[MAINT] use ruff (#109)

* use ruff * fix SIM * fix PATH error flagged by ruff * fix E * fix B008 * fix B028 * fix PLR * fix pandas error * Apply suggestions from code review
bids-standard · Nov 10, 2024 · d207212 · d207212
1 parent a988673
commit d207212
Show file tree

Hide file tree

Showing 11 changed files with 123 additions and 106 deletions.
diff --git a/.flake8 b/.flake8
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,24 +15,6 @@ repos:
     -   id: trailing-whitespace
     -   id: check-toml
 
--   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
-    hooks:
-    -   id: isort
-        args: [--profile, black]
-
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.0
-    hooks:
-    -   id: pyupgrade
-        args: [--py39-plus]
-
--   repo: https://github.com/psf/black
-    rev: 24.10.0
-    hooks:
-    -   id: black
-        args: [--config, pyproject.toml]
-
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
@@ -59,9 +41,12 @@ repos:
         additional_dependencies: [types-requests, types-PyYAML, numpy]
         args: [--config-file=pyproject.toml]
 
--   repo: https://github.com/pyCQA/flake8
-    rev: 7.1.1
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.2
     hooks:
-    -   id: flake8
-        args: [--config, .flake8, --verbose]
-        additional_dependencies: [flake8-docstrings, flake8-use-fstring]
+    # Run the linter.
+    -   id: ruff
+        # args: [--statistics]
+        args: [--fix, --show-fixes]
+    # Run the formatter.
+    -   id: ruff-format
diff --git a/eye2bids/_base.py b/eye2bids/_base.py
@@ -18,7 +18,6 @@ class BasePhysioEventsJson(dict[str, Any]):
     two_eyes: bool
 
     def __init__(self, metadata: None | dict[str, Any] = None) -> None:
-
         self["Columns"] = ["onset", "duration", "trial_type", "blink", "message"]
         self["Description"] = "Messages logged by the measurement device"
         self["ForeignIndexColumn"] = "timestamp"
@@ -69,9 +68,10 @@ def write(
     ) -> None:
         """Write to json."""
         content = {key: value for key, value in self.items() if self[key] is not None}
-        with open(output_dir / self.output_filename(recording=recording), "w") as outfile:
+        with (output_dir / self.output_filename(recording=recording)).open(
+            "w"
+        ) as outfile:
             json.dump(content, outfile, indent=4)
-        # e2b_log.info(f"file generated: {self.output_filename(recording=recording)}")
 
 
 class BaseEventsJson(dict[str, Any]):
@@ -112,7 +112,7 @@ def write(
                 self[key] = value
 
         content = {key: value for key, value in self.items() if self[key] is not None}
-        with open(output_dir / self.output_filename(), "w") as outfile:
+        with (output_dir / self.output_filename()).open("w") as outfile:
             json.dump(content, outfile, indent=4)
 
 
@@ -125,7 +125,6 @@ class BasePhysioJson(dict[str, Any]):
     has_calibration: bool
 
     def __init__(self, manufacturer: str, metadata: dict[str, Any] | None = None) -> None:
-
         self["Manufacturer"] = manufacturer
         self["PhysioType"] = "eyetrack"
 
@@ -199,5 +198,7 @@ def write(
                 self[key] = value
 
         content = {key: value for key, value in self.items() if self[key] is not None}
-        with open(output_dir / self.output_filename(recording=recording), "w") as outfile:
+        with (output_dir / self.output_filename(recording=recording)).open(
+            "w"
+        ) as outfile:
             json.dump(content, outfile, indent=4)
diff --git a/eye2bids/_cli.py b/eye2bids/_cli.py
@@ -15,14 +15,8 @@ def set_verbosity(verbosity: int | list[int]) -> None:
     """Set verbosity level."""
     if isinstance(verbosity, list):
         verbosity = verbosity[0]
-    if verbosity == 0:
-        e2b_log.setLevel("ERROR")
-    elif verbosity == 1:
-        e2b_log.setLevel("WARNING")
-    elif verbosity == 2:
-        e2b_log.setLevel("INFO")
-    elif verbosity == 3:
-        e2b_log.setLevel("DEBUG")
+    verbosity_map = {0: "ERROR", 1: "WARNING", 2: "INFO", 3: "DEBUG"}
+    e2b_log.setLevel(verbosity_map[verbosity])
 
