match is None: + return None + return match.end(1) - 1 + + class Formatter(Parser): def __init__( self, @@ -296,9 +311,34 @@ def format_param( if param_list: val = f"f({val})" extra_spacing = 3 + + # get the index of the last character of the first docstring, if any + docstring_index = index_of_first_docstring(val) + docstring_line_index = None + if docstring_index is not None: + docstring_line_index = val[:docstring_index].count("\n") + lines = val.splitlines() + if docstring_line_index is not None and docstring_line_index + 1 < len(lines): + docstring_has_extra_newline_after = ( + lines[docstring_line_index + 1].strip() == "" + ) + else: + docstring_has_extra_newline_after = False + val = self.run_black_format_str( val, target_indent, extra_spacing, no_nesting=True ) + + # remove newline added after first docstring (black>=24.1) + if docstring_line_index is not None and not docstring_has_extra_newline_after: + lines = val.splitlines() + if docstring_line_index + 1 < len(lines): + line_after_docstring = lines[docstring_line_index + 1] + if line_after_docstring.strip() == "": + # delete the newline + lines.pop(docstring_line_index + 1) + val = "\n".join(lines) + if param_list: match_equal = re.match(r"f\((.*)\)", val, re.DOTALL) val = match_equal.group(1) diff --git a/snakefmt/parser/parser.py b/snakefmt/parser/parser.py index 295b96c..d9c0d45 100644 --- a/snakefmt/parser/parser.py +++ b/snakefmt/parser/parser.py @@ -10,6 +10,7 @@ Vocabulary, add_token_space, is_newline, + re_add_curly_bracket_if_needed, ) from snakefmt.types import TAB, Token, TokenIterator, col_nb @@ -324,3 +325,4 @@ def get_next_queriable(self, snakefile: TokenIterator) -> Status: if not pythonable and token.type != tokenize.COMMENT: pythonable = True buffer += token.string + buffer += re_add_curly_bracket_if_needed(token) diff --git a/snakefmt/parser/syntax.py b/snakefmt/parser/syntax.py index becda7a..c5e9bd7 100644 --- a/snakefmt/parser/syntax.py +++ b/snakefmt/parser/syntax.py @@ -1,6 +1,7 @@ """ Code in charge of parsing and validating Snakemake syntax """ + import sys import tokenize from abc import ABC, abstractmethod @@ -43,6 +44,20 @@ spacing_triggers[tokenize.OP].add(tokenize.FSTRING_START) +def re_add_curly_bracket_if_needed(token: Token) -> str: + result = "" + if ( + token is not None + and sys.version_info >= (3, 12) + and token.type == tokenize.FSTRING_MIDDLE + ): + if token.string.endswith("}"): + result = "}" + elif token.string.endswith("{"): + result = "{" + return result + + def operator_skip_spacing(prev_token: Token, token: Token) -> bool: if prev_token.type != tokenize.OP and token.type != tokenize.OP: return False @@ -332,15 +347,7 @@ def parse_params(self, snakefile: TokenIterator): prev_token = None while True: cur_param = self.process_token(cur_param, prev_token) - if ( - self.token is not None - and sys.version_info >= (3, 12) - and self.token.type == tokenize.FSTRING_MIDDLE - ): - if self.token.string.endswith("}"): - cur_param.value += "}" - elif self.token.string.endswith("{"): - cur_param.value += "{" + cur_param.value += re_add_curly_bracket_if_needed(self.token) try: prev_token = self.token self.token = next(snakefile) diff --git a/snakefmt/snakefmt.py b/snakefmt/snakefmt.py index ef69439..c3b5eb7 100644 --- a/snakefmt/snakefmt.py +++ b/snakefmt/snakefmt.py @@ -288,7 +288,9 @@ def main( if check: if files_unchanged == len(files_to_format): - logger.info(f"All {len(files_to_format)} file(s) would be left unchanged 🎉") + logger.