install_test_standalone.yml

name: Compile and Test CAT Standalone

on:
  workflow_dispatch:
    inputs:
      source:
        description: "Source of standalone binaries"
        required: false
        default: "build"
        type: choice
        options:
          - build
          - release
      release_tag:
        description: "Release tag (only for release source)"
        required: false
        type: string

env:
  MLM_LICENSE_TOKEN: ${{ secrets.MATLAB_BATCH_TOKEN }}
  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true

jobs:
  # ────────────────────────────────────────────────────
  # Job 1: Download release standalone (if source == release)
  # ────────────────────────────────────────────────────
  download_release_standalone:
    name: Download Release Standalone
    if: inputs.source == 'release'
    runs-on: ubuntu-latest
    strategy:
      matrix:
        standalone_os: [Linux, Mac, Mac_arm64, Win]
    steps:
      - name: Download release asset
        env:
          GH_TOKEN: ${{ github.token }}
        run: |
          TAG="${{ inputs.release_tag }}"
          OS="${{ matrix.standalone_os }}"

          ASSET_NAME="CAT_R2023b_MCR_${OS}.zip"

          echo "Downloading $ASSET_NAME from release $TAG"
          gh release download "$TAG" --repo ${{ github.repository }} --pattern "$ASSET_NAME"

      - name: Upload as artifact
        uses: actions/upload-artifact@v4
        with:
          name: cat-standalone-${{ matrix.standalone_os }}
          path: CAT_R2023b_MCR_${{ matrix.standalone_os }}.zip
          retention-days: 1

  # ────────────────────────────────────────────────────
  # Job 2: Build standalone (if source == build or default)
  # ────────────────────────────────────────────────────
  build_standalone:
    name: Build Standalone on ${{ matrix.os_name }}
    if: inputs.source == 'build' || inputs.source == ''
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        version: ["R2023b"]
        os: ["ubuntu-22.04", "macos-13", "macos-latest", "windows-latest"]
        include:
          - os: ubuntu-22.04
            os_name: Linux
            standalone_os: Linux
            mex_ext: mexa64
          - os: macos-13
            os_name: macOS_Intel
            standalone_os: Mac
            mex_ext: mexmaci64
          - os: macos-latest
            os_name: macOS_ARM64
            standalone_os: Mac_arm64
            mex_ext: mexmaca64
          - os: windows-latest
            os_name: Windows
            standalone_os: Win
            mex_ext: mexw64
    steps:
      - name: Checkout CAT
        uses: actions/checkout@v4

      - name: Update
        run: make update

      - name: Install rsync
        if: runner.os == 'Windows'
        run: choco install -y rsync

      - name: Checkout SPM
        uses: actions/checkout@v4
        with:
          repository: spm/spm
          path: spm

      - name: Install CAT in SPM toolbox
        shell: bash
        run: |
          mkdir -p spm/toolbox/CAT
          rsync -a --exclude='.git' \
            --exclude='spm/toolbox/CAT/' \
            --exclude='batches/' \
            --exclude='catQC/' \
            --exclude='check_pipeline/' \
            --exclude='development/' \
            --exclude='html/' \
            --exclude='internal/' \
            --exclude='mexmaca/' \
            --exclude='mexmaci/' \
            --exclude='spm/' \
            --exclude='Makefile' \
            ./ spm/toolbox/CAT/

      - name: Cleanup (Linux/Mac)
        if: runner.os != 'Windows'
        run: rm -rf standalone

      - name: Cleanup (Windows)
        if: runner.os == 'Windows'
        run: Remove-Item -Recurse -Force standalone

      - name: Set up MATLAB
        uses: matlab-actions/setup-matlab@v2
        with:
          release: ${{ matrix.version }}
          products: MATLAB_Compiler

      - name: Set environment variable with MATLAB version
        shell: bash
        run: |
          echo "MATLAB_VERSION=R2023b" >> $GITHUB_ENV

      - name: Compile CAT mex-files
        uses: matlab-actions/run-command@v2
        with:
          command: |
            addpath('spm');
            cd('spm/toolbox/CAT')
            compile

      - name: Install zip on Windows
        if: runner.os == 'Windows'
        run: choco install zip -y
        shell: bash

      # Decompress .nii.gz templates so they are available as .nii in the compiled standalone.
      # Without this, atlas config (cat_conf_ROI.m) fails because it checks exist(...'.nii','file').
      - name: Decompress NII.GZ templates
        shell: bash
        run: |
          echo "Decompressing .nii.gz files in CAT templates..."
          find spm/toolbox/CAT/templates_MNI152NLin2009cAsym -name '*.nii.gz' -exec gunzip -f {} \;
          find spm/toolbox/CAT/templates_surfaces -name '*.nii.gz' -exec gunzip -f {} \;
          find spm/toolbox/CAT/templates_surfaces_32k -name '*.nii.gz' -exec gunzip -f {} \;
          echo "Decompression complete"

      # Build SPM standalone (which includes CAT as toolbox)
      - name: Build MATLAB standalone
        uses: matlab-actions/run-command@v2
        with:
          command: |
            cd('spm');
            addpath(genpath('.'));
            savepath;
            cd('config');
            spm_make_standalone

      - name: Compress standalone to ZIP
        shell: bash
        run: |
          mv spm/toolbox/CAT/standalone standalone/
          mv standalone cat_standalone
          zip -r CAT_${{ env.MATLAB_VERSION }}_MCR_${{ matrix.standalone_os }}.zip cat_standalone/*

      - name: Upload standalone artifact
        uses: actions/upload-artifact@v4
        with:
          name: cat-standalone-${{ matrix.standalone_os }}
          path: CAT_*.zip
          retention-days: 7

  # ────────────────────────────────────────────────────
  # Job 3: Test standalone on each OS
  # ────────────────────────────────────────────────────
  test_standalone:
    name: Test Standalone on ${{ matrix.os_name }}
    needs: [build_standalone, download_release_standalone]
    if: |
      always() &&
      (needs.build_standalone.result == 'success' || needs.download_release_standalone.result == 'success')
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: ["ubuntu-22.04", "macos-13", "macos-latest", "windows-latest"]
        include:
          - os: ubuntu-22.04
            os_name: Linux
            standalone_os: Linux
          - os: macos-13
            os_name: macOS_Intel
            standalone_os: Mac
          - os: macos-latest
            os_name: macOS_ARM64
            standalone_os: Mac_arm64
          - os: windows-latest
            os_name: Windows
            standalone_os: Win

    steps:
      - name: Download standalone artifact
        uses: actions/download-artifact@v4
        with:
          name: cat-standalone-${{ matrix.standalone_os }}
          path: .

      - name: Extract standalone
        shell: bash
        run: |
          unzip -q CAT_*_MCR_${{ matrix.standalone_os }}.zip
          echo "Contents of cat_standalone:"
          ls -la cat_standalone

      # ── Install MATLAB Runtime ──

      - name: Install MATLAB Runtime (Linux)
        if: runner.os == 'Linux'
        shell: bash
        run: |
          # Download MCR R2023b
          echo "Downloading MATLAB Runtime R2023b for Linux..."
          wget -q https://ssd.mathworks.com/supportfiles/downloads/R2023b/Release/10/deployment_files/installer/complete/glnxa64/MATLAB_Runtime_R2023b_Update_10_glnxa64.zip -O mcr.zip
          unzip -q mcr.zip -d mcr_installer

          echo "Installing MATLAB Runtime..."
          sudo ./mcr_installer/install -agreeToLicense yes -destinationFolder /usr/local/MATLAB/MATLAB_Runtime 2>&1

          echo "MCRROOT=/usr/local/MATLAB/MATLAB_Runtime/R2023b" >> $GITHUB_ENV
          echo "LD_LIBRARY_PATH=/usr/local/MATLAB/MATLAB_Runtime/R2023b/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/sys/opengl/lib/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/R2023b/extern/bin/glnxa64" >> $GITHUB_ENV
          echo "MCR_INHIBIT_CTF_LOCK=1" >> $GITHUB_ENV
          echo "SPM_HTML_BROWSER=0" >> $GITHUB_ENV

          rm -rf mcr.zip mcr_installer
          echo "MATLAB Runtime installed at /usr/local/MATLAB/MATLAB_Runtime/R2023b"