 
 def cli(argv: Sequence[str] = sys.argv) -> None:

diff --git a/eye2bids/edf2bids.py b/eye2bids/edf2bids.py
@@ -160,7 +160,6 @@ def _extract_CalibrationCount(df: pd.DataFrame, two_eyes: bool) -> int:
 
 
 def _extract_CalibrationPosition(df: pd.DataFrame) -> list[list[list[int]]]:
-
     calibration_df = df[df[2] == "VALIDATE"]
     calibration_df[5] = pd.to_numeric(calibration_df[5], errors="coerce")
 
@@ -175,7 +174,6 @@ def _extract_CalibrationPosition(df: pd.DataFrame) -> list[list[list[int]]]:
     CalibrationPosition: Any = [[[]] * nb_calibration_postions]
 
     for i_pos in range(nb_calibration_postions):
-
         results_for_this_position = calibration_df[calibration_df[5] == i_pos]
 
         for i, calibration in enumerate(results_for_this_position.iterrows()):
@@ -256,12 +254,13 @@ def _extract_SamplingFrequency(df: pd.DataFrame) -> int:
 
 def _extract_RecordedEye(df: pd.DataFrame) -> str | list[str]:
     eye = df[df[2] == "RECCFG"].iloc[0:1, 5:6].to_string(header=False, index=False)
-    if eye == "L":
-        return "Left"
-    elif eye == "R":
-        return "Right"
-    elif eye == "LR":
-        return ["Left", "Right"]
+    recorded_eye_map: dict[str, str | list[str]] = {
+        "L": "Left",
+        "R": "Right",
+        "LR": ["Left", "Right"],
+    }
+    if eye in recorded_eye_map:
+        return recorded_eye_map[eye]
     return ""
 
 
@@ -313,7 +312,7 @@ def _extract_StopTime(events: list[str]) -> int:
 
 
 def _load_asc_file(events_asc_file: str | Path) -> list[str]:
-    with open(events_asc_file) as f:
+    with Path(events_asc_file).open() as f:
         return f.readlines()
 
 
@@ -425,7 +424,7 @@ def generate_physio_json(
     if metadata_file is None:
         metadata = {}
     else:
-        with open(metadata_file) as f:
+        with Path(metadata_file).open() as f:
             metadata = yaml.load(f, Loader=SafeLoader)
 
     events = _load_asc_file(events_asc_file)
@@ -463,7 +462,6 @@ def generate_physio_json(
         }
 
     if base_json.has_validation:
-
         if CalibrationPosition := _extract_CalibrationPosition(df_ms_reduced):
             base_json["CalibrationCount"] = _extract_CalibrationCount(
                 df_ms_reduced, two_eyes=base_json.two_eyes
@@ -545,7 +543,7 @@ def edf2bids(
     if metadata_file is None:
         metadata = {}
     else:
-        with open(metadata_file) as f:
+        with metadata_file.open() as f:
             metadata = yaml.load(f, Loader=SafeLoader)
 
     events_json = BaseEventsJson(metadata)
@@ -596,7 +594,6 @@ def edf2bids(
     e2b_log.info(f"file generated: {output_filename_eye1}")
 
     if _2eyesmode(df_ms_reduced):
-
         output_filename_eye2 = generate_output_filename(
             output_dir=output_dir,
             input_file=input_file,

diff --git a/eye2bids/logger.py b/eye2bids/logger.py
@@ -6,11 +6,11 @@
 
 from rich.logging import RichHandler
 
+FORMAT = "%(message)s"
+
 
 def eye2bids_logger(log_level: str = "INFO") -> logging.Logger:
     """Create a logger for the eye2bids package."""
-    FORMAT = "%(message)s"
-
     logging.basicConfig(
         level=log_level,
         format=FORMAT,

diff --git a/pyproject.toml b/pyproject.toml
@@ -83,12 +83,6 @@ packages = ["eye2bids"]
 [tool.hatch.version]
 source = "vcs"
 
