os.path to pathlib #5637

Workflow file for this run

.github/workflows/unit_tests.yml at 4c6af9a

	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
	with:
	fetch-depth: 0
	fetch-tags: true
	- 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
	with:
	fetch-depth: 0
	fetch-tags: true
	- 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
	with:
	fetch-depth: 0
	fetch-tags: true
	- 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
	with:
	fetch-depth: 0
	fetch-tags: true
	- name: Test extras install
	run: \|
	python -m pip install .[full]
	python -c 'import mne_bids; print(mne_bids.__version__)'
	python -c 'import defusedxml; print(defusedxml.__version__)'
	python -c 'import edfio; print(edfio.__version__)'
	python -c 'import eeglabio; print(eeglabio.__version__)'
	python -c 'import matplotlib; print(matplotlib.__version__)'
	python -c 'import nibabel; print(nibabel.__version__)'
	python -c 'import pandas; print(pandas.__version__)'
	python -c 'import pybv; print(pybv.__version__)'
	python -c 'import pymatreader; print(pymatreader.__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
	with:
	fetch-depth: 0
	fetch-tags: true

	- 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'
	run: \|
	npm install -g bids-validator

	- name: Download BIDS validator (main)
	if: matrix.bids-validator-version == 'validator-main'
	run: \|
	pushd ..
	git clone --depth 1 https://github.com/bids-standard/legacy-validator
	popd

	- name: Install BIDS validator (main)
	if: matrix.bids-validator-version == 'validator-main'
	run: \|
	pushd ../legacy-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@v5
	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
	with:
	fetch-depth: 0
	fetch-tags: true
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- uses: actions/cache@v4
	with:
	path: ${{ env.pythonLocation }}
	key: build_docs-1-${{ 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
	include-hidden-files: true

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os.path to pathlib #5637

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os.path to pathlib #5637

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