Refactor `get_tau_sigma` and support lists of variables #3752

Workflow file for this run

	name: tests

	on:
	pull_request:
	push:
	branches:
	- main


	# 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@b4ffde65f46336ab88eb53be808477a3936bae11
	with:
	fetch-depth: 0
	- uses: dorny/paths-filter@v3
	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:
	os: [ubuntu-20.04]
	floatx: [float64]
	python-version: ["3.11"]
	test-subset:
	- \|
	tests/test_util.py
	tests/test_pytensorf.py
	tests/test_math.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/distributions/test_continuous.py
	tests/distributions/test_multivariate.py

	- \|
	tests/distributions/test_censored.py
	tests/distributions/test_simulator.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/test_model_graph.py
	tests/ode/test_ode.py
	tests/ode/test_utils.py
	tests/step_methods/hmc/test_quadpotential.py

	- \|
	tests/backends/test_mcbackend.py
	tests/distributions/test_truncated.py
	tests/logprob/test_abstract.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_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_transform_value.py
	tests/logprob/test_transforms.py
	tests/logprob/test_utils.py

	fail-fast: false
	runs-on: ${{ matrix.os }}
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if environment-test.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
	hashFiles('conda-envs/environment-test.yml') }}
	- name: Cache multiple paths
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if requirements.txt has not changed
	CACHE_NUMBER: 0
	with:
	path: \|
	~/.cache/pip
	$RUNNER_TOOL_CACHE/Python/*
	~\AppData\Local\pip\Cache
	key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{
	hashFiles('requirements.txt') }}
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	mamba-version: "*"
	activate-environment: pymc-test
	channel-priority: strict
	environment-file: conda-envs/environment-test.yml
	python-version: ${{matrix.python-version}}
	use-mamba: true
	use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
	- name: Install-pymc
	run: \|
	conda activate pymc-test
	pip install -e .
	pip install --pre -U polyagamma
	python --version
	- name: Run tests
	run: \|
	conda activate pymc-test
	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@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: ${{ matrix.os }} ${{ matrix.floatx }}
	fail_ci_if_error: false

	windows:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	os: [windows-latest]
	floatx: [float64]
	python-version: ["3.9"]
	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

	fail-fast: false
	runs-on: ${{ matrix.os }}
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
	defaults:
	run:
	shell: cmd
	steps:
	- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if conda-envs/windows-environment-test.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
	hashFiles('conda-envs/windows-environment-test.yml') }}
	- name: Cache multiple paths
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if requirements.txt has not changed
	CACHE_NUMBER: 0
	with:
	path: \|
	~/.cache/pip
	$RUNNER_TOOL_CACHE/Python/*
	~\AppData\Local\pip\Cache
	key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{
	hashFiles('requirements.txt') }}
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	mamba-version: "*"
	activate-environment: pymc-test
	channel-priority: strict
	environment-file: conda-envs/windows-environment-test.yml
	python-version: ${{matrix.python-version}}
	use-mamba: true
	use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
	- name: Install-pymc
	run: \|
	conda activate pymc-test
	pip install -e .
	pip install --pre -U polyagamma
	python --version
	- name: Run tests
	# This job uses a cmd shell, therefore the environment variable syntax is different!
	# The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
	run: >-
	conda activate pymc-test &&
	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@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: ${{ matrix.os }} ${{ matrix.floatx }}
	fail_ci_if_error: false

	macos:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	os: [macos-latest]
	floatx: [float64]
	python-version: ["3.10"]
	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/variational/test_updates.py
	fail-fast: false
	runs-on: ${{ matrix.os }}
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if environment-test.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
	hashFiles('conda-envs/environment-test.yml') }}
	- name: Cache multiple paths
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if requirements.txt has not changed
	CACHE_NUMBER: 0
	with:
	path: \|
	~/.cache/pip
	$RUNNER_TOOL_CACHE/Python/*
	~\AppData\Local\pip\Cache
	key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{
	hashFiles('requirements.txt') }}
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	mamba-version: "*"
	activate-environment: pymc-test
	channel-priority: strict
	environment-file: conda-envs/environment-test.yml
	python-version: ${{matrix.python-version}}
	use-mamba: true
	use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
	- name: Install pymc
	run: \|
	conda activate pymc-test
	pip install -e .
	python --version
	- 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@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: ${{ matrix.os }} ${{ matrix.floatx }}
	fail_ci_if_error: false