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 diff --git a/tests/test_config.py b/tests/test_config.py index 913f34d..cc89b45 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -5,7 +5,7 @@ import click import pytest -from snakefmt import DEFAULT_LINE_LENGTH +from snakefmt import DEFAULT_LINE_LENGTH, DEFAULT_TARGET_VERSIONS from snakefmt.config import ( find_pyproject_toml, inject_snakefmt_config, @@ -191,7 +191,9 @@ def test_empty_config_default_line_length_used(self, tmp_path): formatter = setup_formatter("") path = tmp_path / "config.toml" path.touch() - expected = black.FileMode(line_length=DEFAULT_LINE_LENGTH) + expected = black.FileMode( + line_length=DEFAULT_LINE_LENGTH, target_versions=DEFAULT_TARGET_VERSIONS + ) assert formatter.black_mode == expected def test_read_black_config_settings(self, tmp_path): @@ -200,7 +202,9 @@ def test_read_black_config_settings(self, tmp_path): path.write_text(f"[tool.black]\nline_length = {black_line_length}") actual = read_black_config(path) - expected = black.FileMode(line_length=black_line_length) + expected = black.FileMode( + line_length=black_line_length, target_versions=DEFAULT_TARGET_VERSIONS + ) assert actual == expected @@ -213,14 +217,18 @@ def test_snakefmt_line_length_overrides_black(self, tmp_path): # show black gets parsed formatter = setup_formatter("", black_config_file=str(path)) - expected = black.FileMode(line_length=black_line_length) + expected = black.FileMode( + line_length=black_line_length, target_versions=DEFAULT_TARGET_VERSIONS + ) assert formatter.black_mode == expected # Now, add overriding snakefmt line length formatter = setup_formatter( "", line_length=snakefmt_line_length, black_config_file=str(path) ) - expected = black.FileMode(line_length=snakefmt_line_length) + expected = black.FileMode( + line_length=snakefmt_line_length, target_versions=DEFAULT_TARGET_VERSIONS + ) assert formatter.black_mode == expected def test_unrecognised_black_options_in_config_ignored_and_default_line_length_used( @@ -232,7 +240,9 @@ def test_unrecognised_black_options_in_config_ignored_and_default_line_length_us read_black_config(path) actual = formatter.black_mode - expected = black.FileMode(line_length=DEFAULT_LINE_LENGTH) + expected = black.FileMode( + line_length=DEFAULT_LINE_LENGTH, target_versions=DEFAULT_TARGET_VERSIONS + ) assert actual == expected @@ -253,7 +263,9 @@ def test_skip_string_normalisation_handled_with_snakecase(self, tmp_path): read_black_config(path) actual = formatter.black_mode expected = black.FileMode( - line_length=DEFAULT_LINE_LENGTH, string_normalization=True + line_length=DEFAULT_LINE_LENGTH, + string_normalization=True, + target_versions=DEFAULT_TARGET_VERSIONS, ) assert actual == expected @@ -266,7 +278,9 @@ def test_skip_string_normalisation_handled_with_kebabcase(self, tmp_path): read_black_config(path) actual = formatter.black_mode expected = black.FileMode( - line_length=DEFAULT_LINE_LENGTH, string_normalization=True + line_length=DEFAULT_LINE_LENGTH, + string_normalization=True, + target_versions=DEFAULT_TARGET_VERSIONS, ) assert actual == expected @@ -279,5 +293,9 @@ def test_string_normalisation_handled(self, tmp_path): "", line_length=line_length, black_config_file=str(path) ) - expected = black.FileMode(line_length=line_length, string_normalization=False) + expected = black.FileMode( + line_length=line_length, + string_normalization=False, + target_versions=DEFAULT_TARGET_VERSIONS, + ) assert formatter.black_mode == expected diff --git a/tests/test_formatter.py b/tests/test_formatter.py index 67a51f6..2ddc05f 100644 --- a/tests/test_formatter.py +++ b/tests/test_formatter.py @@ -3,6 +3,7 @@ The tests implicitly assume that the input syntax is correct ie that no parsing-related errors arise, as tested in test_parser.py. """ + from io import StringIO from unittest import mock @@ -787,7 +788,6 @@ def test_single_quoted_multiline_string_proper_tabbing(self): assert formatter.get_formatted() == expected def test_docstrings_get_retabbed_for_snakecode_only(self): - """Black only retabs the first tpq in a docstring.""" snakecode = '''def f(): """Does not do much @@ -804,7 +804,8 @@ def test_docstrings_get_retabbed_for_snakecode_only(self): formatter = setup_formatter(snakecode) expected = f'''def f(): {TAB * 1}"""Does not do - much""" +{TAB * 1}much +{TAB * 1}""" {TAB * 1}pass @@ -858,6 +859,19 @@ def test_f_string_with_double_braces_in_input(self): formatter = setup_formatter(snakecode) assert formatter.get_formatted() == snakecode + def test_f_string_with_double_braces_in_python_code(self): + """https://github.com/snakemake/snakefmt/issues/215""" + """def get_test_regions(wildcards): + benchmark = config["variant-calls"][wildcards.callset]["benchmark"] + return f"resources/regions/{benchmark}/test-regions.cov-{{cov}}.bed""" + snakecode = ( + "def get_test_regions(wildcards):\n" + f'{TAB * 1}benchmark = config["variant-calls"][wildcards.callset]["benchmark"]\n' # noqa: E501 + f'{TAB * 1}return f"resources/regions/{{benchmark}}/test-regions.cov-{{{{cov}}}}.bed"\n' # noqa: E501 + ) + formatter = setup_formatter(snakecode) + assert formatter.get_formatted() == snakecode + class TestReformatting_SMK_BREAK: """ @@ -1382,7 +1396,7 @@ def test_wrap_line_in_run_directive(self): def test_shell_indention_long_line(self): """https://github.com/snakemake/snakefmt/issues/186 - test this rule + # test this rule: rule test1: input: "...", @@ -1393,9 +1407,11 @@ def test_shell_indention_long_line(self): "param1", [ "item1", - f"very_long_item2_{very_long_function(other_param)}" - if some_very_long_condition - else "", + ( + f"very_long_item2_{{very_long_function(other_param)}}" + if some_very_long_condition + else "", + ) ], ) @@ -1411,11 +1427,14 @@ def test_shell_indention_long_line(self): f'{TAB * 3}"param1",\n' f"{TAB * 3}[\n" f'{TAB * 4}"item1",\n' - f'{TAB * 4}f"very_long_item2_{{very_long_function(other_param)}}"\n' - f"{TAB * 4}if some_very_long_condition\n" - f'{TAB * 4}else "",\n' + f"{TAB * 4}(\n" + f'{TAB * 5}f"very_long_item2_{{very_long_function(other_param)}}"\n' + f"{TAB * 5}if some_very_long_condition\n" + f'{TAB * 5}else ""\n' + f"{TAB * 4}),\n" f"{TAB * 3}],\n" f"{TAB * 2})\n" ) formatter = setup_formatter(snakecode) + assert formatter.get_formatted() == snakecode diff --git a/tests/test_grammar.py b/tests/test_grammar.py index 3db7dd0..ecc99f6 100644 --- a/tests/test_grammar.py +++ b/tests/test_grammar.py @@ -2,6 +2,7 @@ Completeness tests: checks that the grammar used is a bijection of the snakemake grammar To use the latest snakemake grammar, run `poetry update snakemake` from this repo """ + from snakemake import parser from snakefmt.parser import grammar diff --git a/tests/test_parser.py b/tests/test_parser.py index 486bf25..18d3437 100644 --- a/tests/test_parser.py +++ b/tests/test_parser.py @@ -2,6 +2,7 @@ Examples where we raise errors but snakemake does not are listed as 'SMK_NOBREAK' """ + from io import StringIO import pytest