Add RTD link preview #3099
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name: Tests | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches: | |
- main | |
# Cancels all previous workflow runs for pull requests that have not completed. | |
concurrency: | |
# The concurrency group contains the workflow name and the branch name for pull requests | |
# or the commit hash for any other events. | |
group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }} | |
cancel-in-progress: true | |
jobs: | |
changes: | |
name: "Check for changes" | |
runs-on: ubuntu-latest | |
outputs: | |
changes: ${{ steps.changes.outputs.src }} | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- uses: dorny/paths-filter@v3 | |
id: changes | |
with: | |
filters: | | |
python: &python | |
- 'pytensor/**/*.py' | |
- 'tests/**/*.py' | |
- 'pytensor/**/*.pyx' | |
- 'tests/**/*.pyx' | |
- '*.py' | |
src: | |
- *python | |
- 'pytensor/**/*.c' | |
- 'tests/**/*.c' | |
- 'pytensor/**/*.h' | |
- 'tests/**/*.h' | |
- '.github/workflows/*.yml' | |
- 'setup.cfg' | |
- 'requirements.txt' | |
- '.pre-commit-config.yaml' | |
style: | |
name: Check code style | |
needs: changes | |
runs-on: ubuntu-latest | |
if: ${{ needs.changes.outputs.changes == 'true' }} | |
strategy: | |
matrix: | |
python-version: ["3.10", "3.12"] | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: pre-commit/action@v3.0.1 | |
test_ubuntu: | |
name: "Test py${{ matrix.python-version }} : fast-compile ${{ matrix.fast-compile }} : float32 ${{ matrix.float32 }} : ${{ matrix.part }}" | |
needs: | |
- changes | |
- style | |
runs-on: ubuntu-latest | |
if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }} | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.10", "3.12"] | |
fast-compile: [0, 1] | |
float32: [0, 1] | |
install-numba: [0] | |
install-jax: [0] | |
install-torch: [0] | |
part: | |
- "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link" | |
- "tests --ignore=tests/tensor --ignore=tests/scan --ignore=tests/sparse" | |
- "tests/scan" | |
- "tests/sparse" | |
- "tests/tensor --ignore=tests/tensor/conv --ignore=tests/tensor/rewriting --ignore=tests/tensor/test_math.py --ignore=tests/tensor/test_basic.py --ignore=tests/tensor/test_blas.py --ignore=tests/tensor/test_math_scipy.py --ignore=tests/tensor/test_inplace.py --ignore=tests/tensor/test_elemwise.py" | |
- "tests/tensor/conv" | |
- "tests/tensor/rewriting" | |
- "tests/tensor/test_math.py" | |
- "tests/tensor/test_basic.py tests/tensor/test_inplace.py" | |
- "tests/tensor/test_blas.py tests/tensor/test_elemwise.py tests/tensor/test_math_scipy.py" | |
exclude: | |
- python-version: "3.10" | |
fast-compile: 1 | |
- python-version: "3.10" | |
float32: 1 | |
- python-version: "3.10" | |
part: "tests/tensor/test_math.py" | |
- fast-compile: 1 | |
float32: 1 | |
- part: "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link" | |
float32: 1 | |
- part: "--doctest-modules --ignore=pytensor/misc/check_duplicate_key.py pytensor --ignore=pytensor/link" | |
fast-compile: 1 | |
include: | |
- install-numba: 1 | |
python-version: "3.10" | |
fast-compile: 0 | |
float32: 0 | |
part: "tests/link/numba" | |
- install-numba: 1 | |
python-version: "3.12" | |
fast-compile: 0 | |
float32: 0 | |
part: "tests/link/numba" | |
- install-jax: 1 | |
python-version: "3.10" | |
fast-compile: 0 | |
float32: 0 | |
part: "tests/link/jax" | |
- install-jax: 1 | |
python-version: "3.12" | |
fast-compile: 0 | |
float32: 0 | |
part: "tests/link/jax" | |
- install-torch: 1 | |
python-version: "3.10" | |
fast-compile: 0 | |
float32: 0 | |
part: "tests/link/pytorch" | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-name: pytensor-test | |
micromamba-version: "1.5.10-0" # until https://github.com/mamba-org/setup-micromamba/issues/225 is resolved | |
init-shell: bash | |
post-cleanup: "all" | |
create-args: python=${{ matrix.python-version }} | |
- name: Create matrix id | |
id: matrix-id | |
env: | |
MATRIX_CONTEXT: ${{ toJson(matrix) }} | |
run: | | |
echo $MATRIX_CONTEXT | |
export MATRIX_ID=`echo $MATRIX_CONTEXT | md5sum | cut -c 1-32` | |
echo $MATRIX_ID | |
echo "id=$MATRIX_ID" >> $GITHUB_OUTPUT | |
- name: Install dependencies | |
shell: micromamba-shell {0} | |
run: | | |
micromamba install --yes -q "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service graphviz cython pytest coverage pytest-cov pytest-benchmark pytest-mock | |
if [[ $INSTALL_NUMBA == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" "numba>=0.57"; fi | |
