Create github-actions.yml #73
Workflow file for this run
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| on: push | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| services: | |
| postgres: | |
| image: postgres:latest | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: github_actions | |
| ports: | |
| - 5432:5432 | |
| # needed because the postgres container does not provide a healthcheck | |
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| pip install pip==19.3.1 | |
| pip install --force-reinstall 'setuptools<58.0.0' | |
| pip install -r requirements.txt | |
| pip install -r requirements-toil.txt | |
| #python manage.py migrate | |
| - name: Run migrations | |
| run: python manage.py migrate | |
| - name: Run test | |
| #run: python manage.py test | |
| run: | | |
| coverage run --source='.' manage.py test | |
| coverage report -m --fail-under=75 | |
| - name: Run flake8 | |
| uses: suo/flake8-github-action@releases/v1 | |
| with: | |
| checkName: 'build' # NOTE: this needs to be the same as the job name | |
| env: | |
| #database env variables | |
| RIDGEBACK_DB_NAME: github_actions | |
| RIDGEBACK_DB_PASSWORD: postgres | |
| RIDGEBACK_DB_USERNAME: postgres | |
| #lsf env variables | |
| RIDGEBACK_LSF_WALLTIME: 10:00 | |
| RIDGEBACK_LSF_SLA: SLA | |
| #celery env variables | |
| CELERY_LOG_PATH: /sample_path | |
| CELERY_PID_PATH: /sample_path | |
| CELERY_BEAT_SCHEDULE_PATH: /sample_path | |
| #general env variables | |
| SINGULARITY_PATH: /sample_singularity | |
| RIDGEBACK_VENV: /sample_path | |
| RIDGEBACK_PATH: /sample_path | |
| RIDGEBACK_PORT: 4009 | |
| #general env variables | |
| RIDGEBACK_DEFAULT_QUEUE: sample_queue | |
| RIDGEBACK_RABBITMQ_USERNAME: sample_username | |
| RIDGEBACK_RABBITMQ_PASSWORD: sample_password | |
| #pipeline env variables | |
| ARGOS_JOB_STORE_ROOT: /sample_path | |
| ARGOS_WORK_DIR_ROOT: /sample_path | |
| ARGOS_TMP_DIR_ROOT: /sample_path | |
| TEMPO_JOB_STORE_ROOT: /sample_path | |
| TEMPO_WORK_DIR_ROOT: /sample_path | |
| TEMPO_TMP_DIR_ROOT: /sample_path | |
| ACCESS_JOB_STORE_ROOT: /sample_path | |
| ACCESS_WORK_DIR_ROOT: /sample_path | |
| ACCESS_TMP_DIR_ROOT: /sample_path | |
| CMO_CH_JOB_STORE_ROOT: /sample_path | |
| CMO_CH_WORK_DIR_ROOT: /sample_path | |
| CMO_CH_TMP_DIR_ROOT: /sample_path | |
| ACCESS_HEME_JOB_STORE_ROOT: /sample_path | |
| ACCESS_HEME_WORK_DIR_ROOT: /sample_path | |
| ACCESS_HEME_TMP_DIR_ROOT: /sample_path | |
| DEFAULT_JOB_STORE_ROOT: /sample_path | |
| DEFAULT_WORK_DIR_ROOT: /sample_path | |
| DEFAULT_TMP_DIR_ROOT: /sample_path |