python-test.yml

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

name: CI-PyTest

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]
    

jobs:
  full-test:

    runs-on: ubuntu-latest

    steps:
    - name: Free space
      run: |
        df -h
        sudo rm -rf /opt/ghc
        sudo rm -rf "/usr/local/share/boost"
        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
        sudo rm -rf "$ANDROID_SDK_ROOT"
        df -h
    - name: Checkout
      uses: actions/checkout@v3
    
    # Use changed-files-specific action to collect file changes.
    # The following commented condition applied to a step will run that step only if non-docs files have changed.
    # It should be applied to all functionality-related steps.
    # if: steps.changed-files-specific.outputs.only_modified == 'false'
    - name: Detect and screen file changes
      id: changed-files-specific
      uses: tj-actions/changed-files@v41
      with:
          files: |
            .github/*.md
            .github/ISSUE_TEMPLATE/*.md
            .github/workflows/devcontainer.yml
            .github/workflows/docker-image.yml
            .devcontainer/**
            docs/**
            mlcube/**
            *.md
            LICENSE
            Dockerfile-*

    - name: Summarize docs and non-docs modifications
      run: |
        echo "List of docs files that have changed: ${{ steps.changed-files-specific.outputs.all_modified_files }}"
        echo "Changed non-docs files: ${{ steps.changed-files-specific.outputs.other_modified_files }}"
    
    # This second step is unnecessary but highly recommended because
    # It will cache database and saves time re-downloading it if database isn't stale.
    - name: Cache pip
      uses: actions/cache@v3
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
        restore-keys: |
          ${{ runner.os }}-pip-
    - name: Check dev version
      run: | # Get current canonical version, append current date as an identifier
        currentVer=$(grep -oP '__version__ = \K.*' ./GANDLF/version.py)
        currentVer=${currentVer//\"}
        echo "Current version is $currentVer"
        if [[ $currentVer == *"dev"* ]]; then
          echo "Nightly will be published"
          echo "publish_nightly=true" >> $GITHUB_ENV
        else
          echo "Nightly will not be published"
          echo "publish_nightly=false" >> $GITHUB_ENV
        fi  
    - name: Set up Python 3.9
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      uses: actions/setup-python@v4
      with:
        python-version: 3.9
    - name: Install dependencies and package
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      run: |
        sudo apt-get update
        sudo apt-get install libvips libvips-tools -y
        python -m pip install --upgrade pip==24.0
        python -m pip install wheel
        python -m pip install openvino-dev==2023.0.1 mlcube_docker
        pip install torch==2.1.2 torchvision==0.16.2 torchaudio==2.1.2 --index-url https://download.pytorch.org/whl/cpu
        pip install -e .
    - name: Run generic unit tests
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      run: |
        pytest --cov=. --cov-report=xml -k "generic"        
    - name: Run classification unit tests with histology
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      run: |
        pytest --cov=. --cov-report=xml --cov-append -k "classification and histology"
    - name: Run classification unit tests
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      run: |
        pytest --cov=. --cov-report=xml --cov-append -k "classification and not histology"
    - name: Run segmentation unit tests
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      run: |
        pytest --cov=. --cov-report=xml --cov-append -k "segmentation and not transunet"
    - name: Run regression unit tests
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      run: |
        pytest --cov=. --cov-report=xml --cov-append -k "regression"
    - name: Run transunet unit tests
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      run: |
        pytest --cov=. --cov-report=xml --cov-append -k "transunet"


    - name: Upload coverage
      if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
      uses: codecov/codecov-action@v1
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        file: ./coverage.xml
        flags: unittests