TPTBox/.github/workflows/tests.yml at dd2153efa340fbee932be9a8856e4785227bbc1d · Hendrik-code/TPTBox · GitHub

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: tests

on:
  push:
    branches: [ "main" ]

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-latest]
        python-version: ["3.9", "3.10", "3.11", "3.12"]

    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Configure python
      run: |
        python -m pip install --upgrade pip
        python -m pip install poetry
        python -m pip install flake8 pytest
    - name: Install dependancies
      run: |
        python -m poetry install
    - name: Lint with flake8
      run: |
        # 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: Test with pytest and create coverage report
      run: |
        python -m poetry run coverage run --source=TPTBox -m pytest
        python -m poetry run coverage xml
    - name: Upload coverage results to Codecov (Only on merge to main)
      # Only upload to Codecov after a merge to the main branch
      if: github.ref == 'refs/heads/main' && github.event_name == 'push'
      uses: codecov/codecov-action@v4
      with:
        token: ${{ secrets.CODECOV_TOKEN }}

  build-full-coverage:
    # Authoritative coverage job: installs the heavy optional deps (CPU-only) so
    # the segmentation / registration / dicom / mocked-GPU tests actually run and
    # count towards Codecov. The light `build` matrix above stays fast and skips them.
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3.11
      uses: actions/setup-python@v5
      with:
        python-version: "3.11"
    - name: Configure python
      run: |
        python -m pip install --upgrade pip
        python -m pip install poetry
    - name: Install dependancies
      run: |
        python -m poetry install
    - name: Install heavy optional deps (CPU)
      run: |
        python -m poetry run pip install torch --index-url https://download.pytorch.org/whl/cpu
        python -m poetry run pip install antspyx pydicom numpy-stl nnunetv2 deepali spineps
    - name: Test with pytest and create coverage report
      run: |
        python -m poetry run coverage run --source=TPTBox -m pytest unit_tests/ --ignore=unit_tests/test_auto_segmentation.py
        python -m poetry run coverage xml
    - name: Upload coverage results to Codecov (Only on merge to main)
      if: github.ref == 'refs/heads/main' && github.event_name == 'push'
      uses: codecov/codecov-action@v4
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        flags: full