pytest_conda_linux_image.yml

name: CPU PyTest in Conda Dev/Work Branch Image

on:
  push:
    branches:
      - 'dev'
      - 'work'
    paths-ignore:
      - '.github/workflows/**'
      - 'docs/**'

jobs:
  build-linux-and-start-pytest:
    runs-on: cpu
    steps:
      - uses: actions/checkout@v3
    #   - name: Add conda to system path
    #     run: |
    #       # $CONDA_PREFIX is an environment variable pointing to the root of the miniconda directory
    #       echo $CONDA_PREFIX/bin >> $GITHUB_PATH
      - name: Install dependencies
        run: |
          echo "use conda in $(which conda)"
          conda env update --file tests/workflows_conf/environment_linux_py38.yml --name test_image -q
      - name: Activate conda enviroment
        run: |
          echo "use conda in $(which conda)"
          conda init --all
          source ~/.bashrc
          conda activate test_image
          echo "use pip in $(which pip)"
          echo "use python in $(which python)"
      - name: Install Stereopy dependencies
        run: |
          echo "use conda in $(which conda)"
          conda init --all
          source ~/.bashrc
          conda activate test_image
          echo "use pip in $(which pip)"
          echo "use python in $(which python)"

          pip install -r requirements.txt -q
          # TODO temporarily not install `tests/extra_requirements.txt`
          pip install -r tests/extra_requirements.txt -q
          pip install -r tests/image_requirements.txt -q
          pip install pathlib -q

          python setup.py develop
      - name: Show Env Info
        run: |
          echo "use conda in $(which conda)"
          conda init --all
          source ~/.bashrc          
          conda activate test_image
          echo "use pip in $(which pip)"
          echo "use python in $(which python)"
          conda info
          env
          pip list
      - name: Test with pytest
        run: |
          echo "use conda in $(which conda)"
          conda init --all
          source ~/.bashrc
          conda activate test_image
          echo "use python in $(which python)"
          python -m pytest -m "cell_cut_env" --durations=0