Tests

MAINT: Restore Python 3.11 support #100

Workflow file for this run

	name: Tests

	on: # yamllint disable-line rule:truthy
	push:
	branches: [main]
	pull_request:
	branches: [main]
	schedule:
	- cron: "17 5 * * 1"
	workflow_dispatch:

	concurrency:
	group: ${{ github.workflow }}-${{ github.event.number \|\| github.ref }}
	cancel-in-progress: true

	permissions:
	contents: read

	jobs:
	lint:
	name: Lint
	if: github.event_name != 'schedule'
	runs-on: ubuntu-latest
	timeout-minutes: 10
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
	with:
	python-version: "3.14"
	cache: pip
	- name: Install lint dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install --group lint
	- name: Run repository checks
	run: spin lint

	base-install:
	name: Base install / Python 3.11
	if: github.event_name != 'schedule'
	runs-on: ubuntu-latest
	timeout-minutes: 10
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
	with:
	python-version: "3.11"
	- name: Validate base installation
	run: \|
	base_python="$RUNNER_TEMP/mne-denoise-base/bin/python"
	python -m venv "$RUNNER_TEMP/mne-denoise-base"
	"$base_python" -m pip install --upgrade pip
	"$base_python" -m pip install -e .
	"$base_python" -m pip check
	"$base_python" scripts/check_base_install.py
	- name: Display environment information
	run: \|
	base_python="$RUNNER_TEMP/mne-denoise-base/bin/python"
	"$base_python" --version
	"$base_python" - <<'PY'
	from importlib.metadata import version

	for package in ("mne-denoise", "numpy", "scipy", "scikit-learn", "joblib"):
	print(package, version(package))
	PY

	lower-bound-base:
	name: Lower bound / base dependencies
	if: github.event_name != 'schedule'
	runs-on: ubuntu-latest
	timeout-minutes: 30
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
	with:
	version: ">=0.9"
	python-version: "3.11"
	activate-environment: true
	cache-dependency-glob: \|
	pyproject.toml
	tools/pylock.ci-min-base.toml
	- name: Install shared lockfile checker
	run: >-
	uv pip install
	"mne-tools @ git+https://github.com/mne-tools/mne-tools.git@2e7c4b5469ef311a169e16c7f97cd0ce68508a61"
	- name: Validate base lower-bound lockfile
	run: \|
	python -m mne_tools.check_lockfile \
	"$GITHUB_WORKSPACE" \
	tools/pylock.ci-min-base.toml \
	--groups lockfile_base
	- name: Restore lower-bound Python environment
	run: \|
	base_env="$RUNNER_TEMP/mne-denoise-lower-bound-base"
	uv venv --python 3.11 "$base_env"
	echo "MNE_DENOISE_BASE_ENV=$base_env" >> "$GITHUB_ENV"
	- name: Install lower-bound environment
	run: \|
	base_python="$MNE_DENOISE_BASE_ENV/bin/python"
	uv pip sync --python "$base_python" tools/pylock.ci-min-base.toml
	uv pip install --python "$base_python" pip \
	"mne-tools @ git+https://github.com/mne-tools/mne-tools.git@2e7c4b5469ef311a169e16c7f97cd0ce68508a61"
	uv pip install --python "$base_python" -e . --no-deps
	- name: Check declared lower bounds
	run: \|
	base_python="$MNE_DENOISE_BASE_ENV/bin/python"
	"$base_python" -m mne_tools.check_environment \
	"$GITHUB_WORKSPACE" \
	--groups lockfile_base
	- name: Check base installation boundary
	run: >-
	"$MNE_DENOISE_BASE_ENV/bin/python" scripts/check_base_install.py
	- name: Display environment information
	run: \|
	base_python="$MNE_DENOISE_BASE_ENV/bin/python"
	"$base_python" --version
	"$base_python" - <<'PY'
	from importlib.metadata import version

	for package in (
	"mne-denoise",
	"numpy",
	"scipy",
	"scikit-learn",
	"joblib",
	):
	print(package, version(package))
	PY
	- name: Check installed requirements
	run: >-
	"$MNE_DENOISE_BASE_ENV/bin/python" -m pip check

	mne-minimum:
	name: MNE-Python 1.13.0 minimum integration
	if: github.event_name != 'schedule'
	runs-on: ubuntu-latest
	timeout-minutes: 30
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
	with:
	python-version: "3.11"
	cache: pip
	- name: Install MNE-Python minimum test environment
	run: \|
	python -m pip install --upgrade pip
	python -m pip install -e . --group test "mne==1.13.0"
	- name: Verify MNE-Python minimum version
	run: \|
	python - <<'PY'
	from importlib.metadata import version

