CI/MAINT: add a CI job with ASan and UBSan on macOS, fix one UB issue #471
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - v1.** | |
| pull_request: | |
| branches: | |
| - main | |
| - v1.** | |
| concurrency: | |
| # avoid duplicate runs on both pushes and PRs | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| # Coloured output for GitHub Actions | |
| FORCE_COLOR: 3 | |
| # Some common environment variables for both GNU/Linux and macOS jobs | |
| MPLBACKEND: Agg | |
| CYTHON_TRACE: 1 | |
| CYTHONSPEC: cython | |
| NUMPY_MIN: numpy==1.26.4 | |
| CYTHON_MIN: cython==3.1.3 | |
| jobs: | |
| test_pywavelets_linux: | |
| name: ${{ matrix.runs-on }}-cp${{ matrix.python-version }}-${{ matrix.OPTIONS_NAME }} | |
| runs-on: ${{ matrix.runs-on }} | |
| strategy: | |
| # Ensure that a wheel builder finishes even if another fails | |
| fail-fast: false | |
| matrix: | |
| runs-on: [ubuntu-latest] # Arm runner tested separately, see below | |
| python-version: ["3.12", "3.14"] | |
| MINIMUM_REQUIREMENTS: [0] | |
| USE_SDIST: [0] | |
| REFGUIDE_CHECK: [1] | |
| PIP_FLAGS: [""] | |
| OPTIONS_NAME: ["default"] | |
| include: | |
| # Linux arm64 | |
| - runs-on: ubuntu-22.04-arm | |
| python-version: "3.14" | |
| # Linux amd64 | |
| - runs-on: ubuntu-latest | |
| python-version: "3.12" | |
| MINIMUM_REQUIREMENTS: 1 | |
| OPTIONS_NAME: "minimum-req" | |
| - runs-on: ubuntu-latest | |
| python-version: "3.12" | |
| - runs-on: ubuntu-latest | |
| python-version: "3.14" | |
| USE_SDIST: 1 | |
| OPTIONS_NAME: "install-from-sdist" | |
| - runs-on: ubuntu-latest | |
| python-version: "3.14" | |
| PIP_FLAGS: "--pre" | |
| OPTIONS_NAME: "pre-releases" | |
| - runs-on: ubuntu-latest | |
| python-version: "3.14" | |
| OPTIONS_NAME: "editable-install" | |
| steps: | |
| - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v4.1.2 | |
| - uses: actions/setup-python@2e3e4b15a884dc73a63f962bff250a855150a234 # v5.5.0 | |
| with: | |
| python-version: ${{ matrix.python-version}} | |
| allow-prereleases: true | |
| - name: Build package | |
| env: | |
| VERSION: ${{ matrix.python-version }} | |
| MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }} | |
| PIP_FLAGS: ${{ matrix.PIP_FLAGS }} | |
| USE_SDIST: ${{ matrix.USE_SDIST }} | |
| REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }} | |
| OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }} | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| # ccache -s | |
| which python | |
| python --version | |
| # sudo apt-get install libatlas-base-dev | |
| pip install --upgrade pip build | |
| # Set numpy version first, other packages link against it | |
| if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then | |
| pip install ${CYTHON_MIN} | |
| pip install ${NUMPY_MIN} | |
| else | |
| pip install ${PIP_FLAGS} cython | |
| pip install ${PIP_FLAGS} numpy | |
| fi | |
| pip install ${PIP_FLAGS} matplotlib pytest | |
| set -o pipefail | |
| if [ "${USE_SDIST}" == "1" ]; then | |
| python -m build --sdist | |
| pip install dist/pyw*.tar.gz -v | |
| elif [ "${REFGUIDE_CHECK}" == "1" ]; then | |
| pip install sphinx numpydoc scipy-doctest | |
| pip install . -v | |
| else | |
