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 3.7
        uses: actions/setup-python@v1
        with:
          python-version: 3.7

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

      - 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 (macaque)
        run: |
            python segment_skull.py -data /home/runner/work/skullTo3d/skullTo3d/skullTo3d_CI/cenir-macaque-petra -out /home/runner/work/skullTo3d/skullTo3d/macapype_CI/cenir-macaque-petra/results -soft ANTS_test_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra