pythonpackage.yml

name: pytest

on:
  push:
  pull_request:
    types: [opened, edited, review_requested, synchronize, reopened]

jobs:
  conda-build:
    timeout-minutes: 70
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 4
      matrix:
        python-version: [3.7]

    steps:
      - uses: actions/checkout@v1
      - uses: conda-incubator/setup-miniconda@v2
        with:
          auto-update-conda: true
          python-version: ${{ matrix.python-version }}
          activate-environment: capreolus
          environment-file: environment.yml
          auto-activate-base: false
      - name: Test with pytest
        shell: bash -l {0}
        run: |
          conda activate capreolus
          # delete conda cache to avoid "No space left on device" Exception
          conda list
          conda clean --all
          conda install pytorch=1.8.1 torchvision cpuonly -c pytorch
          conda list
          # hack to force h5py version. 3.0 is not compatible with TF. 
          pip install h5py==2.10.0
          # checks every test except those marked download
          pytest -vvv

  pip-build:
    timeout-minutes: 50
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 4
      matrix:
        python-version: [3.7]

    steps:
    - uses: actions/checkout@v1
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Set up Java 11
      uses: actions/setup-java@v1
      with:
        java-version: '11'
    - name: black
      uses: lgeiger/black-action@master
      with:
        args: ". --check --config capreolus/pyproject.toml"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip==21.1.3
        # cython should be installed seperately due to a pip bug. For some reason, it tries to build pyjnius before building cython
        pip install cython
        pip install -r requirements.txt
        pip install torch==1.8.1+cu101 torchvision==0.9.1+cu101 -f https://download.pytorch.org/whl/torch_stable.html
    - name: Test with pytest
      run: |
        pip install pytest
        export PYTHONPATH=${PYTHONPATH}:/home/runner/work/capreolus/capreolus/
        # checks every test except those marked download
        python -m pytest -vvv
        
  # download:
  #   timeout-minutes: 50
  #   if: github.ref == 'refs/heads/master'
  #   runs-on: ubuntu-latest
  #   strategy:
  #     max-parallel: 4
  #     matrix:
  #       python-version: [3.7]

  #   steps:
  #   - uses: actions/checkout@v1
  #   - name: Set up Python ${{ matrix.python-version }}
  #     uses: actions/setup-python@v1
  #     with:
  #       python-version: ${{ matrix.python-version }}
  #   - name: Set up Java 11
  #     uses: actions/setup-java@v1
  #     with:
  #       java-version: '11'
  #   - name: Install dependencies
  #     run: |
  #       python -m pip install --upgrade pip
  #       # cython should be installed seperately due to a pip bug. For some reason, it tries to build pyjnius before building cython
  #       pip install cython
  #       pip install -r requirements.txt
  #       pip install torch==1.6.0+cu101 torchvision==0.7.0+cu101 -f https://download.pytorch.org/whl/torch_stable.html
  #   - name: Test downloads with pytest
  #     run: |
  #       pip install pytest
  #       export PYTHONPATH=${PYTHONPATH}:/home/runner/work/capreolus/capreolus/
  #       # checks only tests marked download
  #       python -m pytest -vvv -m download