ci_workflow.yaml

name: run workflow with conda envs
on:
  push:
    branches: [main, dev]
  pull_request:
    branches: [main, dev]
  release:
    types: [published]
  schedule:
    - cron: '0 3 * * 3,6'
jobs:
  run-integration-tests-with-conda-install:
    name: ${{ matrix.os }} - Workflow with snakemake conda envs
    runs-on: ${{ matrix.os }}
    defaults:
      run:
        shell: bash -el {0}
    strategy:
      fail-fast: false
      matrix:
        os: [
            "ubuntu-latest",
            "macos-13",
            # "windows-latest" # rrcovNA cannot be build from source on windows-server
          ]
        python-version: ["3.10"]
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Set up Miniconda
        # ! change action https://github.com/mamba-org/setup-micromamba
        uses: conda-incubator/setup-miniconda@v3
        with:
          miniforge-variant: Mambaforge
          use-mamba: true
          channel-priority: disabled
          python-version: ${{ matrix.python-version }}
          environment-file: snakemake_env.yml
          activate-environment: snakemake
          auto-activate-base: true
      - name: inspect-conda-environment
        run: |
          conda info
          conda list
      - name: Dry-run workflow
        run: |
          cd project
          snakemake -p -c1 --configfile config/single_dev_dataset/example/config.yaml -n --use-conda
      - name: Run demo workflow (integration test)
        continue-on-error: true
        run: |
          cd project
          snakemake -p -c4 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda
      - name: Run demo workflow again (in case of installation issues)
        run: |
          cd project
          snakemake -p -c1 -k --configfile config/single_dev_dataset/example/config.yaml --use-conda