slurm.yaml

name: Test SnakemakeProfiles/slurm
env:
  SNAKEMAKE_IMAGE: quay.io/biocontainers/snakemake:7.30.1--hdfd78af_0
  SLURM_IMAGE: giovtorres/docker-centos7-slurm:20.11.8
  DOCKER_COMPOSE: tests/docker-compose.yaml

on: [push, pull_request]

jobs:
  slurmtest:
    name: Test slurm profile in docker containers
    runs-on: ubuntu-latest
    timeout-minutes: 30
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - run: mkdir -p ~/image-cache

      - name: cache conda environment
        uses: actions/cache@v3
        env:
          CACHE_NUMBER: 0
        with:
          path: ~/conda_pkgs_dir
          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('conda-linux-64.lock') }}

      - name: cache images
        uses: actions/cache@v3
        id: cache-images
        env:
          CACHE_NUMBER: 0
        with:
          path: ~/image-cache
          key: image-cache-${{ runner.os }}-${{ env.CACHE_NUMBER }}-${{ env.SNAKEMAKE_IMAGE }}-${{ env.SLURM_IMAGE }}

      - name: install miniconda
        uses: conda-incubator/setup-miniconda@v2
        with:
          miniconda-version: "latest"
          environment-file: conda-linux-64.lock
          use-only-tar-bz2: true

      - 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/slurm.tar

      - name: docker deploy
        shell: bash -l {0}
        env:
          DOCKER_COMPOSE: ${{ env.DOCKER_COMPOSE }}
          SNAKEMAKE_IMAGE: ${{ env.SNAKEMAKE_IMAGE }}
          SLURM_IMAGE: ${{ env.SLURM_IMAGE }}
        run: ./tests/deploystack.sh

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

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

      - name: run tests
        shell: bash -l {0}
        run: |
          pytest -v -s tests/test_cookie.py
          pytest -v -s tests/test_utils.py
          pytest -v -s tests/test_slurm.py --slow
          pytest -v -s tests/test_sidecar.py