build: bump the pip group across 3 directories with 7 updates #38
Workflow file for this run
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| name: medcat-scripts - Test | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| paths: | |
| - 'medcat-scripts/**' | |
| - '.github/workflows/medcat-scripts**' | |
| defaults: | |
| run: | |
| working-directory: ./medcat-scripts | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| strategy: | |
| matrix: | |
| python-version: [ '3.10', '3.11', '3.12', '3.13' ] | |
| max-parallel: 4 | |
| steps: | |
| - uses: actions/checkout@v5 | |
| - name: Install uv for Python ${{ matrix.python-version }} | |
| uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| enable-cache: true | |
| - name: Install the project | |
| run: | | |
| uv venv .venv | |
| source .venv/bin/activate | |
| uv run python -m ensurepip | |
| uv pip install -r requirements.txt | |
| uv pip install -r requirements-dev.txt | |
| # reinstall MedCAT from local to test against changes in core lib | |
| uv pip install "../medcat-v2[spacy,deid,meta-cat,rel-cat]" | |
| - name: Check types | |
| run: | | |
| # NOTE: Only testing against .py files in this folder | |
| uv run python -m mypy `git ls-tree --full-tree --name-only -r HEAD | grep ".py$" | grep "^medcat-scripts" | grep -v "tests/" | sed 's|^medcat-scripts/||'` --explicit-package-bases --follow-imports=normal | |
| - name: Setup for notebook tests | |
| run: | | |
| # NOTE: this will make sure there's something in the den to work with below | |
| uv run python tests/setup_for_tests.py | |
| - name: Install IPython kernel | |
| run: | | |
| uv run python -m ipykernel install --name smoketests --user | |
| - name: Run tests | |
| run: | | |
| uv run pytest tests | |
| - name: Test notebooks | |
| run: | | |
| uv run pytest --collect-only --nbmake **/*.ipynb | |
| uv run pytest --nbmake -n=auto --nbmake-kernel=smoketests --nbmake-timeout=1800 **/*.ipynb |