build_on_prerelease.yml

name: (Prerelease) Build Pipy, Dockerhub image and test

on:
  release:
    types: [prereleased]

jobs:

  build-n-publish-testpypi:
    name: Build and publish Python to Test PyPI
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@master
    - name: Set up Python 3.10.5
      uses: actions/setup-python@v2
      with:
        python-version: 3.10.5
    - name: Install pypa/build
      run: >-
        python -m
        pip install
        build
        --user
    - name: Build a binary wheel and a source tarball
      run: >-
        python -m
        build
        --sdist
        --wheel
        --outdir dist/

    - name: Publish distribution to Test PyPI
      uses: pypa/gh-action-pypi-publish@master
      with:
        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
        repository_url: https://test.pypi.org/legacy/

  docker-build:
    name: Build Docker image and Push to Docker Hub
    needs: build-n-publish-testpypi
    runs-on: ubuntu-latest
    steps:
      - name: Check out the repo
        uses: actions/checkout@v2

      - name: Log in to Docker Hub
        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}

      - name: Extract metadata (tags, labels) for Docker
        id: meta
        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
        with:
          images: macatools/skullTo3d

      - name: Build and push Docker image
        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
        with:
          context: .
          file: Dockerfile_testpypi_nomcr
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}

  run-pretest-spm-macaque:
    name: Running all existing pipelines in skullTo3d_CI.zip (SPM_native macaque)
    needs:  docker-build
    runs-on: ubuntu-latest
    timeout-minutes: 1440

    steps:
      - name: Pull latest docker image
        run:
            docker pull macatools/skullTo3d:latest

      - name: Download dataset
        run: |

            wget --no-check-certificate --content-disposition  "https://amubox.univ-amu.fr/public.php?service=files&t=KJ2L5j6L6orPXxM&download" -O skullTo3d_CI.zip
            unzip -o skullTo3d_CI.zip -d skullTo3d_CI

            pwd
            echo ""

            ls skullTo3d_CI
            echo ""

            ls skullTo3d_CI/cenir-macaque-petra

            ls skullTo3d_CI/cenir-macaque-petra/sub-Magneto/anat

            echo ""

            ls skullTo3d_CI/cerimed-macaque-ct

            ls skullTo3d_CI/cerimed-macaque-ct/sub-Marvin/sub-01/anat

            echo ""

            ls skullTo3d_CI/cerimed-marmo-petra

            ls skullTo3d_CI/cerimed-marmo-petra/sub-Paolina/sub-01/anat

            echo ""

      - name: Running all test pipelines (ANTS deriv pad)
        run: |
            python segment_skull.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_prep_skull -species macaque -sub Magneto -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad

            ls skullTo3d_CI/cenir-macaque-petra/results

            ls skullTo3d_CI/cenir-macaque-petra/results/derivatives

            ls skullTo3d_CI/cenir-macaque-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2/sub-Magneto/anat

            python segment_skull.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_prep_skull -species macaque -sub Marvin -ses 01 -brain_dt T1 T2 -skull_dt T1 CT -deriv -pad

            ls skullTo3d_CI/cerimed-macaque-ct/results

            ls skullTo3d_CI/cerimed-macaque-ct/results/derivatives

            ls skullTo3d_CI/cerimed-macaque-ct/results/derivatives/macapype_crop_aladin_ants_skull_t1_CT_brain_t1_t2/sub-Marvin/-ses-01/anat


            python segment_skull.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_noseg_skull -species marmo -sub Paolina -ses 01 -brain_dt T1 T2 -skull_dt T1 petra -deriv -pad


            ls skullTo3d_CI/cerimed-marmo-petra/results

            ls skullTo3d_CI/cerimed-marmo-petra/results/derivatives

            ls skullTo3d_CI/cerimed-marmo-petra/results/derivatives/macapype_crop_aladin_ants_skull_t1_petra_brain_t1_t2/sub-Paolina/-ses-01/anat