python-dependency-variation.yml

name: TileDB-SOMA Python CI with varying dependencies

on:
  push:
    branches:
      - main
      - 'release-*'
  pull_request:
    paths-ignore:
      - '**.md'
      - 'apis/r/**'
      - 'docs/**'
  workflow_dispatch:

jobs:
  ci:
    strategy:
      fail-fast: false
      matrix:
        include:

          - name: ensemble1
            os: ubuntu-24.04
            python_version: 3.9
            cc: gcc-13
            cxx: g++-13

            anndata: 0.10.8
            numba:   0.60.0
            numpy:   1.25.0
            pandas:  1.5.3
            pyarrow: 11.0.0
            scanpy:  1.9.8
            scipy:   1.13.1

          - name: ensemble2
            os: ubuntu-24.04
            python_version: 3.9
            cc: gcc-13
            cxx: g++-13

            anndata:  0.10.9
            numba:    0.60.0
            numpy:    1.25.0
            pandas:   1.5.3
            pyarrow:  12.0.1
            scanpy:   1.10.3
            scipy:    1.13.1

    runs-on: ${{ matrix.os }}

    steps:
      - uses: actions/checkout@v4

      - name: Show matrix OS
        run: echo "matrix.os:" ${{ matrix.os }}

      - name: Linux CPU info
        if: ${{ matrix.os == 'ubuntu-24.04' }}
        run: cat /proc/cpuinfo

      - name: MacOS CPU info
        if: ${{ matrix.os == 'macOS-latest' }}
        run: sysctl -a | grep cpu

      - name: Select XCode version
        if: startsWith(matrix.os, 'macos')
        uses: maxim-lobanov/setup-xcode@v1
        with:
          xcode-version: '15.4'

      - name: Set up Python ${{ matrix.python_version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python_version }}
          cache: pip
          cache-dependency-path: ./apis/python/setup.py

      - name: Show XCode version
        run: clang --version

      - name: Check out TileDB-SOMA
        uses: actions/checkout@v4
        with:
          fetch-depth: 0  # ensure we get all tags to inform package version determination

      - name: Log pip dependencies
        run: pip list

      - name: Install tiledbsoma
        run: pip -v install -e apis/python[all] -C "--build-option=--no-tiledb-deprecated"
        env:
          CC: ${{ matrix.cc }}
          CXX: ${{ matrix.cxx }}

      - name: Install dependencies
        run: pip install --prefer-binary pytest typeguard

      - name: Install variant dependencies
        run: |
          pip install  \
            anndata==${{matrix.anndata}} \
            numba==${{matrix.numba}} \
            numpy==${{matrix.numpy}} \
            pandas==${{matrix.pandas}} \
            pyarrow==${{matrix.pyarrow}} \
            scanpy==${{matrix.scanpy}} \
            scipy==${{matrix.scipy}}

      - name: Show package versions
        run: python scripts/show-versions.py

      - name: Obtain test data
        shell: bash
        run: |
          cd test
          rm -rf soco
          tar zxf soco.tgz
          cd ..

      - name: Run pytests for Python
        shell: bash
        run: python -m pytest apis/python/tests/*.py -v --durations=20 --maxfail=50