	installed = version("mne")
	if installed != "1.13.0":
	raise SystemExit(f"expected MNE-Python 1.13.0, found {installed}")
	print("MNE-Python:", installed)
	PY
	- name: Display environment information
	run: \|
	python --version
	python - <<'PY'
	from importlib.metadata import version

	for package in (
	"mne-denoise",
	"numpy",
	"scipy",
	"scikit-learn",
	"joblib",
	"mne",
	"matplotlib",
	"seaborn",
	"tqdm",
	):
	print(package, version(package))
	PY
	- name: Check installed requirements
	run: python -m pip check
	- name: Run full test suite
	run: pytest -q

	lower-bound-extras:
	name: Lower bound / standalone extras
	if: github.event_name != 'schedule'
	runs-on: ubuntu-latest
	timeout-minutes: 30
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
	with:
	version: ">=0.9"
	python-version: "3.11"
	activate-environment: true
	cache-dependency-glob: \|
	pyproject.toml
	tools/pylock.ci-min-extras.toml
	- name: Install shared lockfile checker
	run: >-
	uv pip install
	"mne-tools @ git+https://github.com/mne-tools/mne-tools.git@2e7c4b5469ef311a169e16c7f97cd0ce68508a61"
	- name: Validate standalone extras lower-bound lockfile
	run: \|
	python -m mne_tools.check_lockfile \
	"$GITHUB_WORKSPACE" \
	tools/pylock.ci-min-extras.toml \
	--groups lockfile_extras
	- name: Restore lower-bound Python environment
	run: \|
	extras_env="$RUNNER_TEMP/mne-denoise-lower-bound-extras"
	uv venv --python 3.11 "$extras_env"
	echo "MNE_DENOISE_EXTRAS_ENV=$extras_env" >> "$GITHUB_ENV"
	- name: Install lower-bound environment
	run: \|
	extras_python="$MNE_DENOISE_EXTRAS_ENV/bin/python"
	uv pip sync --python "$extras_python" tools/pylock.ci-min-extras.toml
	uv pip install --python "$extras_python" pip \
	"mne-tools @ git+https://github.com/mne-tools/mne-tools.git@2e7c4b5469ef311a169e16c7f97cd0ce68508a61"
	uv pip install --python "$extras_python" -e . --no-deps
	- name: Check declared lower bounds
	run: \|
	extras_python="$MNE_DENOISE_EXTRAS_ENV/bin/python"
	"$extras_python" -m mne_tools.check_environment \
	"$GITHUB_WORKSPACE" --groups lockfile_extras
	- name: Verify MNE-Python remains optional
	run: \|
	"$MNE_DENOISE_EXTRAS_ENV/bin/python" - <<'PY'
	from importlib.util import find_spec

	if find_spec("mne") is not None:
	raise SystemExit(
	"MNE-Python leaked into the standalone extras lower-bound environment"
	)
	PY
	- name: Display environment information
	run: \|
	extras_python="$MNE_DENOISE_EXTRAS_ENV/bin/python"
	"$extras_python" --version
	"$extras_python" - <<'PY'
	from importlib.metadata import version

	for package in (
	"mne-denoise",
	"numpy",
	"scipy",
	"scikit-learn",
	"joblib",
	"matplotlib",
	"seaborn",
	"tqdm",
	):
	print(package, version(package))
	PY
	- name: Check installed requirements
	run: >-
	"$MNE_DENOISE_EXTRAS_ENV/bin/python" -m pip check
	- name: Run standalone public API smoke
	run: \|
	extras_python="$MNE_DENOISE_EXTRAS_ENV/bin/python"
	MPLBACKEND=Agg "$extras_python" - <<'PY'
	import matplotlib.pyplot as plt

	from mne_denoise.progress import TqdmProgress
	from mne_denoise.viz import plot_metric_violins

	data = {
	"subject": ["s1", "s1", "s2", "s2"],
	"group": ["a", "a", "b", "b"],
	"metric": [1.0, 2.0, 3.0, 4.0],
	}

	fig = plot_metric_violins(data, ["metric"], show=False)
	plt.close(fig)

