[pre-commit.ci] pre-commit autoupdate (#246)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.11.13 → v0.12.0](astral-sh/ruff-pre-commit@v0.11.13...v0.12.0)

* bump to 3.10

* run fixes

* fix more

* fix workflows

* add python 3.14

* remove 3.14

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@dandelion.science>

Author: pre-commit-ci[bot]

.github/workflows/doc.yaml

@@ -12,39 +12,28 @@ jobs:
   build:
     timeout-minutes: 30
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
         with:
           path: ./main
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-          architecture: 'x64'
+          python-version: 3.13
       - name: Install linux dependencies
         run: |
           sudo apt update
           sudo apt install optipng
-      - name: Setup headless display
-        uses: pyvista/setup-headless-display-action@main
+      - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off main/.[doc]
-      - name: Display system information
-        run: mne_icalabel-sys_info --developer
-      - name: Build doc
-        run: sphinx-build ./main/doc ./doc-build/dev -W --keep-going
-      - name: Prune sphinx environment
-        run: sudo rm -R ./doc-build/dev/.doctrees
-      - name: Upload documentation
-        uses: actions/upload-artifact@v4
+      - run: mne_icalabel-sys_info --developer
+      - run: sphinx-build ./main/doc ./doc-build/dev -W --keep-going
+      - run: sudo rm -R ./doc-build/dev/.doctrees
+      - uses: actions/upload-artifact@v4
         with:
           name: doc-dev
           path: ./doc-build/dev
@@ -56,19 +45,13 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       contents: write
-    defaults:
-      run:
-        shell: bash
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Download documentation
-        uses: actions/download-artifact@v4
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
         with:
           name: doc-dev
           path: ./doc-dev
-      - name: Deploy
-        uses: JamesIves/github-pages-deploy-action@v4
+      - uses: JamesIves/github-pages-deploy-action@v4
         with:
           folder: ./doc-dev
           target-folder: ./dev

.github/workflows/draft-pdf.yml

@@ -9,19 +9,12 @@ jobs:
     runs-on: ubuntu-latest
     name: Paper Draft
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Build draft PDF
-        uses: openjournals/openjournals-draft-action@master
+      - uses: actions/checkout@v4
+      - uses: openjournals/openjournals-draft-action@master
         with:
           journal: joss
-          # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
-      - name: Upload
-        uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v4
         with:
           name: paper
-          # This is the output path where Pandoc will write the compiled
-          # PDF. Note, this should be the same directory as the input
-          # paper.md
           path: paper/paper.pdf

.github/workflows/publish.yaml

@@ -9,25 +9,19 @@ jobs:
     timeout-minutes: 10
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
-          architecture: 'x64'
-      - name: Setup headless display
-        uses: pyvista/setup-headless-display-action@main
+          python-version: '3.13'
+      - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
       - name: Install dependencies
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off -e .[build,stubs]
-      - name: Display system information
-        run: mne_icalabel-sys_info --developer
-      - name: Generate stub files
-        run: python tools/stubgen.py
+      - run: mne_icalabel-sys_info --developer
+      - run: python tools/stubgen.py
       - name: Build and publish
         env:
           TWINE_USERNAME: __token__

