tests

Allow free-threaded parallel sampling #6963

Workflow file for this run

	name: tests

	permissions: {}

	on:
	pull_request:
	push:
	branches:
	- main
	- "v[0-9]+"

	# Cancel running workflows for updated PRs
	# https://turso.tech/blog/simple-trick-to-save-environment-and-money-when-using-github-actions
	concurrency:
	group: ${{ github.workflow}}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	# Tests are split into multiple jobs to accelerate the CI.
	# Different jobs should be organized to take approximately the same
	# time to complete (and not be prohibitely slow).
	# Because GitHub Actions don't support YAML anchors, we have to place the
	# splitting of testfiles into groups in the strategy/matrix/test-subset
	# and can't re-use the groups across jobs.
	# A pre-commit hook (scripts/check_all_tests_are_covered.py)
	# enforces that test run just once per OS / floatX setting.

	jobs:
	changes:
	name: "Check for changes"
	runs-on: ubuntu-latest
	outputs:
	changes: ${{ steps.changes.outputs.src }}
	steps:
	- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
	with:
	fetch-depth: 0
	persist-credentials: false
	- uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3.0.2
	id: changes
	with:
	filters: \|
	src:
	- ".github/workflows/tests.yml"
	- "pymc/*/.py"
	- "tests/*/.py"
	- "*.py"
	- "conda-envs/*"
	- "requirements*.txt"
	- "codecov.yml"
	- "scripts/*.sh"

	ubuntu:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	linker: [cvm, numba]
	python-version: ["3.14"]
	test-subset:
	- \|
	tests/test_util.py
	tests/test_pytensorf.py
	tests/test_math.py
	tests/test_root_namespace.py
	tests/backends/test_base.py
	tests/backends/test_ndarray.py
	tests/step_methods/hmc/test_hmc.py
	tests/test_func_utils.py
	tests/distributions/test_shape_utils.py
	tests/distributions/test_mixture.py
	tests/test_testing.py
	tests/progress_bar/test_manager.py
	tests/progress_bar/test_marimo.py

	- \|
	tests/distributions/test_continuous.py
	tests/distributions/test_multivariate.py
	tests/distributions/moments/test_means.py

	- \|
	tests/distributions/test_censored.py
	tests/distributions/test_custom.py
	tests/distributions/test_simulator.py
	tests/sampling/test_deterministic.py
	tests/sampling/test_forward.py
	tests/sampling/test_population.py
	tests/stats/test_convergence.py
	tests/stats/test_log_density.py
	tests/distributions/test_distribution.py
	tests/distributions/test_discrete.py

	- \|
	tests/tuning/test_scaling.py
	tests/tuning/test_starting.py
	tests/distributions/test_dist_math.py
	tests/distributions/test_transform.py
	tests/sampling/test_mcmc.py
	tests/sampling/test_parallel.py
	tests/test_printing.py

	- \|
	tests/distributions/test_timeseries.py
	tests/gp/test_cov.py
	tests/gp/test_hsgp_approx.py
	tests/gp/test_gp.py
	tests/gp/test_mean.py
	tests/gp/test_util.py
	tests/model/test_core.py
	tests/model/test_fgraph.py
	tests/model/transform/test_basic.py
	tests/model/transform/test_conditioning.py
	tests/model/transform/test_deterministic.py
	tests/model/transform/test_optimization.py
	tests/model/test_transform_values.py
	tests/test_model_graph.py
	tests/ode/test_ode.py
	tests/ode/test_utils.py
	tests/step_methods/hmc/test_quadpotential.py
	tests/step_methods/test_state.py

	- \|
	tests/backends/test_mcbackend.py
	tests/backends/test_zarr.py
	tests/distributions/test_truncated.py
	tests/logprob/test_abstract.py
	tests/logprob/test_arithmetic.py
	tests/logprob/test_basic.py
	tests/logprob/test_binary.py
	tests/logprob/test_checks.py
	tests/logprob/test_censoring.py
	tests/logprob/test_composite_logprob.py
	tests/logprob/test_cumsum.py
	tests/logprob/test_linalg.py
	tests/logprob/test_mixture.py
	tests/logprob/test_order.py
	tests/logprob/test_rewriting.py
	tests/logprob/test_scan.py
	tests/logprob/test_tensor.py
	tests/logprob/test_switch.py
	tests/logprob/test_transform_value.py
	tests/logprob/test_transforms.py
	tests/logprob/test_utils.py