| pip install . -v | |
| fi | |
| if [ "${OPTIONS_NAME}" == "editable-install" ]; then | |
| pip install meson-python>=0.16.0 matplotlib pytest ninja | |
| pip install -e . --no-build-isolation | |
| fi | |
| - name: Run tests | |
| env: | |
| USE_SDIST: ${{ matrix.USE_SDIST }} | |
| REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }} | |
| OPTIONS_NAME: ${{ matrix.OPTIONS_NAME }} | |
| run: | | |
| set -o pipefail | |
| # Move out of source directory to avoid finding local pywt | |
| pushd demo | |
| if [ "${USE_SDIST}" == "1" ]; then | |
| pytest --pyargs pywt | |
| python ../pywt/tests/test_doc.py | |
| elif [ "${REFGUIDE_CHECK}" == "1" ]; then | |
| # doctest docstrings | |
| pytest --doctest-modules --pyargs pywt -v --doctest-collect=api | |
| # Run Sphinx HTML docs builder, converting warnings to errors | |
| # Move back out of demo/ to root directory | |
| cd .. | |
| pip install -r util/readthedocs/requirements.txt | |
| sphinx-build -b html -W --keep-going -d _build/doctrees doc/source doc/build | |
| else | |
| pytest --pyargs pywt | |
| fi | |
| popd | |
| test_pywavelets_linux_free_threaded: | |
| name: linux-cp${{ matrix.python-version }}-default | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.13t", "3.14t"] | |
| steps: | |
| - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v4.1.2 | |
| - uses: actions/setup-python@2e3e4b15a884dc73a63f962bff250a855150a234 # v5.5.0 | |
| with: | |
| python-version: ${{ matrix.python-version}} | |
| - name: Build package | |
| run: | | |
| pip install --upgrade pip build | |
| pip install cython numpy meson-python ninja pytest | |
| pip install . -v --no-build-isolation | |
| - name: Run tests | |
| run: | | |
| # Move out of source directory to avoid finding local pywt | |
| cd demo | |
| pytest --pyargs pywt | |
| test_pywavelets_macos: | |
| name: macos-cp${{ matrix.python-version }}-${{ matrix.OPTIONS_NAME }} | |
| runs-on: macos-latest | |
| strategy: | |
| # Ensure that a wheel builder finishes even if another fails | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.12", "3.14"] | |
| MINIMUM_REQUIREMENTS: [0] | |
| USE_SDIST: [0] | |
| REFGUIDE_CHECK: [0] | |
| PIP_FLAGS: [""] | |
| OPTIONS_NAME: ["default"] | |
| include: | |
| - python-version: "3.12" | |
| MINIMUM_REQUIREMENTS: 1 | |
| OPTIONS_NAME: "osx-minimum-req" | |
| - python-version: "3.14" | |
| PIP_FLAGS: "--pre" | |
| OPTIONS_NAME: "pre-releases" | |
| steps: | |
| - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v4.1.2 | |
| - uses: actions/setup-python@2e3e4b15a884dc73a63f962bff250a855150a234 # v5.5.0 | |
| with: | |
| python-version: ${{ matrix.python-version}} | |
| allow-prereleases: true | |
| - name: Build package | |
| env: | |
| VERSION: ${{ matrix.python-version }} | |
| MINIMUM_REQUIREMENTS: ${{ matrix.MINIMUM_REQUIREMENTS }} | |
| PIP_FLAGS: ${{ matrix.PIP_FLAGS }} | |
| USE_SDIST: ${{ matrix.USE_SDIST }} | |
| REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }} | |
| CC: /usr/bin/clang | |
| CXX: /usr/bin/clang++ | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| which python | |
| python --version | |
| pip install --upgrade pip build | |
