spatialdata/.github/workflows/test.yaml at 175fbea8a7ef8937a86523dcf18fdbb67888c4d8 · scverse/spatialdata · GitHub

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name: Test

on:
    push:
        branches: [main]
        tags:
            - "v*"
    pull_request:
        branches: "*"

jobs:
    test:
        runs-on: ${{ matrix.os }}
        defaults:
            run:
                shell: bash  # bash also on windows

        strategy:
            fail-fast: false
            matrix:
                include:
                    - {os: windows-latest, python: "3.11", dask-version: "2025.12.0", name: "Dask 2025.12.0"}
                    - {os: windows-latest, python: "3.13", dask-version: "latest", name: "Dask latest"}
                    - {os: ubuntu-latest, python: "3.11", dask-version: "latest", name: "Dask latest"}
                    - {os: ubuntu-latest, python: "3.13", dask-version: "latest", name: "Dask latest"}
                    - {os: macos-latest, python: "3.11", dask-version: "latest", name: "Dask latest"}
                    - {os: macos-latest, python: "3.13", prerelease: "allow", name: "Python 3.13 (pre-release)"}
        env:
            OS: ${{ matrix.os }}
            PYTHON: ${{ matrix.python }}
            DASK_VERSION: ${{ matrix.dask-version }}
            PRERELEASE: ${{ matrix.prerelease }}

        steps:
            - uses: actions/checkout@v6
            - uses: astral-sh/setup-uv@v7
              id: setup-uv
              with:
                  version: "latest"
                  python-version: ${{ matrix.python }}
            - name: Install dependencies
              run: |
                  if [[ "${PRERELEASE}" == "allow" ]]; then
                    sed -i '' 's/requires-python.*//' pyproject.toml # otherwise uv complains that anndata requires python>=3.12 and we only do >=3.11 😱
                    uv add git+https://github.com/scverse/anndata.git
                    uv add pandas>=3.dev0
                  fi
                  if [[ -n "${DASK_VERSION}" ]]; then
                    if [[ "${DASK_VERSION}" == "latest" ]]; then
                      uv add dask
                    else
                      uv add dask==${DASK_VERSION}
                    fi
                  fi
                  uv sync --group=test
            # Start storage emulators (S3, Azure, GCS) only on Linux; Docker service containers are not available on
            # Windows/macOS runners, so tests/io/remote_storage/ is skipped there (see Test step). Remote I/O is still
            # exercised on every PR via the Ubuntu matrix jobs.
            - name: Build and start storage emulators
              if: matrix.os == 'ubuntu-latest'
              run: |
                  docker build -f tests/io/remote_storage/Dockerfile.emulators -t spatialdata-emulators .
                  docker run --rm -d --name spatialdata-emulators \
                    -p 5000:5000 -p 10000:10000 -p 4443:4443 \
                    spatialdata-emulators
            - name: Wait for emulator ports
              if: matrix.os == 'ubuntu-latest'
              run: |
                  echo "Waiting for S3 (5000), Azure (10000), GCS (4443)..."
                  python3 -c "
                  import socket, time
                  for _ in range(45):
                      try:
                          for p in (5000, 10000, 4443):
                              socket.create_connection(('127.0.0.1', p), timeout=2)
                          print('Emulators ready.')
                          break
                      except (socket.error, OSError):
                          time.sleep(2)
                  else:
                      raise SystemExit('Emulators did not become ready.')
                  "
            # On Linux, emulators run above so full suite (incl. tests/io/remote_storage/) runs. On Windows/macOS, skip remote_storage.
            - name: Test
              env:
                  MPLBACKEND: agg
                  PLATFORM: ${{ matrix.os }}
                  DISPLAY: :42
                  # gcsfs otherwise defaults to ExtendedGcsFileSystem (prod Storage Control gRPC; breaks fake-gcs-server).
                  GCSFS_EXPERIMENTAL_ZB_HNS_SUPPORT: "false"
              run: |
                  if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
                    uv run pytest --cov --color=yes --cov-report=xml
                  else
                    uv run pytest --cov --color=yes --cov-report=xml --ignore=tests/io/remote_storage/
                  fi
            - name: Upload coverage to Codecov
              uses: codecov/codecov-action@v5
              with:
                  name: coverage
                  verbose: true
              env:
                  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}