[pre-commit.ci] pre-commit autoupdate #5417
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name: test_suite | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }} | |
cancel-in-progress: true | |
on: | |
push: | |
branches: ['**'] | |
tags: ['**'] | |
pull_request: | |
branches: ['**'] | |
schedule: | |
- cron: "0 4 * * *" | |
jobs: | |
style: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.12"] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: actions/cache@v4 | |
with: | |
path: ${{ env.pythonLocation }} | |
key: style-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install ruff | |
- name: Display versions and environment information | |
run: | | |
python --version | |
which python | |
- name: Run style & documentation tests | |
run: make pep | |
build: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest] | |
python-version: ["3.10", "3.12"] # Oldest and newest supported versions | |
steps: | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: actions/cache@v4 | |
with: | |
path: ${{ env.pythonLocation }} | |
key: build-1-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install build twine | |
- uses: actions/checkout@v4 | |
- name: Build sdist | |
run: python -m build --sdist | |
- name: Check sdist | |
run: twine check --strict dist/* | |
- name: Install sdist | |
run: python -m pip install ./dist/mne_bids-* | |
- name: Clean up working directory | |
run: rm -rf ./* | |
- name: Try importing mne_bids | |
run: python -c 'import mne_bids; print(mne_bids.__version__)' | |
- name: Try cli mne_bids | |
run: mne_bids --version | |
- name: Remove sdist install | |
run: python -m pip uninstall -y mne-bids | |
- uses: actions/checkout@v4 | |
- name: Build wheel | |
run: python -m build --wheel | |
- name: Check wheel | |
run: twine check --strict dist/* | |
- name: Install wheel | |
run: python -m pip install ./dist/mne_bids-*.whl | |
- name: Clean up working directory | |
run: rm -rf ./* | |
- name: Try importing mne_bids | |
run: python -c 'import mne_bids; print(mne_bids.__version__)' | |
- name: Try cli mne_bids | |
run: mne_bids --version | |
- name: Remove wheel install | |
run: python -m pip uninstall -y mne-bids | |
- uses: actions/checkout@v4 | |
- name: Test extras install | |
run: | | |
python -m pip install .[full] | |
python -c 'import mne_bids; print(mne_bids.__version__)' | |
python -c 'import nibabel; print(nibabel.__version__)' | |
python -c 'import pybv; print(pybv.__version__)' | |
python -c 'import eeglabio; print(eeglabio.__version__)' | |
python -c 'import pymatreader; print(pymatreader.__version__)' | |
python -c 'import matplotlib; print(matplotlib.__version__)' | |
python -c 'import pandas; print(pandas.__version__)' | |
python -c 'import EDFlib; print("EDFlib has no .__version__")' | |
python -c 'import edfio; print(edfio.__version__)' | |
test: | |
# For GitHub "required" CI checks, add in branch protection: | |
# | |
# 8 checks: | |
# for each machine type (ubuntu, macos, macos-13, windows): | |
# (NOTE: macos-13=x86_64, macos>13=arm64) | |
# 3.10 / mne-stable / full / validator-stable | |
# 3.12 / mne-stable / full / validator-stable | |
# | |
# 3 additional checks with alternative MNE-Python and BIDS validator versions: | |
# ubuntu / 3.12 / mne-main / full / validator-main | |
# ubuntu / 3.10 / mne-prev / full / validator-stable | |
# ubuntu / 3.12 / mne-stable / minimal / validator-stable | |
timeout-minutes: 60 | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, macos-latest, macos-13, windows-latest] | |
python-version: ["3.10", "3.12"] # Oldest and newest supported versions | |
mne-version: [mne-stable] | |
mne-bids-install: [full] | |
bids-validator-version: [validator-stable] | |
include: | |
# special test runs running only on single CI systems to save resources | |
# Test development versions | |
- os: ubuntu-latest | |
python-version: "3.12" | |
mne-version: mne-main | |
mne-bids-install: full | |
bids-validator-version: validator-main | |
# Test previous MNE stable version | |
- os: ubuntu-latest | |
python-version: "3.10" | |
mne-version: mne-prev-stable | |
mne-bids-install: full | |
bids-validator-version: validator-stable | |
# Test minimal mne-bids install | |
- os: ubuntu-latest | |
python-version: "3.12" | |
mne-version: mne-stable | |
mne-bids-install: minimal | |
bids-validator-version: validator-stable | |
