Derive logprob for exp2, log2, log10, log1p, expm1, log1mexp, log1pexp (softplus), and sigmoid transformations #2934
Workflow file for this run
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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@v3 | |
with: | |
fetch-depth: 0 | |
- uses: dorny/paths-filter@v2 | |
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_bound.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_likelihood.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/test_model.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_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@v3 | |
- name: Cache conda | |
uses: actions/cache@v3 | |
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@v3 | |
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@v3 | |
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/test_model.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@v3 | |
- name: Cache conda | |
uses: actions/cache@v3 | |
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@v3 | |
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@v3 | |
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/test_model.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@v3 | |
- name: Cache conda | |
uses: actions/cache@v3 | |
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@v3 | |
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@v3 | |
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@v3 | |
- name: Cache conda | |
uses: actions/cache@v3 | |
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@v3 | |
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: Install external samplers | |
run: | | |
conda activate pymc-test | |
pip install "numpyro>=0.8.0" | |
pip install git+https://github.com/blackjax-devs/[email protected] | |
- 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@v3 | |
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@v3 | |
- name: Cache conda | |
uses: actions/cache@v3 | |
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@v3 | |
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@v3 | |
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 |