| # Set numpy version first, other packages link against it | |
| if [ "${MINIMUM_REQUIREMENTS}" == "1" ]; then | |
| pip install ${CYTHON_MIN} ${NUMPY_MIN} | |
| else | |
| pip install ${PIP_FLAGS} cython numpy | |
| fi | |
| pip install ${PIP_FLAGS} matplotlib pytest | |
| set -o pipefail | |
| if [ "${USE_SDIST}" == "1" ]; then | |
| python -m build --sdist | |
| pip install pywavelets* -v | |
| elif [ "${REFGUIDE_CHECK}" == "1" ]; then | |
| pip install sphinx numpydoc scipy-doctest | |
| pip install . -v | |
| else | |
| pip install . -v | |
| fi | |
| - name: Run tests | |
| env: | |
| PIP_FLAGS: ${{ matrix.PIP_FLAGS }} | |
| USE_SDIST: ${{ matrix.USE_SDIST }} | |
| REFGUIDE_CHECK: ${{ matrix.REFGUIDE_CHECK }} | |
| run: | | |
| # Move out of source directory to avoid finding local pywt | |
| pushd demo | |
| if [ "${USE_SDIST}" == "1" ]; then | |
| pytest --pyargs pywt | |
| python ../pywt/tests/test_doc.py | |
| elif [ "${REFGUIDE_CHECK}" == "1" ]; then | |
| # doctests docstrings | |
| pytest --doctest-modules --doctest-only-doctests=true --pyargs pywt -v --doctest-collect=api | |
| pytest --doctest-modules --doctest-only-doctests=true --pyargs pywt.data -v | |
| else | |
| pytest --pyargs pywt | |
| fi | |
| popd | |
| clang_ASan_UBSan: | |
| name: Test under ASan and UBSan | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 | |
| with: | |
| submodules: recursive | |
| fetch-tags: true | |
| persist-credentials: false | |
| - name: Set up pyenv | |
| run: | | |
| git clone https://github.com/pyenv/pyenv.git "$HOME/.pyenv" | |
| PYENV_ROOT="$HOME/.pyenv" | |
| PYENV_BIN="$PYENV_ROOT/bin" | |
| PYENV_SHIMS="$PYENV_ROOT/shims" | |
| echo "$PYENV_BIN" >> $GITHUB_PATH | |
| echo "$PYENV_SHIMS" >> $GITHUB_PATH | |
| echo "PYENV_ROOT=$PYENV_ROOT" >> $GITHUB_ENV | |
| - name: Set up LLVM | |
| run: | | |
| brew install llvm@19 | |
| LLVM_PREFIX=$(brew --prefix llvm@19) | |
| echo CC="$LLVM_PREFIX/bin/clang" >> $GITHUB_ENV | |
| echo CXX="$LLVM_PREFIX/bin/clang++" >> $GITHUB_ENV | |
| echo LDFLAGS="-L$LLVM_PREFIX/lib" >> $GITHUB_ENV | |
| echo CPPFLAGS="-I$LLVM_PREFIX/include" >> $GITHUB_ENV | |
| - name: Build Python with AddressSanitizer | |
| run: | | |
| CONFIGURE_OPTS="--with-address-sanitizer" pyenv install 3.14 | |
| pyenv global 3.14 | |
| - name: Install NumPy dependencies from PyPI | |
| run: | | |
| pip install meson-python ninja cython | |
| - name: Build NumPy with ASan | |
| run: | | |
| pip install numpy --no-binary numpy --no-build-isolation -Csetup-args="-Db_sanitize=address" -v | |
| - name: Install dependencies from PyPI | |
| run: | | |
| pip install spin pytest pytest-timeout | |
| - name: Build PyWavelets with ASan and UBSan | |
| run: | | |
| export CFLAGS=-fno-sanitize=function # suppressed upstream, see cython#7437 | |
| spin build -- -Db_sanitize=address,undefined -Db_lundef=false | |
| - name: Test | |
| run: | | |
| # pass -s to pytest to see ASAN errors and warnings, otherwise pytest captures them | |
| ASAN_OPTIONS=detect_leaks=0:symbolize=1:strict_init_order=true:allocator_may_return_null=1:use_sigaltstack=0 \ | |
| UBSAN_OPTIONS=halt_on_error=1 \ | |
| spin test -- -v -s --timeout=600 --durations=10 |