villa/.github/workflows/test-vesuvius.yml at main · ScrollPrize/villa · GitHub

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name: Test vesuvius Python

on:
  pull_request:
    paths:
      - 'vesuvius/**'
      - 'lasagna/**'
      # Local source dependencies installed by uv sync --extra all.
      - 'volume-cartographer/**'
      - 'vc_object_store/**'
      - 'vc_reader/**'
      - '.github/workflows/test-vesuvius.yml'

jobs:
  test-vesuvius-python:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
            # Limit the test matrix to ubuntu-latest for now, as other platforms may not
            # support all dependencies yet.  Extend this list once the build scripts
            # for macOS and Windows are confirmed.
            os: [blacksmith-4vcpu-ubuntu-2404]
            zarr: ['2.18.7', '3.2.1']
    defaults:
      run:
        shell: bash
        working-directory: ./vesuvius

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Install native build dependencies on Linux
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          # Native dependency closure for the Python-only scikit-build
          # configurations of volume-cartographer (apps, UI tracer, flatboi,
          # tests: OFF) and vc_object_store (tools: OFF).
          # qt6-base-dev: utils links Qt6::Core (SFTP remote access, #1941).
          sudo apt-get install -y --no-install-recommends \
            build-essential \
            curl \
            git \
            libblosc-dev \
            libboost-dev \
            libceres-dev \
            libcurl4-openssl-dev \
            libeigen3-dev \
            liblz4-dev \
            libopencv-contrib-dev \
            libopencv-dev \
            libsuitesparse-dev \
            libjpeg-dev \
            libpng-dev \
            libtiff-dev \
            libzstd-dev \
            ninja-build \
            nlohmann-json3-dev \
            pkg-config \
            qt6-base-dev \
            zlib1g-dev

      - name: Install uv and restore dependency cache
        uses: astral-sh/setup-uv@v10.3.3
        with:
          enable-cache: true
          # Preserve downloaded wheels as well as built wheels; the ML stack
          # is expensive to download again. Never cache the virtualenv itself.
          prune-cache: false
          cache-suffix: vesuvius-zarr-${{ matrix.zarr }}
          # Include transitive reader sources: volume-cartographer's own uv
          # wheel cache keys do not currently cover this sibling dependency.
          cache-dependency-glob: |
            .github/workflows/test-vesuvius.yml
            vesuvius/uv.lock
            vesuvius/pyproject.toml
            volume-cartographer/pyproject.toml
            vc_object_store/pyproject.toml
            vc_reader/**
            gpu_manager/pyproject.toml
            segmentation/models/batchgeneratorsv2/pyproject.toml
            segmentation/models/arch/nnunet/pyproject.toml

      - name: Sync dependencies
        run: uv sync --extra all

      - name: Select Zarr version
        run: uv pip install "zarr==${{ matrix.zarr }}"

      - name: Run tests
        env:
          PYTHONPATH: ${{ github.workspace }}
        run: uv run --no-sync pytest tests -m "not slow and not network"