      - name: Install MATLAB Runtime (macOS)
        if: runner.os == 'macOS'
        shell: bash
        run: |
          ARCH=$(uname -m)
          if [ "$ARCH" = "arm64" ]; then
            echo "Downloading MATLAB Runtime R2023b for macOS ARM64..."
            wget -q https://ssd.mathworks.com/supportfiles/downloads/R2023b/Release/10/deployment_files/installer/complete/maca64/MATLAB_Runtime_R2023b_Update_10_maca64.dmg -O mcr.dmg
          else
            echo "Downloading MATLAB Runtime R2023b for macOS Intel..."
            wget -q https://ssd.mathworks.com/supportfiles/downloads/R2023b/Release/10/deployment_files/installer/complete/maci64/MATLAB_Runtime_R2023b_Update_10_maci64.dmg.zip -O mcr.dmg.zip
            unzip -q mcr.dmg.zip
            MCR_DMG=$(ls *.dmg | head -n 1)
            mv "$MCR_DMG" mcr.dmg
          fi

          echo "Mounting DMG..."
          hdiutil attach mcr.dmg -mountpoint /Volumes/MCR

          echo "Installing MATLAB Runtime..."
          # Find the installer app and its actual executable (name varies by architecture)
          INSTALLER_APP=$(find /Volumes/MCR -name "*.app" -maxdepth 1 | head -n 1)
          if [ -z "$INSTALLER_APP" ]; then
            echo "ERROR: No installer .app found in DMG"
            ls -la /Volumes/MCR/
            exit 1
          fi
          # The executable name matches the app name (e.g., InstallForMacOSAppleSilicon)
          APP_NAME=$(basename "$INSTALLER_APP" .app)
          INSTALLER_BIN="$INSTALLER_APP/Contents/MacOS/$APP_NAME"
          if [ ! -f "$INSTALLER_BIN" ]; then
            # Fallback: find the actual executable inside the app bundle
            INSTALLER_BIN=$(find "$INSTALLER_APP/Contents/MacOS" -type f -perm +111 | head -n 1)
          fi
          echo "Using installer: $INSTALLER_BIN"
          sudo "$INSTALLER_BIN" -agreeToLicense yes -destinationFolder "$HOME/MATLAB_Runtime" 2>&1 | tee install.log
          sleep 2

          sudo chown -R $USER "$HOME/MATLAB_Runtime"
          sudo chown -R $USER "$HOME/.matlab" 2>/dev/null || true

          hdiutil detach /Volumes/MCR 2>/dev/null || true

          echo "MCRROOT=$HOME/MATLAB_Runtime/R2023b" >> $GITHUB_ENV
          echo "MCR_INHIBIT_CTF_LOCK=1" >> $GITHUB_ENV
          echo "SPM_HTML_BROWSER=0" >> $GITHUB_ENV

          rm -f mcr.dmg mcr.dmg.zip
          echo "MATLAB Runtime installed at $HOME/MATLAB_Runtime/R2023b"

      - name: Install MATLAB Runtime (Windows)
        if: runner.os == 'Windows'
        shell: bash
        run: |
          echo "Downloading MATLAB Runtime R2023b for Windows..."
          curl -sL -o mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2023b/Release/10/deployment_files/installer/complete/win64/MATLAB_Runtime_R2023b_Update_10_win64.zip
          unzip -q mcr.zip -d mcr_installer

          echo "Installing MATLAB Runtime..."
          INSTALLER=$(find mcr_installer -name "setup.exe" | head -n 1)
          "$INSTALLER" -agreeToLicense yes -destinationFolder "C:\\MATLAB_Runtime"
          echo "Installation command completed"

          echo "C:\\MATLAB_Runtime\\R2023b\\runtime\\win64" >> $GITHUB_PATH
          echo "MCRROOT=C:\\MATLAB_Runtime\\R2023b" >> $GITHUB_ENV
          echo "MCR_INHIBIT_CTF_LOCK=1" >> $GITHUB_ENV
          echo "SPM_HTML_BROWSER=0" >> $GITHUB_ENV

          rm -rf mcr.zip mcr_installer
          echo "MATLAB Runtime installed at C:\\MATLAB_Runtime\\R2023b"

      # ── Setup and extract CTF ──

      - name: Setup CAT standalone (Linux)
        if: runner.os == 'Linux'
        shell: bash
        run: |
          chmod +x cat_standalone/spm25
          echo "Extracting CTF archive..."
          cat_standalone/spm25 function exit || true
          echo "CAT standalone setup complete"

      - name: Setup CAT standalone (macOS)
        if: runner.os == 'macOS'
        shell: bash
        run: |
          # Remove quarantine attributes to avoid Gatekeeper blocking binaries
          xattr -dr com.apple.quarantine cat_standalone 2>/dev/null || true
          chmod -R +x cat_standalone/
          echo "Extracting CTF archive..."
          cd cat_standalone
          ./run_spm25.sh "$MCRROOT" function exit || true
          cd ..
          echo "CAT standalone setup complete"

