build.yaml

name: CI

on:
  push:
    paths:
      - '.github/**'
      - 'wsidata/**'
      - 'tests/**'
      - 'pyproject.toml'
  pull_request:
    paths:
      - '.github/**'
      - 'wsidata/**'
      - 'tests/**'
      - 'pyproject.toml'

jobs:
  Test:
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-latest, macos-latest]
        python-version: ['3.9', '3.10', '3.11', '3.12']

    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v4
      - name: Setup Miniconda
        uses: conda-incubator/setup-miniconda@v3.0.4
        with:
          activate-environment: test-env
          python-version: ${{ matrix.python-version }}
      - name: Test project installation
        run: |
          python -m pip install --upgrade pip
          pip install .[all,dev]
          pip install torch torchstain
      - name: Install OpenSlide
        if: matrix.os != 'windows-latest'
        run: |
          conda install -c conda-forge openslide-python
      - name: Install scyjava
        run: |
          conda install -c conda-forge scyjava
      - name: Test with pytest
        run: |
          pip install pytest
          pytest tests/

#  Upload_to_test_pypi:
#    runs-on: ubuntu-latest
#    steps:
#      - uses: actions/checkout@v3
#      - name: Set up Python
#        uses: actions/setup-python@v4
#        with:
#          python-version: '3.10'
#
#      - name: Install dependencies
#        run: |
#          python -m pip install --upgrade pip
#          pip install flit
#          pip install .

#      - name: Publish to test.ipynb pypi
#        env:
#          FLIT_INDEX_URL: https://test.ipynb.pypi.org/legacy/
#          FLIT_USERNAME: ${{ secrets.PYPI_USERNAME }}
#          FLIT_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
#        run: flit publish || exit 0
#
#      - name: Publish to pypi
#        if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
#        env:
#          FLIT_INDEX_URL: https://upload.pypi.org/legacy/
#          FLIT_USERNAME: ${{ secrets.PYPI_USERNAME }}
#          FLIT_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
#        run: flit publish