	external_samplers:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	os: [ubuntu-20.04]
	floatx: [float64]
	python-version: ["3.11"]
	test-subset:
	- tests/sampling/test_jax.py tests/sampling/test_mcmc_external.py
	fail-fast: false
	runs-on: ${{ matrix.os }}
	env:
	TEST_SUBSET: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=native'
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if environment-jax.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
	hashFiles('conda-envs/environment-jax.yml') }}
	- name: Cache multiple paths
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if requirements.txt has not changed
	CACHE_NUMBER: 0
	with:
	path: \|
	~/.cache/pip
	$RUNNER_TOOL_CACHE/Python/*
	~\AppData\Local\pip\Cache
	key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{
	hashFiles('requirements.txt') }}
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	mamba-version: "*"
	activate-environment: pymc-test
	channel-priority: strict
	environment-file: conda-envs/environment-jax.yml
	python-version: ${{matrix.python-version}}
	use-mamba: true
	use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
	- name: Install pymc
	run: \|
	conda activate pymc-test
	pip install -e .
	python --version
	- 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@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: JAX tests - ${{ matrix.os }} ${{ matrix.floatx }}
	fail_ci_if_error: false

	float32:
	needs: changes
	if: ${{ needs.changes.outputs.changes == 'true' }}
	strategy:
	matrix:
	os: [windows-latest]
	floatx: [float32]
	python-version: ["3.11"]
	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: ${{ matrix.test-subset }}
	PYTENSOR_FLAGS: floatX=${{ matrix.floatx }},gcc__cxxflags='-march=core2'
	defaults:
	run:
	shell: cmd
	steps:
	- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11
	- name: Cache conda
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if conda-envs/windows-environment-test.yml has not changed
	CACHE_NUMBER: 0
	with:
	path: ~/conda_pkgs_dir
	key: ${{ runner.os }}-py${{matrix.python-version}}-conda-${{ env.CACHE_NUMBER }}-${{
	hashFiles('conda-envs/windows-environment-test.yml') }}
	- name: Cache multiple paths
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if requirements.txt has not changed
	CACHE_NUMBER: 0
	with:
	path: \|
	~/.cache/pip
	$RUNNER_TOOL_CACHE/Python/*
	~\AppData\Local\pip\Cache
	key: ${{ runner.os }}-build-${{ matrix.python-version }}-${{ env.CACHE_NUMBER }}-${{
	hashFiles('requirements.txt') }}
	- uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	mamba-version: "*"
	activate-environment: pymc-test
	channel-priority: strict
	environment-file: conda-envs/windows-environment-test.yml
	python-version: ${{matrix.python-version}}
	use-mamba: true
	use-only-tar-bz2: false # IMPORTANT: This may break caching of conda packages! See https://github.com/conda-incubator/setup-miniconda/issues/267
	- name: Install-pymc
	run: \|
	conda activate pymc-test
	pip install -e .
	pip install --pre -U polyagamma
	python --version
	- name: Run tests
	# This job uses a cmd shell, therefore the environment variable syntax is different!
	# The ">-" in the next line replaces newlines with spaces (see https://stackoverflow.com/a/66809682).
	run: >-
	conda activate pymc-test &&
	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@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }} # use token for more robust uploads
	env_vars: TEST_SUBSET
	name: ${{ matrix.os }} ${{ matrix.floatx }}
	fail_ci_if_error: false

	all_tests:
	if: ${{ always() }}
	runs-on: ubuntu-latest
	needs: [ changes, ubuntu, windows, macos, external_samplers, 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.external_samplers.result != 'success' \|\|
	needs.float32.result != 'success' ) }}
	run: exit 1

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Refactor `get_tau_sigma` and support lists of variables #3752

Workflow file

Refactor `get_tau_sigma` and support lists of variables #3752

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Workflow file for this run

Refactor get_tau_sigma and support lists of variables #3752

Workflow file

Workflow file for this run

Refactor `get_tau_sigma` and support lists of variables #3752