monalisa-python/.github/workflows/ci.yml at main · MattechLab/monalisa-python · GitHub

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name: CI

on:
  push:
    branches: [main]
  pull_request:
  workflow_dispatch:
    inputs:
      parity:
        description: "Record MATLAB golden calls (static2d) and replay them"
        type: boolean
        default: false

jobs:
  test:
    name: Lint and unit tests (no MATLAB)
    runs-on: ubuntu-latest
    # In the official Python image (Debian 13, as the Dockerfile), not on the runner itself: since
    # 2026-11-09 apt-get fails on the GitHub runners (Ubuntu 26.04 cannot resolve the Ubuntu
    # package servers; Ubuntu 24.04 fails at the same step), while Debian's servers work.
    container: python:${{ matrix.python-version }}-slim-trixie
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.10", "3.12"]
    steps:
      # System libraries of Qt and Mesa's OpenGL (napari, dialogs) and a virtual display, as in
      # the Dockerfile.
      - name: Qt system libraries
        run: |
          apt-get update -q
          apt-get install -y -q --no-install-recommends \
            git xvfb xauth libgl1 libegl1 libegl-mesa0 libopengl0 libglx-mesa0 libgl1-mesa-dri \
            libglib2.0-0t64 libfontconfig1 libfreetype6 libdbus-1-3 \
            libx11-6 libx11-xcb1 libxext6 libxrender1 libxi6 libxkbcommon0 libxkbcommon-x11-0 \
            libxcb1 libxcb-cursor0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 \
            libxcb-render-util0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 \
            libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1
      - uses: actions/checkout@v5
      - run: pip install -e ".[dev]" scikit-image h5py
      - run: ruff check src tests examples tools demo
      - run: xvfb-run -a pytest tests/unit -q

  test-macos-windows:
    name: Unit tests (${{ matrix.os }}, pip install as in the README)
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macos-latest, windows-latest]
    steps:
      - uses: actions/checkout@v5
      - uses: actions/setup-python@v6
        with:
          python-version: "3.12"
      # pytest-github-actions-annotate-failures: each failing test becomes an annotation of the run
      # (its message is readable on the run page and through the API, unlike the log)
      - run: pip install -e ".[dev,io]" scikit-image pytest-github-actions-annotate-failures
      # The napari viewer tests need OpenGL, which these runners do not offer to napari (Windows:
      # GLError on the canvas; macOS: crash): skipped here, run by the Linux job. Two worker
      # processes (-n 2): a test that crashes Python is reported as that test's failure.
      - run: pytest tests/unit -q -rfE --tb=short -n 2
        env:
          MONALISA_TESTS_NO_OPENGL: "1"

  parity:
    name: MATLAB parity (static2d)
    if: github.event_name == 'workflow_dispatch' && inputs.parity
    runs-on: ubuntu-latest
    env:
      UPSTREAM_COMMIT: 0cb5cf93c699870bcd93a00b2e2cd787bef73fcc
    steps:
      - uses: actions/checkout@v5
      - uses: actions/checkout@v5
        with:
          repository: MattechLab/monalisa
          ref: ${{ env.UPSTREAM_COMMIT }}
          path: upstream
      - uses: matlab-actions/setup-matlab@v2
        with:
          products: Image_Processing_Toolbox Statistics_and_Machine_Learning_Toolbox
      - name: Compile upstream MEX files
        uses: matlab-actions/run-command@v2
        with:
          command: addpath(genpath('upstream/src')); compile_mex_for_monalisa
      - name: Record golden calls
        uses: matlab-actions/run-command@v2
        with:
          command: addpath('tools/matlab_capture'); run_capture('static2d', fullfile(pwd,'fixtures','matlab'), fullfile(pwd,'upstream'), 'maxBytes', 20e6)
      - uses: actions/setup-python@v6
        with:
          python-version: "3.12"
      - run: pip install -e ".[dev]" scikit-image h5py
      - run: pytest tests/parity -q -n auto