	progress = TqdmProgress(disable=True)
	progress.close()
	PY

	stable:
	name: ${{ matrix.name }}
	if: github.event_name != 'schedule'
	runs-on: ${{ matrix.os }}
	timeout-minutes: 30
	strategy:
	fail-fast: false
	matrix:
	include:
	- os: ubuntu-latest
	python-version: "3.12"
	name: Python 3.12
	coverage: "false"
	- os: ubuntu-latest
	python-version: "3.13"
	name: Python 3.13
	coverage: "false"
	- os: ubuntu-latest
	python-version: "3.14"
	name: Latest / Python 3.14
	coverage: "true"
	- os: windows-latest
	python-version: "3.14"
	name: Windows / Python 3.14
	coverage: "false"
	- os: macos-latest
	python-version: "3.14"
	name: macOS ARM / Python 3.14
	coverage: "false"
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
	with:
	python-version: ${{ matrix.python-version }}
	cache: pip
	- name: Install stable test environment
	run: \|
	python -m pip install --upgrade pip
	python -m pip install -e . --group test
	- name: Verify macOS ARM runner
	if: matrix.name == 'macOS ARM / Python 3.14'
	run: \|
	python - <<'PY'
	import platform

	print("machine:", platform.machine())
	print("platform:", platform.platform())
	if platform.machine() != "arm64":
	raise SystemExit("macOS compatibility job is not running on arm64")
	PY
	- name: Display environment information
	run: \|
	python --version
	python - <<'PY'
	from importlib.metadata import version

	for package in (
	"mne-denoise",
	"numpy",
	"scipy",
	"scikit-learn",
	"joblib",
	"mne",
	"matplotlib",
	"seaborn",
	"tqdm",
	):
	print(package, version(package))
	PY
	- name: Check installed requirements
	run: python -m pip check
	- name: Run tests
	if: matrix.coverage == 'false'
	run: pytest -q
	- name: Run tests with coverage
	if: matrix.coverage == 'true'
	run: pytest --cov=mne_denoise --cov-report=xml -q
	- name: Upload coverage to Codecov
	if: matrix.coverage == 'true'
	uses: codecov/codecov-action@0b35c9ecc4f0529d0eb674914510c22f85b196b4 # v7.1.0
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: ./coverage.xml
	flags: unittests
	fail_ci_if_error: false

	mne-main:
	name: MNE main
	runs-on: ubuntu-latest
	timeout-minutes: 30
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
	with:
	python-version: "3.14"
	cache: pip
	- name: Install stable mne-denoise test environment
	run: \|
	python -m pip install --upgrade pip
	python -m pip install -e . --group test
	python -c "import mne; print(mne.__version__)" > "$RUNNER_TEMP/mne-stable-version"
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	repository: mne-tools/mne-python
	path: .ci/mne-python
	fetch-depth: 0
	persist-credentials: false
	- name: Install MNE-Python main
	run: python -m pip install --upgrade ./.ci/mne-python
	- name: Verify MNE-Python main installation
	run: \|
	git -C .ci/mne-python rev-parse HEAD
	python - <<'PY'
	import os
	from importlib.metadata import version

	import mne

	stable_version = open(
	os.path.join(os.environ["RUNNER_TEMP"], "mne-stable-version"),
	encoding="utf-8",
	).read().strip()
	print("mne.__version__:", mne.__version__)
	print("mne metadata:", version("mne"))
	print("mne path:", mne.__file__)
	if mne.__version__ == stable_version:
	raise SystemExit("MNE main installation did not replace stable MNE")
	PY
	- name: Display environment information
	run: \|
	python --version
	echo "MNE git SHA: $(git -C .ci/mne-python rev-parse HEAD)"
	python - <<'PY'
	from importlib.metadata import version

	for package in (
	"mne-denoise",
	"numpy",
	"scipy",
	"scikit-learn",
	"joblib",
	"mne",
	"matplotlib",
	"seaborn",
	"tqdm",
	):
	print(package, version(package))
	PY
	- name: Check installed requirements
	run: python -m pip check
	- name: Run tests
	run: pytest -q

	prerelease:
	name: Prerelease dependencies
	continue-on-error: true
	runs-on: ubuntu-latest
	timeout-minutes: 30
	defaults:
	run:
	shell: bash
	steps:
	- uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
	with:
	python-version: "3.14"
	cache: pip
	- name: Install stable test environment
	run: \|
	python -m pip install --upgrade pip
	python -m pip install -e . --group test
	- name: Upgrade scientific dependencies to prereleases
	run: \|
	python -m pip install --upgrade --pre \
	numpy scipy scikit-learn joblib matplotlib seaborn tqdm
	- name: Display environment information
	run: \|
	python --version
	python - <<'PY'
	from importlib.metadata import version

	for package in (
	"mne-denoise",
	"numpy",
	"scipy",
	"scikit-learn",
	"joblib",
	"mne",
	"matplotlib",
	"seaborn",
	"tqdm",
	):
	print(package, version(package))
	PY
	- name: Check installed requirements
	run: python -m pip check
	- name: Run tests
	run: pytest -q

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MAINT: Restore Python 3.11 support #100

Workflow file

MAINT: Restore Python 3.11 support #100

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Workflow file for this run