if [[ $INSTALL_JAX == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" jax jaxlib numpyro && pip install tensorflow-probability; fi | |
if [[ $INSTALL_TORCH == "1" ]]; then micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" pytorch pytorch-cuda=12.1 "mkl<=2024.0" -c pytorch -c nvidia; fi | |
pip install pytest-sphinx | |
pip install -e ./ | |
micromamba list && pip freeze | |
python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))' | |
python -c 'import pytensor; assert pytensor.config.blas__ldflags != "", "Blas flags are empty"' | |
env: | |
PYTHON_VERSION: ${{ matrix.python-version }} | |
INSTALL_NUMBA: ${{ matrix.install-numba }} | |
INSTALL_JAX: ${{ matrix.install-jax }} | |
INSTALL_TORCH: ${{ matrix.install-torch}} | |
- name: Run tests | |
shell: micromamba-shell {0} | |
run: | | |
if [[ $FAST_COMPILE == "1" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,mode=FAST_COMPILE; fi | |
if [[ $FLOAT32 == "1" ]]; then export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,floatX=float32; fi | |
export PYTENSOR_FLAGS=$PYTENSOR_FLAGS,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe | |
python -m pytest -r A --verbose --runslow --durations=50 --cov=pytensor/ --cov-report=xml:coverage/coverage-${MATRIX_ID}.xml --no-cov-on-fail $PART --benchmark-skip | |
env: | |
MATRIX_ID: ${{ steps.matrix-id.outputs.id }} | |
MKL_THREADING_LAYER: GNU | |
MKL_NUM_THREADS: 1 | |
OMP_NUM_THREADS: 1 | |
PART: ${{ matrix.part }} | |
FAST_COMPILE: ${{ matrix.fast-compile }} | |
FLOAT32: ${{ matrix.float32 }} | |
- name: Upload coverage file | |
uses: actions/upload-artifact@v4 | |
with: | |
name: coverage-${{ steps.matrix-id.outputs.id }} | |
path: coverage/coverage-${{ steps.matrix-id.outputs.id }}.xml | |
benchmarks: | |
name: "Benchmarks" | |
needs: | |
- changes | |
- style | |
runs-on: ubuntu-latest | |
if: ${{ needs.changes.outputs.changes == 'true' && needs.style.result == 'success' }} | |
strategy: | |
fail-fast: false | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python 3.10 | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-name: pytensor-test | |
micromamba-version: "1.5.10-0" # until https://github.com/mamba-org/setup-micromamba/issues/225 is resolved | |
init-shell: bash | |
post-cleanup: "all" | |
- name: Install dependencies | |
shell: micromamba-shell {0} | |
run: | | |
micromamba install --yes -q -c conda-forge "python~=${PYTHON_VERSION}=*_cpython" mkl numpy scipy pip mkl-service cython pytest "numba>=0.57" jax jaxlib pytest-benchmark | |
pip install -e ./ | |
micromamba list && pip freeze | |
python -c 'import pytensor; print(pytensor.config.__str__(print_doc=False))' | |
python -c 'import pytensor; assert pytensor.config.blas__ldflags != "", "Blas flags are empty"' | |
env: | |
PYTHON_VERSION: 3.10 | |
- name: Download previous benchmark data | |
uses: actions/cache@v4 | |
with: | |
path: ./cache | |
key: ${{ runner.os }}-benchmark | |
- name: Run benchmarks | |
shell: micromamba-shell {0} | |
run: | | |
export PYTENSOR_FLAGS=mode=FAST_COMPILE,warn__ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise,gcc__cxxflags=-pipe | |
python -m pytest --runslow --benchmark-only --benchmark-json output.json | |
- name: Store benchmark result | |
uses: benchmark-action/github-action-benchmark@v1 | |
with: | |
name: Python Benchmark with pytest-benchmark | |
tool: "pytest" | |
output-file-path: output.json | |
external-data-json-path: ./cache/benchmark-data.json | |
alert-threshold: "200%" | |
github-token: ${{ secrets.GITHUB_TOKEN }} | |
comment-on-alert: false | |
fail-on-alert: false | |
auto-push: false | |
all-checks: | |
if: ${{ always() }} | |
runs-on: ubuntu-latest | |
name: "All tests" | |
needs: [changes, style, test_ubuntu] | |
steps: | |
- name: Check build matrix status | |
if: ${{ needs.changes.outputs.changes == 'true' && (needs.style.result != 'success' || needs.test_ubuntu.result != 'success') }} | |
run: exit 1 | |
upload-coverage: | |
runs-on: ubuntu-latest | |
name: "Upload coverage" | |
needs: [changes, all-checks] | |
if: ${{ needs.changes.outputs.changes == 'true' && needs.all-checks.result == 'success' }} | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.12" | |
- name: Install dependencies | |
run: | | |
python -m pip install -U coverage>=5.1 coveralls | |
- name: Download coverage file | |
uses: actions/download-artifact@v4 | |
with: | |
pattern: coverage-* | |
path: coverage | |
merge-multiple: true | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v4 | |
with: | |
directory: ./coverage/ | |
fail_ci_if_error: true | |
token: ${{ secrets.CODECOV_TOKEN }} | |