htcondor.yaml

name: Test SnakemakeProfiles/htcondor
on: [push, pull_request]

jobs:
  htcondortest:
    name: Test htcondor profile in docker containers
    runs-on: ubuntu-latest
    timeout-minutes: 30
    strategy:
      matrix:
        snakemake_image:
          - "quay.io/biocontainers/snakemake:7.32.4--hdfd78af_1"
          - "quay.io/biocontainers/snakemake:8.9.0--hdfd78af_0"
        htcondor_image:
          - "htcondor/mini:23.5.2-el8"

    steps:
      - uses: actions/checkout@v2
      - run: mkdir -p ~/image-cache
      - name: cache-conda
        uses: actions/cache@v4
        env:
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('test-environment.yml') }}

      - uses: actions/cache@v4
        id: cache-images
        env:
          CACHE_NUMBER: 0
        with:
          path: ~/image-cache
          key: image-cache-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ matrix.snakemake_image }}-${{ matrix.htcondor_image }}

      - name: install miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          channels: conda-forge,bioconda,defaults
          channel-priority: true
          environment-file: test-environment.yml

      - name: docker swarm init
        run: docker swarm init

      - if: steps.cache-images.outputs.cache-hit == 'true'
        run: docker load -i ~/image-cache/snakemake.tar

      - if: steps.cache-images.outputs.cache-hit == 'true'
        run: docker load -i ~/image-cache/htcondor.tar

      - name: docker deploy
        shell: bash -l {0}
        env:
          DOCKER_COMPOSE: "tests/docker-compose.yaml"
          SNAKEMAKE_IMAGE: ${{ matrix.snakemake_image }}
          HTCONDOR_IMAGE: ${{ matrix.htcondor_image }}
        run: ./tests/deploystack.sh

      - if: steps.cache-images.outputs.cache-hit != 'true'
        run: docker save -o ~/image-cache/snakemake.tar ${{ matrix.snakemake_image }}

      - if: steps.cache-images.outputs.cache-hit != 'true'
        run: docker save -o ~/image-cache/htcondor.tar ${{ matrix.htcondor_image }}

      - name: run tests
        shell: bash -l {0}
        run: |
          pytest -v -s tests/test_cookie.py
          pytest -v -s tests/test_submit.py