MAINT: Enable more ruff rules (#838)

.github/workflows/run-tests.yml

@@ -15,6 +15,8 @@ jobs:
     steps:
     - uses: actions/checkout@v3
     - uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
     - run: pip install --upgrade pip
     - run: pip install -ve .[tests] codespell tomli
     - run: make codespell-error

.pre-commit-config.yaml

@@ -9,6 +9,7 @@ repos:
     rev: v0.1.14
     hooks:
       - id: ruff
+        args: ["--fix"]
       - id: ruff-format
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.6

docs/hooks.py

@@ -1,9 +1,9 @@
 import logging
-from typing import Dict, Any
+from typing import Any
 
 from mkdocs.config.defaults import MkDocsConfig
-from mkdocs.structure.pages import Page
 from mkdocs.structure.files import Files
+from mkdocs.structure.pages import Page
 
 logger = logging.getLogger("mkdocs")
 
@@ -13,7 +13,7 @@
 # Ideally there would be a better hook, but it's unclear if context can
 # be obtained any earlier
 def on_template_context(
-    context: Dict[str, Any],
+    context: dict[str, Any],
     template_name: str,
     config: MkDocsConfig,
 ) -> None:

docs/source/examples/gen_examples.py

@@ -1,19 +1,21 @@
 #!/usr/bin/env python
 
-from collections import defaultdict
 import contextlib
 import logging
 import shutil
-from pathlib import Path
 import sys
-from typing import Union, Iterable
+from collections import defaultdict
+from collections.abc import Iterable
+from pathlib import Path
+from typing import Union
+
+from tqdm import tqdm
 
 import mne_bids_pipeline
-from mne_bids_pipeline._config_import import _import_config
 import mne_bids_pipeline.tests.datasets
-from mne_bids_pipeline.tests.test_run import TEST_SUITE
+from mne_bids_pipeline._config_import import _import_config
 from mne_bids_pipeline.tests.datasets import DATASET_OPTIONS
-from tqdm import tqdm
+from mne_bids_pipeline.tests.test_run import TEST_SUITE
 
 this_dir = Path(__file__).parent
 root = Path(mne_bids_pipeline.__file__).parent.resolve(strict=True)

docs/source/features/gen_steps.py

@@ -3,6 +3,7 @@
 
 import importlib
 from pathlib import Path
+
 from mne_bids_pipeline._config_utils import _get_step_modules
 
 pre = """\

docs/source/v1.6.md.inc

@@ -21,5 +21,5 @@
 ### :medical_symbol: Code health
 
 - The package build backend has been switched from `setuptools` to `hatchling`. (#825 by @hoechenberger)
-- Code formatting now uses `ruff format` instead of `black` (#834 by @larsoner)
+- Code formatting now uses `ruff format` instead of `black` (#834, #838 by @larsoner)
 - Code caching is now tested using GitHub Actions (#836 by @larsoner)

mne_bids_pipeline/__init__.py

@@ -1,4 +1,4 @@
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
 
 try:
     __version__ = version("mne_bids_pipeline")

mne_bids_pipeline/_config.py

@@ -1,18 +1,17 @@
 # Default settings for data processing and analysis.
 
-from typing import Optional, Union, Iterable, List, Tuple, Dict, Callable, Literal
+from typing import Callable, Iterable, Literal, Optional, Union
 
 from mne import Covariance
 from mne_bids import BIDSPath
 
 from mne_bids_pipeline.typing import (
-    PathLike,
     ArbitraryContrast,
-    FloatArrayLike,
     DigMontageType,
+    FloatArrayLike,
+    PathLike,
 )
 
-
 ###############################################################################
 # Config parameters
 # -----------------
@@ -84,7 +83,7 @@
     Enabling interactive mode deactivates parallel processing.
 """
 
-sessions: Union[List, Literal["all"]] = "all"
+sessions: Union[list, Literal["all"]] = "all"
 """
 The sessions to process. If `'all'`, will process all sessions found in the
 BIDS dataset.
@@ -101,7 +100,7 @@
 BIDS dataset.
 """
 
-exclude_runs: Optional[Dict[str, List[str]]] = None
+exclude_runs: Optional[dict[str, list[str]]] = None
 """
 Specify runs to exclude from analysis, for each participant individually.
 
