test.yml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Debug some tests

on:
  workflow_dispatch:

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v2
      - name: Set up Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8
      #----------------------------------------------
      #  -----  install & configure conda
      #----------------------------------------------
      - uses: conda-incubator/setup-miniconda@v2
        with:
          python-version: 3.8
          mamba-version: "*"
          channels: conda-forge,defaults
          channel-priority: true

      - shell: bash -l {0}
        run: |
          conda info
          conda list
          conda config --show-sources
          conda config --show
          printenv | sort
      - shell: bash -l {0}
        run: |
          mamba env update -n test --file environment.yml
      - name: Create mongoDB Docker container
        run: sudo docker run -d -p 27017:27017 mongo:latest

      #----------------------------------------------
      #              run tests
      #----------------------------------------------
      - name: Run tests
        shell: bash -l {0}
        run: |
          conda info
          conda activate test
          pytest --capture=no tests/test_R.py