Check BMT initialization daily #327
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: Check BMT initialization daily | |
| on: | |
| pull_request: | |
| schedule: | |
| - cron: '0 5 * * *' # once per day at midnight ET | |
| workflow_dispatch: | |
| # Allows you to run this workflow manually from the Actions tab | |
| types: trigger-run-check-toolkit-initialization | |
| jobs: | |
| # This workflow contains a single job called "build" | |
| build: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: [ "3.9", "3.10", "3.11" ] | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v2 | |
| name: setup python environment | |
| with: | |
| python-version: ${{ matrix.python }} | |
| # this step we remove and rebuild the poetry.lock file to ensure that the tests that follow can be run | |
| # with the latest dependencies | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install poetry | |
| rm -rf poetry.lock | |
| poetry install | |
| - name: Run bmt tests | |
| run: | | |
| make test | |
| - name: Clone KGX and install dev branch of bmt | |
| run: | | |
| cd ../ | |
| pwd | |
| git clone https://github.com/biolink/kgx.git | |
| cd kgx | |
| poetry install # this will install a different version of hdmf from the current one | |
| poetry remove bmt | |
| ls -al ../ | |
| poetry add /home/runner/work/biolink-model-toolkit/biolink-model-toolkit | |
| - name: Setup Neo4j Docker | |
| run: | | |
| cd ../ | |
| pwd | |
| cd kgx | |
| docker run --detach --name kgx-neo4j-unit-test -p 8484:7474 -p 8888:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0 | |
| docker run --detach --name kgx-neo4j-integration-test -p 7474:7474 -p 7687:7687 --env NEO4J_AUTH=neo4j/test neo4j:4.3.0 | |
| docker ps -a | |
| - name: Wait | |
| uses: jakejarvis/wait-action@master | |
| with: | |
| time: '45s' | |
| - name: Run kgx tests | |
| run: | | |
| cd ../ | |
| pwd | |
| cd kgx | |
| poetry run pytest tests/unit/test_source/*.py | |
| poetry run pytest tests/unit/test_sink/*.py | |
| poetry run pytest tests/unit/*.py | |
| poetry run pytest tests/integration/*.py |