@@ -117,7 +116,7 @@
     did not understand the instructions, etc.).
 """
 
-crop_runs: Optional[Tuple[float, float]] = None
+crop_runs: Optional[tuple[float, float]] = None
 """
 Crop the raw data of each run to the specified time interval `[tmin, tmax]`,
 in seconds. The runs will be cropped before Maxwell or frequency filtering is
@@ -288,7 +287,7 @@
     ```
 """
 
-eeg_bipolar_channels: Optional[Dict[str, Tuple[str, str]]] = None
+eeg_bipolar_channels: Optional[dict[str, tuple[str, str]]] = None
 """
 Combine two channels into a bipolar channel, whose signal is the **difference**
 between the two combined channels, and add it to the data.
@@ -688,7 +687,7 @@
 Number of extended SSS (eSSS) basis projectors to use from empty-room data.
 """
 
-mf_esss_reject: Optional[Dict[str, float]] = None
+mf_esss_reject: Optional[dict[str, float]] = None
 """
 Rejection parameters to use when computing the extended SSS (eSSS) basis.
 """
@@ -980,7 +979,7 @@
     ```
 """  # noqa: E501
 
-conditions: Optional[Union[Iterable[str], Dict[str, str]]] = None
+conditions: Optional[Union[Iterable[str], dict[str, str]]] = None
 """
 The time-locked events based on which to create evoked responses.
 This can either be name of the experimental condition as specified in the
@@ -1048,7 +1047,7 @@
 and when the annotations do not contain any stimulation or behavior events.
 """
 
-baseline: Optional[Tuple[Optional[float], Optional[float]]] = (None, 0)
+baseline: Optional[tuple[Optional[float], Optional[float]]] = (None, 0)
 """
 Specifies which time interval to use for baseline correction of epochs;
 if `None`, no baseline correction is applied.
@@ -1059,7 +1058,7 @@
     ```
 """
 
-contrasts: Iterable[Union[Tuple[str, str], ArbitraryContrast]] = []
+contrasts: Iterable[Union[tuple[str, str], ArbitraryContrast]] = []
 """
 The conditions to contrast via a subtraction of ERPs / ERFs. The list elements
 can either be tuples or dictionaries (or a mix of both). Each element in the
@@ -1156,12 +1155,12 @@
 
 # Rejection based on SSP
 # ~~~~~~~~~~~~~~~~~~~~~~
-n_proj_eog: Dict[str, float] = dict(n_mag=1, n_grad=1, n_eeg=1)
+n_proj_eog: dict[str, float] = dict(n_mag=1, n_grad=1, n_eeg=1)
 """
 Number of SSP vectors to create for EOG artifacts for each channel type.
 """
 
-n_proj_ecg: Dict[str, float] = dict(n_mag=1, n_grad=1, n_eeg=1)
+n_proj_ecg: dict[str, float] = dict(n_mag=1, n_grad=1, n_eeg=1)
 """
 Number of SSP vectors to create for ECG artifacts for each channel type.
 """
@@ -1189,7 +1188,7 @@
 `'separate'` otherwise.
 """
 
-ssp_reject_ecg: Optional[Union[Dict[str, float], Literal["autoreject_global"]]] = None
+ssp_reject_ecg: Optional[Union[dict[str, float], Literal["autoreject_global"]]] = None
 """
 Peak-to-peak amplitude limits of the ECG epochs to exclude from SSP fitting.
 This allows you to remove strong transient artifacts, which could negatively
@@ -1207,7 +1206,7 @@
     ```
 """
 
-ssp_reject_eog: Optional[Union[Dict[str, float], Literal["autoreject_global"]]] = None
+ssp_reject_eog: Optional[Union[dict[str, float], Literal["autoreject_global"]]] = None
 """
 Peak-to-peak amplitude limits of the EOG epochs to exclude from SSP fitting.
 This allows you to remove strong transient artifacts, which could negatively
@@ -1233,11 +1232,11 @@
 
 # Rejection based on ICA
 # ~~~~~~~~~~~~~~~~~~~~~~
-ica_reject: Optional[Union[Dict[str, float], Literal["autoreject_local"]]] = None
+ica_reject: Optional[Union[dict[str, float], Literal["autoreject_local"]]] = None
 """
 Peak-to-peak amplitude limits to exclude epochs from ICA fitting. This allows you to
 remove strong transient artifacts from the epochs used for fitting ICA, which could
-negatively affect ICA performance. 
+negatively affect ICA performance.
 
 The parameter values are the same as for [`reject`][mne_bids_pipeline._config.reject],
 but `"autoreject_global"` is not supported. `"autoreject_local"` here behaves
@@ -1264,7 +1263,7 @@
     to **not** specify rejection thresholds for EOG and ECG channels here –
     otherwise, ICA won't be able to "see" these artifacts.
 
-???+ info 
+???+ info
     This setting is applied only to the epochs that are used for **fitting** ICA. The
     goal is to make it easier for ICA to produce a good decomposition. After fitting,
     ICA is applied to the epochs to be analyzed, usually with one or more components
@@ -1280,7 +1279,7 @@
     ica_reject = "autoreject_global"  # find global (per channel type) PTP thresholds before fitting ICA
     ica_reject = "autoreject_local"  # find local (per channel) thresholds and repair epochs before fitting ICA
     ```
-"""
+"""  # noqa: E501
 
 ica_algorithm: Literal[
     "picard", "fastica", "extended_infomax", "picard-extended_infomax"
@@ -1373,7 +1372,7 @@
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 reject: Optional[
-    Union[Dict[str, float], Literal["autoreject_global", "autoreject_local"]]
+    Union[dict[str, float], Literal["autoreject_global", "autoreject_local"]]
 ] = None
 """
 Peak-to-peak amplitude limits to mark epochs as bad. This allows you to remove
@@ -1386,7 +1385,7 @@
 
 If `None` (default), do not apply artifact rejection.
 