	- \|
	tests/dims/distributions/test_core.py
	tests/dims/distributions/test_censored.py
	tests/dims/distributions/test_scalar.py
	tests/dims/distributions/test_vector.py
	tests/dims/test_model.py

	fail-fast: false
	runs-on: ubuntu-latest
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: linker=${{ matrix.linker }}
	defaults:
	run:
	shell: bash -leo pipefail {0}
	steps:
	- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
	with:
	persist-credentials: false
	- uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
	with:
	environment-file: conda-envs/environment-test.yml
	create-args: >-
	python=${{matrix.python-version}}
	environment-name: pymc-test
	init-shell: bash
	cache-environment: true
	- name: Install-pymc
	run: \|
	pip install -e .
	python --version
	micromamba list
	- name: Run tests
	run: \|
	python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	env_vars: TEST_SUBSET
	name: Ubuntu py${{ matrix.python-version }} linker=${{ matrix.linker }}
	fail_ci_if_error: false

	windows:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	linker: [cvm, numba]
	python-version: ["3.12"]
	test-subset:
	- tests/variational/test_approximations.py tests/variational/test_callbacks.py tests/variational/test_inference.py tests/variational/test_opvi.py tests/test_initial_point.py
	- tests/model/test_core.py tests/sampling/test_mcmc.py
	- tests/gp/test_cov.py tests/gp/test_gp.py tests/gp/test_mean.py tests/gp/test_util.py tests/ode/test_ode.py tests/ode/test_utils.py tests/smc/test_smc.py tests/sampling/test_parallel.py
	- tests/step_methods/test_metropolis.py tests/step_methods/test_slicer.py tests/step_methods/hmc/test_nuts.py tests/step_methods/test_compound.py tests/step_methods/hmc/test_hmc.py tests/step_methods/test_state.py

	fail-fast: false
	runs-on: windows-2022
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: linker=${{ matrix.linker }}
	defaults:
	run:
	shell: bash -leo pipefail {0}
	steps:
	- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
	with:
	persist-credentials: false
	- uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
	with:
	environment-file: conda-envs/windows-environment-test.yml
	micromamba-version: "2.6.0-0"
	create-args: >-
	python=${{matrix.python-version}}
	environment-name: pymc-test
	init-shell: bash
	cache-environment: true
	- name: Install-pymc
	run: \|
	pip install -e .
	python --version
	micromamba list
	- name: Run tests
	run: \|
	python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	env_vars: TEST_SUBSET
	name: Windows py${{ matrix.python-version }} linker=${{ matrix.linker }}
	fail_ci_if_error: false

	macos:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	linker: [cvm, numba]
	python-version: ["3.14"]
	test-subset:
	- \|
	tests/sampling/test_parallel.py
	tests/test_data.py
	tests/variational/test_minibatch_rv.py
	tests/model/test_core.py

	- \|
	tests/sampling/test_mcmc.py

	- \|
	tests/backends/test_arviz.py
	tests/backends/test_zarr.py
	tests/variational/test_updates.py
	fail-fast: false
	runs-on: macos-latest
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: linker=${{ matrix.linker }}
	defaults:
	run:
	shell: bash -leo pipefail {0}
	steps:
	- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
	with:
	persist-credentials: false
	- uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
	with:
	environment-file: conda-envs/environment-test.yml
	create-args: >-
	python=${{matrix.python-version}}
	environment-name: pymc-test
	init-shell: bash
	cache-environment: true
	- name: Install pymc
	run: \|
	pip install -e .
	python --version
	micromamba list
	- name: Run tests
	run: \|
	python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: MacOS py${{ matrix.python-version }} linker=${{ matrix.linker }}
	fail_ci_if_error: false

	alternative_backends:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	linker: [cvm, numba]
	# nutpie depends on PyMC, and it will require an extra release cycle to support
	# the next PyMC release and therefore Python 3.14.
	python-version: ["3.13"]
	test-subset:
	- \|
	tests/distributions/test_random_alternative_backends.py
	tests/sampling/test_jax.py
	tests/sampling/test_mcmc_external.py

