check_on_PR.yml

name: Checking unit-tests, PEP8 and standard pipeline congruency

on:

  pull_request:
    branches:
      - main


jobs:
  build:

    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@main
      - name: Set up Python 3.10.5
        uses: actions/setup-python@v2
        with:
            python-version: 3.10.5

      - name: Install dependencies
        run: |
            pip install codecov pytest pytest-cov
            pip install flake8
            sudo apt-get install build-essential  graphviz libgraphviz-dev
            pip install --upgrade pygraphviz graphviz

            # pip install --no-deps --index-url https://test.pypi.org/simple/ --pre macapype

            pip install -e .

            python -c "import skullTo3d; print(skullTo3d.__version__)"

            python -c "import macapype; print( macapype.__version__)"

            cd ..
            git clone https://github.com/macatools/macapype.git

            cd macapype
            python setup.py develop

            python -c "import macapype; print(macapype.__version__)"

            cd ../skullTo3d
            pwd


      - name: Test with pytest
        run:
            py.test --cov skullTo3d

      - name: Flake8
        run:
            flake8 --count skullTo3d

      - name: Download dataset
        run: |
            wget --no-check-certificate --content-disposition  "https://amubox.univ-amu.fr/public.php?service=files&t=swYxNZ3P6LjfqN4&download" -O skullTo3d_CI.zip
            unzip -o skullTo3d_CI.zip -d skullTo3d_CI

      - name: Running all test pipelines (ANTS SPM)
        run: |
            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft ANTS_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft ANTS_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft ANTS_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra


            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft SPM_native_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft SPM_native_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft SPM_native_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra

      - name: Running all test pipelines (ANTS SPM deriv pad)
        run: |
            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft ANTS_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft ANTS_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft ANTS_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad


            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra/results -soft SPM_native_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-macaque-ct/results -soft SPM_native_test_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad

            python workflows/segment_petra.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra -out /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cerimed-marmo-petra/results -soft SPM_native_test_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad