Adding REST rtf only pipeline, cleaning up Java warnings, adjusting to MTAP changes #993
Workflow file for this run
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| name: Continuous Integration | |
| on: | |
| pull_request: | |
| branches: main | |
| schedule: | |
| - cron: 0 8 * * * | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 2 | |
| matrix: | |
| python-version: ['3.9', '3.11'] | |
| include: | |
| - java-version: '11' | |
| python-version: '3.9' | |
| - java-version: '21' | |
| python-version: '3.11' | |
| name: ubuntu-latest, py${{ matrix.python-version }}, java${{ matrix.java-version }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: actions/cache@v3 | |
| id: cache | |
| with: | |
| path: ~/.biomedicus/data | |
| key: ${{ hashFiles('python/biomedicus/data_version.py') }} | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: 'temurin' | |
| java-version: ${{ matrix.java-version }} | |
| - uses: actions/setup-go@v5 | |
| with: | |
| go-version: '1.20' | |
| - name: Install dependencies (not release) | |
| if: ${{ !startsWith(github.head_ref, 'release') && success() }} | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| pip install flake8 pytest | |
| pip install git+https://github.com/nlpie/mtap@main#egg=mtap ./biomedicus_client .[test,stanza] --extra-index-url https://download.pytorch.org/whl/cpu | |
| go install github.com/nlpie/mtap/go/mtap-gateway@latest | |
| - name: Install dependencies (release) | |
| if: ${{ startsWith(github.head_ref, 'release') && success() }} | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| pip install flake8 pytest | |
| SETUPTOOLS_SCM_PRETEND_VERSION=${GITHUB_HEAD_REF##*/} pip install ./biomedicus_client .[test,stanza] --extra-index-url https://download.pytorch.org/whl/cpu | |
| go install github.com/nlpie/mtap/go/mtap-gateway@latest | |
| - name: Lint with flake8 | |
| run: | | |
| pip install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Download models | |
| run: b9 download-data --with-stanza | |
| - name: Test with pytest | |
| run: pytest -s python/tests --integration --timeout 120.0 |