python-package.yml

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Python package

permissions:
  contents: read

on:
  push:
    branches: [ develop, pre-release, master, main ]
    tags: v*
  pull_request:
    branches: [ develop, pre-release, master, main ]

jobs:
  build:

    runs-on: ubuntu-24.04
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.11", "3.12", "3.13"]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        sudo apt update
        sudo apt-get install -y libopenjp2-7 libopenjp2-tools
        python -m pip install --upgrade pip
        python -m pip install ruff==0.15.4 pytest pytest-cov pytest-runner
        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
        pip install -r requirements/requirements.txt
    - name: Cache tiatoolbox static assets
      uses: actions/cache@v4
      with:
        key: tiatoolbox-home-static
        path: ~/.tiatoolbox
    - name: Print Version Information
      run: |
        echo "---SQlite---"
        sqlite3 --version
        sqlite3 ":memory:" -list ".output stdout" "pragma compile_options" ".exit"
        echo "---OpenJPEG---"
        opj_dump -h | head -n 5
        echo "---Python---"
        python -c "import sys; print('Python %s' % sys.version)"
        python -c "import sqlite3; print('SQLite %s' % sqlite3.sqlite_version)"
        python -c "import numpy; print('Numpy %s' % numpy.__version__)"
        python -c "import openslide; print('OpenSlide %s' % openslide.__version__)"
    - name: Lint with ruff
      run: |
        # stop the build if there are Python syntax errors or undefined names
        ruff check .
    - name: Test with pytest
      run: |
        pytest --basetemp={envtmpdir} \
           --cov=tiatoolbox --cov-report=term --cov-report=xml --cov-config=pyproject.toml \
           --capture=sys \
           --durations=10 --durations-min=1.0 \
           --maxfail=1
    - name: Report test coverage to Codecov
      uses: codecov/codecov-action@v4
      env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
      with:
        files: coverage.xml
        fail_ci_if_error: false
        verbose: true

    - name: Report test coverage to DeepSource
      uses: deepsourcelabs/test-coverage-action@master
      with:
        key: python
        coverage-file: coverage.xml
        dsn: ${{ secrets.DEEPSOURCE_DSN }}
        fail-ci-on-error: false
    - name: List tiatoolbox contents
      run: ls -lahR ~/.tiatoolbox
    - name: Delete Hugging Face cache for large models
      run: |
        find ~/.tiatoolbox/models -type f -size +250M -exec bash -c '
          for model_path; do
            model_name=$(basename "$model_path")
            cache_dir="$HOME/.tiatoolbox/models/.cache/huggingface/download"
            rm -vf "$cache_dir/${model_name}.lock" "$cache_dir/${model_name}.metadata"
          done
          ' bash {} +

  release:
    runs-on: ubuntu-24.04
    timeout-minutes: 15
    needs: build
    if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/pre-release' || startsWith(github.ref, 'refs/tags/v')

    steps:
    - uses: actions/checkout@v4

    - name: Set up Python 3.11
      uses: actions/setup-python@v4
      with:
        python-version: '3.11'
        cache: 'pip'

    - name: Install dependencies
      run: |
        sudo apt-get install -y libopenslide-dev libopenjp2-7
        python -m pip install --upgrade pip
        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
        pip install -r requirements/requirements.txt
        pip install build
    - name: Build package
      run: python -m build

    - name: Publish package to Test PyPI
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
        repository_url: https://test.pypi.org/legacy/
        skip_existing: true  # Ignore errors if the current version exists already

    - name: Publish package to PyPI
      if: startsWith(github.ref, 'refs/tags/v')  # Only run on tags starting with v
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        user: __token__
        password: ${{ secrets.PYPI_API_TOKEN }}