[MAINT] switch to ruff

Author: Remi-Gau

.flake8

@@ -5,15 +5,25 @@ repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
-    -   id: end-of-file-fixer
-    -   id: check-added-large-files
+    -   id: check-ast
     -   id: check-case-conflict
     -   id: check-json
     -   id: check-merge-conflict
+    -   id: check-toml
     -   id: check-yaml
-    -   id: debug-statements
+    -   id: end-of-file-fixer
+    -   id: mixed-line-ending
+        args: [--fix=lf]
     -   id: trailing-whitespace
 
+    # Checks for .rst files
+-   repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+    -   id: rst-backticks
+    -   id: rst-directive-colons
+    -   id: rst-inline-touching-normal
+
 -   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
     rev: 0.2.3
     hooks:
@@ -36,12 +46,8 @@ repos:
     rev: v2.10
     hooks:
     -   id: import-linter
-
--   repo: https://github.com/pycqa/isort
-    rev: 8.0.1
-    hooks:
-    -   id: isort
-        args: [--settings-path, pyproject.toml]
+        args: [--verbose]
+        language: python
 
 -   repo: https://github.com/adamchainz/blacken-docs
     rev: 1.20.0
@@ -56,6 +62,16 @@ repos:
     -   id: black
         args: [--config=pyproject.toml]
 
+    # Lint and format Python code
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.1
+    hooks:
+    -   id: ruff-check
+        # args: [--statistics]
+        args: [--fix, --show-fixes, --unsafe-fixes]
+    -   id: ruff-format
+        # args: [--diff]
+
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.19.1
     hooks:
@@ -71,13 +87,7 @@ repos:
         args: [--toml=pyproject.toml]
         additional_dependencies: [tomli]
 
--   repo: https://github.com/pycqa/flake8
-    rev: 7.3.0
-    hooks:
-    -   id: flake8
-        exclude: tests_.*.py|version.*.py|setup.py # ignore tests and versioneer related code
-        args: [--config, .flake8, --verbose]
-        additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions, flake8-bugbear]
-
 ci:
     autoupdate_commit_msg: 'chore: update pre-commit hooks'
+    autofix_commit_msg: 'style: pre-commit fixes'
+    autoupdate_schedule: monthly

.pre-commit-config.yaml

@@ -10,7 +10,7 @@
 def _base_parser(formatter_class: type[HelpFormatter] = HelpFormatter) -> ArgumentParser:
     parser = ArgumentParser(
         description=(
-            "BIDS app using deepMReye to decode " "eye motion for fMRI time series data."
+            "BIDS app using deepMReye to decode eye motion for fMRI time series data."
         ),
         epilog="""
         For a more readable version of this help section,

bidsmreye/_parsers.py

@@ -36,11 +36,8 @@ def check_layout(cfg: Config, layout: BIDSLayout, for_file: str = "bold") -> Non
     :raises RuntimeError: _description_
     """
     desc = layout.get_dataset_description()
-    if (
-        "DatasetType" not in desc
-        and "PipelineDescription" not in desc
-        or "DatasetType" in desc
-        and desc["DatasetType"] != "derivative"
+    if ("DatasetType" not in desc and "PipelineDescription" not in desc) or (
+        "DatasetType" in desc and desc["DatasetType"] != "derivative"
     ):
         raise RuntimeError(
             "DatasetType must be 'derivative' in dataset_description.json\n."

bidsmreye/bids_utils.py

@@ -74,7 +74,7 @@ def __attrs_post_init__(self) -> None:
             self.bids_filter = get_bids_filter_config()
 
         self.output_dir = self.output_dir / "bidsmreye"
-        if not self.output_dir:
+        if not self.output_dir.exists():
             self.output_dir.mkdir(parents=True, exist_ok=True)
 
         database_path = self.input_dir / "pybids_db"
@@ -136,7 +136,7 @@ def check_argument(self, attribute: str, layout_in: BIDSLayout) -> Config:
         self.listify(attribute)
 
         # convert all run values to integers
-        if attribute in {"run"}:
+        if attribute == "run":
             for i, j in enumerate(value):
                 value[i] = int(j)
             tmp = [int(j) for j in getattr(self, attribute)]
@@ -155,7 +155,7 @@ def check_argument(self, attribute: str, layout_in: BIDSLayout) -> Config:
         # run and space can be empty if their entity are not used
         # we will figure out the values for run
         # in subject / task wise manner later on
-        if attribute not in ["run"]:
+        if attribute != "run":
             setattr(self, attribute, value)
 
         if attribute not in ["run", "space"] and not getattr(self, attribute):
@@ -236,7 +236,7 @@ def get_config(config_file: Path | None = None, default: str = "") -> dict[str,
         my_path = Path(__file__).absolute().parent / "config"
         config_file = my_path / default
 
-    if config_file is None or not Path(config_file).exists():
+    if not Path(config_file).exists():
         raise FileNotFoundError(f"Config file {config_file} not found")
 
     with open(config_file) as ff:

bidsmreye/configuration.py

@@ -29,7 +29,7 @@ def methods(
     :rtype: Path
     """
     if output_dir is None:
-        output_dir = Path(".")
+        output_dir = Path()
     if isinstance(output_dir, str):
         output_dir = Path(output_dir)
     output_dir = output_dir / "logs"

bidsmreye/methods.py

@@ -325,7 +325,7 @@ def compute_robust_outliers(
             indices.pop(i)
 
             tmp = time_series[indices]
-            tmp.dropna(inplace=True)
+            tmp = tmp.dropna()
 
