Add variant related models #497
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: ReSDK CI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - "[0-9]+.[0-9]+.[0-9]+*" | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| unittest: | |
| runs-on: arc-runner | |
| env: | |
| TOX_COMMAND: "tox --skip-missing-interpreters false" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| toxenv: [py38, py39, py310, py311, py312, docs, linters, package] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Assert PR is up-to-date | |
| if: github.event_name == 'pull_request' | |
| run: | | |
| git fetch origin ${{ github.base_ref }} | |
| git fetch origin HEAD --unshallow | |
| git_change_target_merge_base=$(git merge-base HEAD origin/${{ github.base_ref }}) | |
| git_change_target_sha=$(git rev-parse origin/${{ github.base_ref }}) | |
| if [[ "${git_change_target_merge_base}" != "${git_change_target_sha}" ]]; then | |
| echo 'Pull request is not up-to-date!' | |
| echo "Please, rebase your pull request on top of '${{ github.base_ref }}' (commit: ${git_change_target_sha})." | |
| exit 1 | |
| fi | |
| - name: Run Tests | |
| run: > | |
| ${{ env.TOX_COMMAND }} -e ${{ matrix.toxenv }} | |
| e2e: | |
| runs-on: arc-runner | |
| needs: unittest | |
| env: | |
| GENESIS_POSTGRESQL_NAME: genialis-base | |
| GENESIS_POSTGRESQL_USER: genialis-base | |
| GENESIS_POSTGRESQL_PASSWORD: genialis-base | |
| GENESIS_POSTGRESQL_PORT: 55434 | |
| GENESIS_REDIS_PORT: 56381 | |
| GENESIS_RESDK_PATH: ".." | |
| GENESIS_REST_THROTTLING: '{"login": "100000/hour", "credentials": "100000/hour", "email": "100000/hour"}' | |
| services: | |
| postgres: | |
| image: public.ecr.aws/docker/library/postgres:14 | |
| env: | |
| POSTGRES_USER: genialis-base | |
| POSTGRES_DB: genialis-base | |
| POSTGRES_PASSWORD: genialis-base | |
| ports: | |
| - 55434:5432 | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| redis: | |
| image: public.ecr.aws/docker/library/redis:7-alpine | |
| ports: | |
| - 56381:6379 | |
| options: >- | |
| --health-cmd "redis-cli ping" | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| steps: | |
| - name: Checkout resolwe-bio-py | |
| uses: actions/checkout@v4 | |
| - name: Checkout genialis-base | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: genialis/genialis-base | |
| path: genialis-base | |
| ssh-key: ${{ secrets.GHA_SSH_PRIVATE_KEY_GENIALIS_DEPLOY }} | |
| - name: Run tests | |
| run: | | |
| cd genialis-base | |
| # Prepare frontend configuration | |
| mkdir -p frontend/genjs/schema | |
| echo '{}' > frontend/genjs/schema/configuration.json | |
| # Make sure `python` refers to the tox environment's Python | |
| export PATH=`pwd`/.tox/py310-e2e-resdk/bin:$PATH | |
| tox --skip-missing-interpreters false -e py310-e2e-resdk | |
| build: | |
| runs-on: arc-runner | |
| needs: [unittest, e2e] | |
| if: startsWith(github.ref, 'refs/tags') | |
| env: | |
| PYTHON: "python3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install build | |
| run: ${{ env.PYTHON }} -m pip install --user build | |
| - name: Build a binary wheel and a source tarball | |
| run: ${{ env.PYTHON }} -m build --sdist --wheel --outdir dist/ . | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| file: .coverage | |
| - name: Publish distribution to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1.8 | |
| with: | |
| password: ${{ secrets.pypi_password }} |