python-app.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: Python application

on:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

permissions:
  contents: read

jobs:
  build:

    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3
    - name: Set up Python 3.10
      uses: actions/setup-python@v3
      with:
        python-version: "3.10"
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pytest
        pip install pytest-cov
        pip install coverage
        pip install -r requirements.txt
        pip install platipy
        #pip install numpy==1.22.4
    - name: Install elastix
      run: |
        wget -P ~/ElastixDownload "https://github.com/SuperElastix/elastix/releases/download/5.0.1/elastix-5.0.1-linux.tar.bz2"
        #bzip2 -d /home/runner/ElastixDownload/elastix-5.0.1-linux.tar.bz2
        #tar -xvjf /home/runner/ElastixDownload/elastix-5.0.1-linux.tar.bz2
        #ls /home/runner
        #ls /home/runner/ElastixDownload
        #PATH=$PATH:~/ElastixDownload/elastix-5.0.1-linux/bin
        #PATH=$PATH:/home/runner/work/CTHeadDeformation/CTHeadDeformation/elastix-5.0.1-linux/bin/elastix
        #echo "$PATH"
        #ls /home/runner
        #find /home/runner -name elastix -type f -print
        #ls /home/runner/ElastixDownload/elastix-5.0.1-linux/
        #whereis elastix.exe
        #which elastix.exe                
        #ls ~/elastix-5.0.1-linux/bin/elastix
        #ls ~/ElastixDownload/elastix-5.0.1-linux/bin/elastix

    - name: Test with pytest & Coverage
      run: |        
        mkdir /home/runner/elastix
        tar -xvjf /home/runner/ElastixDownload/elastix-5.0.1-linux.tar.bz2 -C /home/runner/elastix        
        PATH=$PATH:~/elastix/elastix-5.0.1-linux/bin
        LD_LIBRARY_PATH=$LD_LIBRARY_PATH:~/elastix/elastix-5.0.1-linux/lib
        echo "$PATH"
        echo "$LD_LIBRARY_PATH"
        #ls /home/runner/elastix/elastix-5.0.1-linux/bin/elastix
        #find /home/runner -name elastix.exe -type f -print
        #elastix -h
        #/home/runner/elastix/elastix-5.0.1-linux/bin/elastix.exe -h
        pytest --cov=DeformHeadCT/ --cov-report=xml
        #coverage run -m pytest
    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v3