      - name: Setup CAT standalone (Windows)
        if: runner.os == 'Windows'
        shell: bash
        run: |
          echo "Extracting CTF archive..."
          cd cat_standalone
          # On Windows, spm25.exe should find MCR via PATH/registry
          ./spm25.exe function exit 2>&1 || true
          cd ..
          echo "CAT standalone setup complete"
          echo "Standalone contents after setup:"
          find cat_standalone -maxdepth 3 -type d | head -20

      # ── Find test data (single_subj_T1.nii from SPM canonical directory) ──

      - name: Locate test data
        shell: bash
        run: |
          echo "Searching for single_subj_T1.nii inside standalone..."
          T1=$(find cat_standalone -name "single_subj_T1.nii" -type f 2>/dev/null | head -n 1)
          # If not found as .nii, try .nii.gz and decompress
          if [ -z "$T1" ]; then
            T1GZ=$(find cat_standalone -name "single_subj_T1.nii.gz" -type f 2>/dev/null | head -n 1)
            if [ -n "$T1GZ" ]; then
              echo "Found compressed: $T1GZ — decompressing..."
              gunzip -k "$T1GZ"
              T1="${T1GZ%.gz}"
            fi
          fi
          if [ -z "$T1" ]; then
            echo "ERROR: single_subj_T1.nii not found in standalone"
            echo "Listing all directories:"
            find cat_standalone -maxdepth 4 -type d 2>/dev/null
            echo "Listing all .nii and .nii.gz files:"
            find cat_standalone -name "*.nii" -o -name "*.nii.gz" 2>/dev/null | head -30
            exit 1
          fi
          echo "Found test data: $T1"
          # Copy to working directory so output goes there
          cp "$T1" ./single_subj_T1.nii
          echo "Test data ready: ./single_subj_T1.nii"

      # ── Run CAT segmentation test ──

      - name: Test CAT segmentation (Linux)
        if: runner.os == 'Linux'
        timeout-minutes: 60
        shell: bash
        run: |
          SPMROOT=$(pwd)/cat_standalone
          BATCH="${SPMROOT}/spm25_mcr/spm25/toolbox/CAT/standalone/cat_standalone_segment.m"

          # If batch not at expected location, search for it
          if [ ! -f "$BATCH" ]; then
            BATCH=$(find cat_standalone -name "cat_standalone_segment.m" -type f | head -n 1)
          fi

          echo "Using batch file: $BATCH"
          echo "Running CAT segmentation on single_subj_T1.nii..."

          "${SPMROOT}/run_spm25.sh" "$MCRROOT" batch "$BATCH" "$(pwd)/single_subj_T1.nii"

      - name: Test CAT segmentation (macOS)
        if: runner.os == 'macOS'
        timeout-minutes: 60
        shell: bash
        run: |
          SPMROOT=$(pwd)/cat_standalone
          BATCH=$(find cat_standalone -name "cat_standalone_segment.m" -type f | head -n 1)

          echo "Using batch file: $BATCH"
          echo "Running CAT segmentation on single_subj_T1.nii..."

          "${SPMROOT}/run_spm25.sh" "$MCRROOT" batch "$BATCH" "$(pwd)/single_subj_T1.nii"

      - name: Test CAT segmentation (Windows)
        if: runner.os == 'Windows'
        timeout-minutes: 60
        shell: bash
        run: |
          SPMROOT=$(pwd)/cat_standalone
          BATCH=$(find cat_standalone -name "cat_standalone_segment.m" -type f | head -n 1)

          echo "Using batch file: $BATCH"
          echo "Running CAT segmentation on single_subj_T1.nii..."

          "${SPMROOT}/spm25.exe" batch "$BATCH" "$(pwd)/single_subj_T1.nii"

      # ── Verify outputs ──

      - name: Verify segmentation outputs
        shell: bash
        run: |
          echo "Checking for segmentation output files..."

          # Look for typical CAT output files
          found=0
          for pattern in "mri/mwp1*" "mri/p0*" "report/cat_*" "surf/lh.thickness*"; do
            matches=$(find . -path "./$pattern" 2>/dev/null)
            if [ -n "$matches" ]; then
              echo "Found: $matches"
              found=1
            fi
          done

          if [ "$found" -eq 0 ]; then
            echo "WARNING: No standard CAT output files found in current directory"
            echo "Checking all nii files created:"
            find . -name "*.nii" -newer single_subj_T1.nii 2>/dev/null || echo "No new .nii files"
            find . -name "*.gii" 2>/dev/null || echo "No .gii files"
            find . -name "*.xml" -path "*/report/*" 2>/dev/null || echo "No report XMLs"
          fi

          echo "Test completed successfully"