.github/workflows/pytest.yaml

@@ -17,33 +17,27 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu, macos, windows]
-        python-version: [3.9, "3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     name: ${{ matrix.os }} - py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}-latest
     defaults:
       run:
         shell: bash
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Setup headless display
-        uses: pyvista/setup-headless-display-action@main
+      - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off .[test]
-      - name: Display system information
-        run: mne_icalabel-sys_info --developer
-      - name: Run pytest
-        run: pytest mne_icalabel --cov=mne_icalabel --cov-report=xml --cov-config=pyproject.toml
-      - name: Upload to codecov
-        uses: codecov/codecov-action@v5
+      - run: mne_icalabel-sys_info --developer
+      - run: pytest mne_icalabel --cov=mne_icalabel --cov-report=xml --cov-config=pyproject.toml
+      - uses: codecov/codecov-action@v5
         with:
           files: ./coverage.xml
           flags: unittests  # optional
@@ -59,18 +53,12 @@ jobs:
         python-version: ["3.11"]
     name: pip pre-release - py${{ matrix.python-version }}
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Setup Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Setup headless display
-        uses: pyvista/setup-headless-display-action@main
+      - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
       - name: Install dependencies
@@ -80,12 +68,9 @@ jobs:
           python -m pip install --progress-bar off --upgrade git+https://github.com/mne-tools/mne-python
           python -m pip install --progress-bar off --upgrade git+https://github.com/mne-tools/mne-bids
           python -m pip install --progress-bar off --upgrade --pre --only-binary :all: -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple --timeout=180 numpy scipy matplotlib
-      - name: Display system information
-        run: mne_icalabel-sys_info --developer
-      - name: Run pytest
-        run: pytest mne_icalabel --cov=mne_icalabel --cov-report=xml --cov-config=pyproject.toml
-      - name: Upload to codecov
-        uses: codecov/codecov-action@v5
+      - run: mne_icalabel-sys_info --developer
+      - run: pytest mne_icalabel --cov=mne_icalabel --cov-report=xml --cov-config=pyproject.toml
+      - uses: codecov/codecov-action@v5
         with:
           files: ./coverage.xml
           flags: unittests  # optional

.github/workflows/stubs.yaml

@@ -12,29 +12,20 @@ jobs:
   generate:
     timeout-minutes: 10
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
     steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
-          architecture: 'x64'
-      - name: Setup headless display
-        uses: pyvista/setup-headless-display-action@main
+          python-version: 3.13
+      - uses: pyvista/setup-headless-display-action@main
         with:
           qt: true
       - name: Install package
         run: |
           python -m pip install --progress-bar off --upgrade pip setuptools
           python -m pip install --progress-bar off -e .[stubs]
-      - name: Display system information
-        run: mne_icalabel-sys_info --developer
-      - name: Generate stub files
-        run: python tools/stubgen.py
+      - run: mne_icalabel-sys_info --developer
+      - run: python tools/stubgen.py
       - name: Push stub files
         if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
         env:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.11.13
+      rev: v0.12.0
       hooks:
           - id: ruff
             name: ruff linter

doc/conf.py

@@ -9,7 +9,6 @@
 import sys
 from datetime import date
 from importlib import import_module
-from typing import Optional
 
 import mne
 from sphinx_gallery.sorting import FileNameSortKey
@@ -260,7 +259,7 @@
 # https://www.sphinx-doc.org/en/master/usage/extensions/linkcode.html
 
 
-def linkcode_resolve(domain: str, info: dict[str, str]) -> Optional[str]:
+def linkcode_resolve(domain: str, info: dict[str, str]) -> str | None:
     """Determine the URL corresponding to a Python object.
 
     Parameters

mne_icalabel/annotation/bids.py

@@ -10,12 +10,11 @@
 
 if TYPE_CHECKING:
     from pathlib import Path
-    from typing import Union
 
     from mne.preprocessing import ICA
 
 
-def write_components_tsv(ica: ICA, fname: Union[str, Path]):
+def write_components_tsv(ica: ICA, fname: str | Path):
     """Write channels tsv file for ICA components.
 
     Will create an accompanying JSON sidecar to explain the
@@ -102,7 +101,7 @@ def write_components_tsv(ica: ICA, fname: Union[str, Path]):
 
 def mark_component(
     component: int,
-    fname: Union[str, Path],
+    fname: str | Path,
     method: str,
     label: str,
     author: str,

mne_icalabel/config.py

@@ -5,9 +5,9 @@
 from .iclabel import iclabel_label_components
 
 if TYPE_CHECKING:
-    from typing import Callable, Optional
+    from collections.abc import Callable
 
-ICALABEL_METHODS: dict[str, Optional[Callable]] = {
+ICALABEL_METHODS: dict[str, Callable | None] = {
     "iclabel": iclabel_label_components,
     "manual": None,
 }

mne_icalabel/config.pyi

@@ -1,4 +1,4 @@
-from typing import Callable
+from collections.abc import Callable
 
 from .iclabel import iclabel_label_components as iclabel_label_components