-If a dictionary, manually specify rejection thresholds (see examples). 
+If a dictionary, manually specify rejection thresholds (see examples).
 The thresholds provided here must be at least as stringent as those in
 [`ica_reject`][mne_bids_pipeline._config.ica_reject] if using ICA. In case of
 `'autoreject_global'`, thresholds for any channel that do not meet this
@@ -1409,7 +1408,7 @@
     reject = "autoreject_global"  # find global (per channel type) PTP thresholds
     reject = "autoreject_local"  # find local (per channel) thresholds and repair epochs
     ```
-"""
+"""  # noqa: E501
 
 reject_tmin: Optional[float] = None
 """
@@ -1689,7 +1688,7 @@
     ```
 """
 
-decoding_csp_freqs: Optional[Dict[str, FloatArrayLike]] = None
+decoding_csp_freqs: Optional[dict[str, FloatArrayLike]] = None
 """
 The edges of the frequency bins to use for CSP decoding.
 
@@ -1733,7 +1732,7 @@
     }
 """
 
-time_frequency_baseline: Optional[Tuple[float, float]] = None
+time_frequency_baseline: Optional[tuple[float, float]] = None
 """
 Baseline period to use for the time-frequency analysis. If `None`, no baseline.
 ???+ example "Example"
@@ -1964,7 +1963,7 @@ def mri_landmarks_kind(bids_path):
 """
 
 noise_cov: Union[
-    Tuple[Optional[float], Optional[float]],
+    tuple[Optional[float], Optional[float]],
     Literal["emptyroom", "rest", "ad-hoc"],
     Callable[[BIDSPath], Covariance],
 ] = (None, 0)
@@ -2031,7 +2030,7 @@ def noise_cov(bids_path):
     ```
 """
 
-source_info_path_update: Optional[Dict[str, str]] = dict(suffix="ave")
+source_info_path_update: Optional[dict[str, str]] = dict(suffix="ave")
 """
 When computing the forward and inverse solutions, by default the pipeline
 retrieves the `mne.Info` object from the cleaned evoked data. However, in
@@ -2049,7 +2048,7 @@ def noise_cov(bids_path):
     ```
 """
 
-inverse_targets: List[Literal["evoked"]] = ["evoked"]
+inverse_targets: list[Literal["evoked"]] = ["evoked"]
 """
 
 On which data to apply the inverse operator. Currently, the only supported

mne_bids_pipeline/_config_import.py

@@ -1,22 +1,21 @@
 import ast
 import copy
-from dataclasses import field
 import difflib
-from functools import partial
 import importlib
 import os
 import pathlib
+from dataclasses import field
+from functools import partial
 from types import SimpleNamespace
-from typing import Optional, List
+from typing import Optional
 
 import matplotlib
-import numpy as np
 import mne
-
+import numpy as np
 from pydantic import ValidationError
 from pydantic.dataclasses import dataclass
 
-from ._logging import logger, gen_log_kwargs
+from ._logging import gen_log_kwargs, logger
 from .typing import PathLike
 
 
@@ -150,7 +149,7 @@ def _update_with_user_config(
     config_path: Optional[PathLike],
     overrides: Optional[SimpleNamespace],
     log: bool = False,
-) -> List[str]:
+) -> list[str]:
     # 1. Basics and hidden vars
     from . import __version__
 
@@ -433,8 +432,8 @@ def _pydantic_validate(
 def _check_misspellings_removals(
     config: SimpleNamespace,
     *,
-    valid_names: List[str],
-    user_names: List[str],
+    valid_names: list[str],
+    user_names: list[str],
     log: bool,
 ) -> None:
     # for each name in the user names, check if it's in the valid names but

mne_bids_pipeline/_config_template.py

@@ -1,8 +1,6 @@
 from pathlib import Path
-from typing import List
-
-from ._logging import logger, gen_log_kwargs
 
+from ._logging import gen_log_kwargs, logger
 
 CONFIG_SOURCE_PATH = Path(__file__).parent / "_config.py"
 
@@ -17,8 +15,8 @@ def create_template_config(
         raise FileExistsError(f"The specified path already exists: {target_path}")
 
     # Create a template by commenting out most of the lines in _config.py
-    config: List[str] = []
-    with open(CONFIG_SOURCE_PATH, "r", encoding="utf-8") as f:
+    config: list[str] = []
+    with open(CONFIG_SOURCE_PATH, encoding="utf-8") as f:
         for line in f:
             line = (
                 line if line.startswith(("#", "\n", "import", "from")) else f"# {line}"