-[tool.isort]
-combine_as_imports = true
-line_length = 90
-profile = "black"
-skip_gitignore = true
-
 [tool.mypy]
 check_untyped_defs = true
 disallow_any_generics = true
@@ -121,3 +115,66 @@ module = [
 addopts = "-ra --strict-config --strict-markers -q -vv --cov eye2bids --durations=0"
 norecursedirs = "data"
 testpaths = ["tests/"]
+
+[tool.ruff]
+include = ["pyproject.toml", "eye2bids/**/*.py", "tools/**/*.py"]
+indent-width = 4
+line-length = 90
+
+[tool.ruff.format]
+docstring-code-format = true
+docstring-code-line-length = "dynamic"
+indent-style = "space"
+line-ending = "auto"
+quote-style = "double"
+skip-magic-trailing-comma = false
+
+[tool.ruff.lint]
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+fixable = ["ALL"]
+ignore = [
+    "D205",
+    "N802",
+    "N806"
+]
+# List of all the ruff rules (includes why the rule matters)
+# https://docs.astral.sh/ruff/rules/
+select = [
+    "ARG",
+    "B",
+    "C4",
+    "C90",
+    "D",
+    "E",
+    "ERA",
+    "F",
+    "FLY",
+    "I",
+    "N",
+    "NPY",
+    "PERF",
+    "PTH",
+    "PD",
+    "PLR",
+    "RUF",
+    "SIM",
+    "UP",
+    "W"
+]
+unfixable = []
+
+[tool.ruff.lint.mccabe]
+max-complexity = 21
+
+[tool.ruff.lint.per-file-ignores]
+"**/{tests}/*" = ["D100", "D103", "PLR2004"]
+"__init__.py" = ["D100", "D104"]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.lint.pylint]
+# https://docs.astral.sh/ruff/settings/#lint_pylint_max-branches
+max-branches = 17
+# https://docs.astral.sh/ruff/settings/#lint_pylint_max-statements
+max-statements = 71
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -10,20 +10,24 @@ def data_dir() -> Path:
     return Path(__file__).parent / "data"
 
 
-def asc_test_files(input_dir: Path = data_dir(), suffix: str = "*") -> list[Path]:
+def asc_test_files(input_dir: Path | None = None, suffix: str = "*") -> list[Path]:
+    if input_dir is None:
+        input_dir = data_dir()
     files = input_dir.glob(f"**/{suffix}.asc")
     tmp = list(files)
     if not tmp:
-        warn(f"No .asc file found in: {input_dir}.")
+        warn(f"No .asc file found in: {input_dir}.", stacklevel=2)
     return tmp
 
 
-def edf_test_files(input_dir: Path = data_dir()) -> list[Path]:
+def edf_test_files(input_dir: Path | None = None) -> list[Path]:
+    if input_dir is None:
+        input_dir = data_dir()
     files = list(input_dir.glob("**/*.edf"))
-    EDF_files = list(input_dir.glob("**/*.EDF"))
-    files.extend(EDF_files)
+    edf_files = list(input_dir.glob("**/*.EDF"))
+    files.extend(edf_files)
     if not files:
-        warn(f"No EDF file found in: {input_dir}")
+        warn(f"No EDF file found in: {input_dir}", stacklevel=2)
     return files
 
 

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -19,7 +19,6 @@ def root_dir() -> Path:
 @pytest.mark.parametrize("output_dir", [data_dir() / "output", None])
 @pytest.mark.parametrize("use_relative_path", [False, True])
 def test_edf_cli(use_relative_path, output_dir, eyelink_test_data_dir):
-
     metadata_file = data_dir() / "metadata.yml"
 
     input_dir = eyelink_test_data_dir / "satf"