Biolink model 4.0 and permissible value descendants and children methods #16
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| name: Check Dependencies in Pyproject.toml | |
| # Controls when the action will run. | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| types: trigger-run-check-dependencies | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| 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" ] | |
| # 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 | |
| continue-on-error: true | |
| 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 | |
| continue-on-error: true | |
| 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 |