phantoms #320
Workflow file for this run
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| name: phantoms | |
| on: | |
| workflow_call: | |
| push: | |
| branches: | |
| - main | |
| - switch-phantoms-to-s3 | |
| 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: Check dcm2niix is installed and on path | |
| if: runner.os != 'Windows' | |
| run: | |
| dcm2niix -h | |
| - 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 . | |
| - name: Install Poetry Build Package | |
| run: | | |
| make installpoetry | |
| make buildpackage | |
| make installpackage | |
| dcm2niix4pet -h | |
| - name: Set Up Node | |
| uses: actions/setup-node@v4 | |
| - name: Install BIDS Validator | |
| run: npm install -g bids-validator@1.14.6 | |
| - name: Collect Phantoms | |
| if: ${{ steps.cache-phantoms.outputs.cache-hit != 'true' }} && ${{ !env.ACT }} | |
| run: wget -O PHANTOMS.zip https://openneuropet.s3.amazonaws.com/US-sourced-OpenNeuroPET-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 | |
| # note matlab-actions/setup-matlab@v2 breaks this script, don't update unless you're forced to | |
| #with: | |
| #release: 'R2023a' | |
| #cache: true | |
| - 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: 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: Validate Matlab Conversion | |
| run: | | |
| bids-validator OpenNeuroPET-Phantoms/matlab |