medcat-scripts_main.yml

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@v7
      - 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