             # median of all pair-wise distances
             distance.append(np.median(abs(this_timepoint - tmp)))

bidsmreye/quality_control.py

@@ -66,7 +66,6 @@ def generate_report(output_dir: Path, subject_label: str, action: str) -> None:
 
 
 if __name__ == "__main__":
-
     cwd = Path("/home/remi/github/cpp-lln-lab/bidsMReye")
 
     output_dir = cwd / "outputs" / "moae_fmriprep" / "derivatives" / "bidsmreye"

bidsmreye/report.py

@@ -17,14 +17,14 @@
 from bidsmreye.utils import check_if_file_found, set_this_filter
 
 LINE_WIDTH = 3
-FONT_SIZE = dict(size=14)
+FONT_SIZE = {"size": 14}
 GRID_COLOR = "grey"
 LINE_COLOR = "rgb(0, 150, 175)"
 BG_COLOR = "rgb(255,255,255)"
 HEAT_MAP_COLOR = "gnbu"
 MARKER_SIZE = 10
 
-TICK_FONT = dict(family="arial", color="black", size=14)
+TICK_FONT = {"family": "arial", "color": "black", "size": 14}
 
 X_POSITION_1 = 1
 X_POSITION_2 = 1.5
@@ -113,7 +113,7 @@ def plot_group_boxplot(
             go.Box(
                 x=np.ones(nb_data_points) * X_POSITION[i],
                 y=qc_data[this_column],
-                marker=dict(size=MARKER_SIZE, color=COLORS[i]),
+                marker={"size": MARKER_SIZE, "color": COLORS[i]},
                 name=trace_names[i],
             ),
             row=row,
@@ -128,7 +128,7 @@ def plot_group_boxplot(
     fig.update_yaxes(
         row=row,
         col=col,
-        title=dict(text=yaxes_title, font=FONT_SIZE),
+        title={"text": yaxes_title, "font": FONT_SIZE},
     )
 
 
@@ -186,7 +186,7 @@ def group_report(cfg: Config) -> None:
     )
 
     fig.update_yaxes(
-        title=dict(standoff=0, font=FONT_SIZE),
+        title={"standoff": 0, "font": FONT_SIZE},
         showline=True,
         linewidth=LINE_WIDTH - 1,
         linecolor="black",
@@ -215,9 +215,9 @@ def group_report(cfg: Config) -> None:
         boxmean=True,
         width=0.2,
         hovertext=qc_data["filename"],
-        marker=dict(size=MARKER_SIZE),
+        marker={"size": MARKER_SIZE},
         fillcolor="rgb(200, 200, 200)",
-        line=dict(color="black"),
+        line={"color": "black"},
     )
 
     fig.update_layout(
@@ -226,17 +226,17 @@ def group_report(cfg: Config) -> None:
         paper_bgcolor=BG_COLOR,
         height=800,
         width=800,
-        title=dict(
-            text=f"""<b>bidsmreye: group report</b><br>
+        title={
+            "text": f"""<b>bidsmreye: group report</b><br>
     <b>Summary</b><br>
     - Date and time: {datetime.now():%Y-%m-%d, %H:%M}<br>
     - bidsmreye version: {__version__}<br>
             """,
-            x=0.05,
-            y=0.95,
-            font=dict(size=19, color="black"),
-        ),
-        margin=dict(t=150, b=10, l=100, r=10, pad=0),
+            "x": 0.05,
+            "y": 0.95,
+            "font": {"size": 19, "color": "black"},
+        },
+        margin={"t": 150, "b": 10, "l": 100, "r": 10, "pad": 0},
     )
 
     fig.show()
@@ -288,7 +288,7 @@ def visualize_eye_gaze_data(
     fig.update_xaxes(
         row=3,
         col=1,
-        title=dict(text="Time (s)", standoff=16, font=FONT_SIZE),
+        title={"text": "Time (s)", "standoff": 16, "font": FONT_SIZE},
         tickfont=TICK_FONT,
     )
 
@@ -376,7 +376,7 @@ def plot_time_series(
         griddash="dot",
         gridwidth=0.5,
         ticksuffix="°",
-        title=dict(text=title_text, standoff=0, font=FONT_SIZE),
+        title={"text": title_text, "standoff": 0, "font": FONT_SIZE},
         tickfont=FONT_SIZE,
     )
 
@@ -428,7 +428,7 @@ def plot_heat_map(fig: Any, eye_gaze_data: pd.DataFrame) -> None:
             x=X,
             y=Y,
             opacity=0.4,
-            line=dict(color="black", width=1, dash="dash"),
+            line={"color": "black", "width": 1, "dash": "dash"},
         ),
         row=1,
         col=3,
@@ -448,15 +448,15 @@ def plot_heat_map(fig: Any, eye_gaze_data: pd.DataFrame) -> None:
         col=3,
         range=value_range(X),
         ticksuffix="°",
-        title=dict(text="X", standoff=16, font=FONT_SIZE),
+        title={"text": "X", "standoff": 16, "font": FONT_SIZE},
         tickfont=TICK_FONT,
     )
     fig.update_yaxes(
         row=1,
         col=3,
         range=value_range(Y),
         ticksuffix="°",
-        title=dict(text="Y", standoff=16, font=FONT_SIZE),
+        title={"text": "Y", "standoff": 16, "font": FONT_SIZE},
         tickfont=TICK_FONT,
     )