env: | |
TZ: Europe/Berlin | |
FORCE_COLOR: true | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Node.js | |
uses: actions/setup-node@v4 | |
with: | |
node-version: 20 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Restore cache | |
uses: actions/cache@v4 | |
with: | |
path: ${{ env.pythonLocation }} | |
key: test-0-${{ env.pythonLocation }}-${{ env.os }}-${{ hashFiles('pyproject.toml') }} | |
- name: Install Python dependencies using pip | |
# This would be nicer once this feature is implemented: https://github.com/pypa/pip/issues/11440 | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install -e .[test] | |
- name: Install MNE (stable) | |
if: matrix.mne-version == 'mne-stable' | |
run: | | |
git clone --single-branch --branch maint/1.8 https://github.com/mne-tools/mne-python.git | |
python -m pip install -e ./mne-python | |
- name: Install MNE (previous stable) | |
if: matrix.mne-version == 'mne-prev-stable' | |
# Have to install NumPy<2.1 here because of a change in positional arg handling + MNE 1.7 | |
# XXX: drop when mne < 1.8 is no longer supported | |
run: | | |
git clone --single-branch --branch maint/1.7 https://github.com/mne-tools/mne-python.git | |
python -m pip install -e ./mne-python "numpy<2.1" | |
- name: Install MNE (main) | |
if: matrix.mne-version == 'mne-main' | |
run: | | |
git clone --single-branch --branch main https://github.com/mne-tools/mne-python.git | |
python -m pip install -e ./mne-python | |
- name: Install BIDS validator (stable) | |
if: matrix.bids-validator-version == 'validator-stable' | |
# XXX: Remove pin once this is solved: https://github.com/bids-standard/bids-validator/issues/2124 | |
run: | | |
npm install -g [email protected] | |
- name: Download BIDS validator (main) | |
if: matrix.bids-validator-version == 'validator-main' | |
run: | | |
pushd .. | |
git clone --depth 1 https://github.com/bids-standard/bids-validator | |
popd | |
- name: Install BIDS validator (main) | |
if: matrix.bids-validator-version == 'validator-main' | |
run: | | |
pushd ../bids-validator | |
# Generate the full development node_modules | |
npm install | |
# Build & bundle the bids-validator CLI package | |
npm -w bids-validator run build | |
# Generate a package to install globally | |
npm -w bids-validator pack | |
# Install the package globally | |
npm install -g bids-validator-*.tgz | |
popd | |
- name: Display versions and environment information | |
run: | | |
echo $TZ | |
date | |
echo "npm"; npm --version | |
echo "node"; node --version | |
echo "bids-validator"; bids-validator --version | |
echo "python"; python --version | |
which python | |
mne sys_info | |
- name: Install MNE-BIDS (minimal) | |
if: matrix.mne-bids-install == 'minimal' | |
run: python -m pip install -e . | |
- name: Install MNE-BIDS (full) | |
if: matrix.mne-bids-install == 'full' | |
run: python -m pip install -e .[full] | |
# Only run on a limited set of jobs | |
- name: Run pytest without testing data | |
run: make test | |
if: ${{ matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest' && matrix.mne-version == 'mne-main' }} | |
# Get testing data | |
- run: ./tools/get_testing_version.sh | |
working-directory: mne-python | |
shell: bash | |
name: 'Get testing version' | |
- uses: actions/cache@v4 | |
with: | |
key: ${{ env.TESTING_VERSION }} | |
path: ~/mne_data | |
name: 'Cache testing data' | |
- run: ./tools/github_actions_download.sh | |
shell: bash | |
working-directory: mne-python | |
- name: Run pytest | |
shell: bash | |
run: make test | |
- name: Upload coverage stats to codecov | |
uses: codecov/codecov-action@v4 | |
with: | |
files: ./coverage.xml | |
token: ${{ secrets.CODECOV_TOKEN }} | |
verbose: true | |
build_docs: | |
runs-on: ubuntu-latest | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.12"] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: actions/cache@v4 | |
with: | |
path: ${{ env.pythonLocation }} | |
key: build_docs-0-${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
python -m pip install --upgrade https://github.com/mne-tools/mne-python/archive/refs/heads/main.zip | |
python -m pip install -e .[test,doc] | |
- name: Build the documentation | |
run: | | |
make build-doc | |
- name: Upload artifacts | |
uses: actions/upload-artifact@v4 | |
with: | |
name: documentation | |
path: doc/_build/html |