phantoms.yaml

name: phantoms
on:
  workflow_call:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
      - dev
  workflow_dispatch:
    inputs:
      debug_enabled:
        type: boolean
        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
        required: false
        default: false

jobs:
  phantoms:
    runs-on: ${{ matrix.os }}
    env:
      DCM2NIIX_WIN_PATH: dcm2niix_win/dcm2niix.exe
      MATLAB_CODE_PATH: ${{ github.workspace }}/matlab/
      METADATA_PATH: ${{ github.workspace }}/metadata/

    strategy:
      matrix:
        os: [ubuntu-20.04]
        python: ["3.10"]
      fail-fast: false

    steps:
      - name: Checkout Repo
        uses: actions/checkout@v2

      - name: Cache Node Posix
        if: runner.os != 'Windows' && !env.ACT
        uses: actions/cache@v3
        with:
          path: ~/.npm
          key: npm-${{ runner.os }}-${{ env.cache-name }}

      - name: Cache Phantoms
        if: ${{ !env.ACT }}
        id: phantom-cache
        uses: actions/cache@v3
        env:
          cache-name: cache-phantoms
        with:
          path: PHANTOMS.zip
          key: ${{ runner.os }}-${{ env.cache-name }}-${{ hashFiles('PHANTOMS.zip') }}
          restore-keys: |
            ${{ runner.os }}-${{ env.cache-name }}-
            ${{ runner.os }}- 

      - name: Install dcm2niix posix
        if: runner.os != 'Windows'
        run: |
          if [ "$RUNNER_OS" == "Linux" ]; then
            mkdir dcm2niix_install/ && cd dcm2niix_install/
            curl -fLO https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20230411/dcm2niix_lnx.zip
            unzip dcm2niix*.zip
            echo "${{ github.workspace }}/dcm2niix_install/" >> $GITHUB_PATH
          elif [ "$RUNNER_OS" == "macOS" ]; then
            brew install dcm2niix
          fi

      - name: Install dcm2niix windows
        if: runner.os == 'Windows'
        run: |
          curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_win.zip
          powershell -command "Expand-Archive dcm2niix_win.zip"
          
      - name: Set up python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python }}
          cache: 'pip'
          cache-dependency-path: |
            pypet2bids/pyproject.toml

      - name: Install Python Dependencies
        run: |
          cd pypet2bids
          pip install .
          pip install gdown

      - name: Install Poetry Build Package
        run: |
          make installpoetry
          make buildpackage
          make installpackage
          dcm2niix4pet -h

      - name: Set Up Node
        uses: actions/setup-node@v3

      - name: Install BIDS Validator
        run: npm install -g bids-validator

      - name: Collect Phantoms from Google Drive
        if: ${{ steps.cache-phantoms.outputs.cache-hit != 'true' }} && ${{ !env.ACT }}
        run: gdown ${{ secrets.ZIPPED_OPEN_NEURO_PET_PHANTOMS_URL }} -O PHANTOMS.zip

      - name: Decompress phantoms windows
        if: steps.cache-phantoms.outputs.cache-hit != 'true' && !env.ACT && runner.os == 'Windows'
        run: powershell -command "Expand-Archive PHANTOMS.zip"

      - name: Decompress phantoms posix
        if: steps.cache-phantoms.outputs.cache-hit != 'true' && !env.ACT && runner.os != 'Windows'
        run: unzip PHANTOMS.zip

      - name: Copy Conversion Scripts from Version Control
        run: |
          mkdir -p OpenNeuroPET-Phantoms/code/
          cp scripts/matlab_conversions.m OpenNeuroPET-Phantoms/code/matlab_conversions.m
          cp scripts/python_conversions.sh OpenNeuroPET-Phantoms/code/python_conversions.sh

      - name: Debug
        uses: mxschmitt/action-tmate@v3
        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
        timeout-minutes: 15
        with:
          limit-access-to-actor: true

      - name: Run Python Conversion Script on Phantoms
        run: |
          cd OpenNeuroPET-Phantoms/code
          bash python_conversions.sh

      - name: SetupMatlab
        if: ${{ matrix.os == 'ubuntu-20.04' }}
        uses: matlab-actions/setup-matlab@v1

      - name: Run Matlab Conversion Script on Phantoms
        if: ${{ matrix.os == 'ubuntu-20.04' }}
        uses: matlab-actions/run-command@v1
        with:
          command: |
            addpath('${{ github.workspace }}/OpenNeuroPET-Phantoms/code')
            addpath('${{ env.MATLAB_CODE_PATH }}');
            addpath('${{ env.MATLAB_CODE_PATH }}/unit_tests');
            addpath('${{ env.MATLAB_CODE_PATH }}/template_txt');
            addpath('${{ env.SMALLER_ECAT_PATH }}');
            addpath('${{ env.METADATA_PATH }}');
            matlab_conversions

      - name: Check Parity
        run: |
          python scripts/compare_jsons.py OpenNeuroPET-Phantoms/python OpenNeuroPET-Phantoms/matlab

      - name: Validate Python Conversion
        run: |
          bids-validator OpenNeuroPET-Phantoms/python

      - name: Validate Matlab Conversion
        run: |
          bids-validator OpenNeuroPET-Phantoms/matlab