	fail-fast: false
	runs-on: ubuntu-latest
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: linker=${{ matrix.linker }}
	defaults:
	run:
	shell: bash -leo pipefail {0}
	steps:
	- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
	with:
	persist-credentials: false
	- uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
	with:
	environment-file: conda-envs/environment-alternative-backends.yml
	create-args: >-
	python=${{matrix.python-version}}
	environment-name: pymc-test
	init-shell: bash
	cache-environment: true
	- name: Install pymc
	run: \|
	pip install -e .
	# Track nutpie main so we exercise unreleased changes. Expected to be
	# red until nutpie main drops its `arviz.InferenceData` references.
	pip install "nutpie @ git+https://github.com/pymc-devs/nutpie@main"
	python --version
	micromamba list
	- name: Run tests
	run: \|
	python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: Alternative backends py${{ matrix.python-version }} linker=${{ matrix.linker }}
	fail_ci_if_error: false

	free_threading:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	# A small, sampling-focused subset that exercises the thread-based parallel
	# sampling path used on free-threaded (no-GIL) builds. The GIL-stays-disabled
	# check is a pytest_sessionfinish hook in tests/conftest.py.
	test-subset:
	- \|
	tests/sampling/test_parallel.py
	tests/step_methods/test_compound.py
	fail-fast: false
	runs-on: ubuntu-latest
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	# Intentionally leave PYTHON_GIL unset. Setting it to 0 would force the GIL
	# off and hide a dependency that fails to support free-threading; leaving it
	# unset lets such a dependency re-enable the GIL, which the conftest
	# pytest_sessionfinish hook asserts against.
	defaults:
	run:
	shell: bash -leo pipefail {0}
	steps:
	- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
	with:
	persist-credentials: false
	- uses: actions/setup-python@ece7cb06caefa5fff74198d8649806c4678c61a1 # v6.3.0
	with:
	python-version: "3.14t"
	- name: Install pymc and test dependencies
	run: \|
	python -m pip install --upgrade pip
	# Install from PyPI (free-threaded wheels), not conda-forge. numba is
	# included as the free-threading-safe PyTensor backend.
	pip install -e . numba pytest pytest-cov
	# Free-threaded sampling needs the (still unreleased) PyTensor
	# free-threading support; track its branch until it is released.
	pip install "pytensor @ git+https://github.com/pymc-devs/pytensor@free_threaded"
	python --version
	python -c "import sys, sysconfig; print('Py_GIL_DISABLED =', sysconfig.get_config_var('Py_GIL_DISABLED'), '\| gil_enabled =', sys._is_gil_enabled())"
	pip list
	- name: Run tests
	run: \|
	python -m pytest -vv --durations=25 $TEST_SUBSET

	float32:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	linker: [cvm, numba]
	os: [windows-2022]
	python-version: ["3.14"]
	test-subset:
	- tests/sampling/test_mcmc.py tests/ode/test_ode.py tests/ode/test_utils.py tests/distributions/test_transform.py
	fail-fast: false
	runs-on: ${{ matrix.os }}
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: floatX=float32
	defaults:
	run:
	shell: bash -leo pipefail {0}
	steps:
	- uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
	with:
	persist-credentials: false
	- uses: mamba-org/setup-micromamba@add3a49764cedee8ee24e82dfde87f5bc2914462 # v2.0.7
	with:
	environment-file: conda-envs/windows-environment-test.yml
	micromamba-version: "2.6.0-0"
	create-args: >-
	python=${{matrix.python-version}}
	environment-name: pymc-test
	init-shell: bash
	cache-environment: true
	- name: Install-pymc
	run: \|
	pip install -e .
	python --version
	micromamba list
	- name: Run tests
	run: \|
	python -m pytest -vv --cov=pymc --cov-report=xml --no-cov-on-fail --cov-report term --durations=50 $TEST_SUBSET
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6.0.0
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: float32 ${{ matrix.os }} py${{ matrix.python-version }} linker=${{ matrix.linker }}
	fail_ci_if_error: false

	all_tests:
	if: ${{ always() }}
	runs-on: ubuntu-latest
	needs: [changes, ubuntu, windows, macos, alternative_backends, free_threading, float32]
	steps:
	- name: Check build matrix status
	if: ${{ needs.changes.outputs.changes == 'true' &&
	( needs.ubuntu.result != 'success' \|\|
	needs.windows.result != 'success' \|\|
	needs.macos.result != 'success' \|\|
	needs.alternative_backends.result != 'success' \|\|
	needs.free_threading.result != 'success' \|\|
	needs.float32.result != 'success' ) }}
	run: exit 1

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Allow free-threaded parallel sampling #6963

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Allow free-threaded parallel sampling #6963

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Workflow file for this run