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Speedup sample and allow specifying compile_kwargs (several major changes related to step samplers) #4785

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Speedup sample and allow specifying compile_kwargs (several major changes related to step samplers)

Speedup sample and allow specifying compile_kwargs (several major changes related to step samplers) #4785

Workflow file for this run

.github/workflows/tests.yml at f7f8bc5
name: tests
on:
pull_request:
push:
branches:
- main
# 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@11bd71901bbe5b1630ceea73d27597364c9af683
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: ["3.12"]
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/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_optimization.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/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_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_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@11bd71901bbe5b1630ceea73d27597364c9af683
- 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 .
# TODO: https://github.com/pymc-devs/pymc/issues/7417
pip install --pre -U 'polyagamma<1.3.7'
python --version
conda list
- 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: ["3.10"]
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: ${{ 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@11bd71901bbe5b1630ceea73d27597364c9af683
- 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<1.3.7'
python --version
conda list
- 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: ["3.12"]
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@11bd71901bbe5b1630ceea73d27597364c9af683
- 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
conda 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@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: ["3.12"]
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@11bd71901bbe5b1630ceea73d27597364c9af683
- 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
conda 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@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: ["3.12"]
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@11bd71901bbe5b1630ceea73d27597364c9af683
- 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<1.3.7'
python --version
conda list
- 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