Tests workflow (PyWavelets/pywt)

The Tests workflow from PyWavelets/pywt, explained and optimized by Latchkey.

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Source: PyWavelets/pywt.github/workflows/tests.ymlLicense MITView source

What it does

This is the Tests workflow from the PyWavelets/pywt repository, a real project running GitHub Actions. It is shown here with attribution under its MIT license.

Below, Latchkey shows a faster, safer version produced by its optimization engine.

The workflow

workflow (.yml)

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@0c366fd6a839edf440554fa01a7085ccba70ac98 # 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@0c366fd6a839edf440554fa01a7085ccba70ac98 # 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@0c366fd6a839edf440554fa01a7085ccba70ac98 # 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@0c366fd6a839edf440554fa01a7085ccba70ac98 # 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

The same workflow, on Latchkey

Estimated ~20% faster on cache hits, plus fewer wasted runs and a safer supply chain. Added and changed lines are highlighted.

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:
    timeout-minutes: 30
    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: latchkey-small-arm
            python-version: "3.14"
          # Linux amd64
          - runs-on: latchkey-small
            python-version: "3.12"
            MINIMUM_REQUIREMENTS: 1
            OPTIONS_NAME: "minimum-req"
          - runs-on: latchkey-small
            python-version: "3.12"
          - runs-on: latchkey-small
            python-version: "3.14"
            USE_SDIST: 1
            OPTIONS_NAME: "install-from-sdist"
          - runs-on: latchkey-small
            python-version: "3.14"
            PIP_FLAGS: "--pre"
            OPTIONS_NAME: "pre-releases"
          - runs-on: latchkey-small
            python-version: "3.14"
            OPTIONS_NAME: "editable-install"
    steps:
      - uses: actions/checkout@0c366fd6a839edf440554fa01a7085ccba70ac98 # v4.1.2
      - uses: actions/setup-python@2e3e4b15a884dc73a63f962bff250a855150a234 # v5.5.0
        with:
          cache: 'pip'
          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:
    timeout-minutes: 30
    name: linux-cp${{ matrix.python-version }}-default
    runs-on: latchkey-small
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.13t", "3.14t"]
    steps:
      - uses: actions/checkout@0c366fd6a839edf440554fa01a7085ccba70ac98 # v4.1.2
      - uses: actions/setup-python@2e3e4b15a884dc73a63f962bff250a855150a234 # v5.5.0
        with:
          cache: 'pip'
          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:
    timeout-minutes: 30
    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@0c366fd6a839edf440554fa01a7085ccba70ac98 # v4.1.2
      - uses: actions/setup-python@2e3e4b15a884dc73a63f962bff250a855150a234 # v5.5.0
        with:
          cache: 'pip'
          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:
    timeout-minutes: 30
    name: Test under ASan and UBSan
    runs-on: macos-latest
    steps:
      - uses: actions/checkout@0c366fd6a839edf440554fa01a7085ccba70ac98 # 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

What changed

Run on Latchkey managed runners with one line (runs-on), which apply the fixes below automatically and self-heal transient failures. This example uses latchkey-small; pick the runner size that fits the job.
Cache dependency installs on the setup step so they are served from cache.
Add a job timeout so a hung step cannot burn hours of runner time.

What Latchkey heals here

This workflow has steps that commonly fail on transient issues (network, registries, flaky browsers). On Latchkey managed runners they are detected, retried, and self-healed instead of failing your build:

Dependency installs

This workflow runs 4 jobs (7 with the matrix expanded) per trigger. On Latchkey the same minutes cost up to 58% less than GitHub-hosted, with zero queue time.

Actions used in this workflow

actions/checkout actions/setup-python