python-package-conda.yml

name: Python Package using Conda

on: [push]

jobs:
  build-linux:
    runs-on: ubuntu-latest
    strategy:
      max-parallel: 5
    defaults:
      run:
        shell: bash -el {0} # use default shell

    steps:

      - name: Checkout
        uses: actions/checkout@v3.5.2
        
      - name: Setup_conda_and_cache
        uses: actions/cache@v2
        env:
          # Increase this value to reset cache if etc/example-environment.yml has not changed
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key:
            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
            hashFiles('atlasenv.yml') }}
      - uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: atlasenv
          use-mamba: true
          python-version: 3.11
          mamba-version: "*"
          channels: conda-forge,bioconda,defaults
          environment-file: atlasenv.yml
          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!


      - name: Install atlas
        run: |
           echo "You are using env '$CONDA_PREFIX'"
           python -m pip install . --no-deps -vv
      - name: Test atlas
        run: |
          atlas --help
          atlas --version
      - name: Import atlas
        run: |
          python -c "from atlas import utils"

      - name: Dryrun
        run: |
          test/dryrun.sh