Add hdf5-native Maven JARs and SciJava native-lib-loader integration

.github/actions/setup-jextract/action.yml

@@ -2,7 +2,7 @@ name: 'Setup jextract'
 description: 'Install jextract for FFM binding generation across all platforms'
 inputs:
   java-version:
-    description: 'Java version for jextract (24, 25, latest)'
+    description: 'Java version for jextract (25)'
     required: false
     default: '25'
 
@@ -21,47 +21,45 @@ runs:
       id: setup-jextract-unix
       if: runner.os != 'Windows'
       shell: bash
+      env:
+        INPUT_JAVA_VERSION: ${{ inputs.java-version }}
       run: |
-        echo "Installing jextract for $RUNNER_OS..."
+        echo "Installing jextract 25 for $RUNNER_OS..."
+
+        if [[ "$INPUT_JAVA_VERSION" != "25" ]]; then
+          echo "ERROR: Only jextract 25 is supported (requested: $INPUT_JAVA_VERSION)"
+          exit 1
+        fi
 
         # Determine platform
         if [[ "$RUNNER_OS" == "macOS" ]]; then
-          PLATFORM="macos-x64"
+          if [[ "$(uname -m)" == "arm64" ]]; then
+            PLATFORM="macos-aarch64"
+          else
+            PLATFORM="macos-x64"
+          fi
+        elif [[ "$(uname -m)" == "aarch64" ]]; then
+          PLATFORM="linux-aarch64"
         else
           PLATFORM="linux-x64"
         fi
 
-        # Try different jextract versions (from latest to older)
-        # Check https://jdk.java.net/jextract/ for available builds
-        JEXTRACT_URLS=(
-          "https://download.java.net/java/early_access/jextract/22/6/openjdk-22-jextract+6-47_${PLATFORM}_bin.tar.gz"
-          "https://download.java.net/java/early_access/jextract/21/5/openjdk-21-jextract+5-31_${PLATFORM}_bin.tar.gz"
-          "https://download.java.net/java/early_access/jextract/20/1/openjdk-20-jextract+1-2_${PLATFORM}_bin.tar.gz"
-        )
+        # Use fixed jextract 25 version
+        JEXTRACT_URL="https://download.java.net/java/early_access/jextract/25/2/openjdk-25-jextract+2-4_${PLATFORM}_bin.tar.gz"
+        echo "Downloading jextract 25 from: $JEXTRACT_URL"
 
         mkdir -p $HOME/jextract
         cd $HOME/jextract
 
-        SUCCESS=false
-        for URL in "${JEXTRACT_URLS[@]}"; do
-          echo "Trying to download from: $URL"
-          if curl -L -f -o jextract.tar.gz "$URL" 2>/dev/null; then
-            echo "✓ Download successful from $URL"
-            tar -xzf jextract.tar.gz --strip-components=1
-            rm jextract.tar.gz
-            SUCCESS=true
-            break
-          else
-            echo "✗ Failed to download from $URL, trying next..."
-          fi
-        done
-
-        if [ "$SUCCESS" = false ]; then
-          echo "ERROR: Failed to download jextract from any known source"
-          echo "Please check https://jdk.java.net/jextract/ for available builds"
+        if ! curl -L -f -o jextract.tar.gz "$JEXTRACT_URL"; then
+          echo "ERROR: Failed to download jextract 25 from $JEXTRACT_URL"
+          echo "See https://jdk.java.net/jextract/25/ for available builds"
           exit 1
         fi
 
+        tar -xzf jextract.tar.gz --strip-components=1
+        rm jextract.tar.gz
+
         # Set outputs
         echo "jextract-home=$HOME/jextract" >> $GITHUB_OUTPUT
 
@@ -70,6 +68,10 @@ runs:
           VERSION=$($HOME/jextract/bin/jextract --version 2>&1 | head -1 || echo "unknown")
           echo "jextract-version=$VERSION" >> $GITHUB_OUTPUT
           echo "✓ jextract installed successfully: $VERSION"
+          if [[ "$VERSION" != jextract\ 25* ]]; then
+            echo "ERROR: Expected jextract 25, got: $VERSION"
+            exit 1
+          fi
         else
           echo "jextract-version=unknown" >> $GITHUB_OUTPUT
           echo "✓ jextract installed (version check not supported)"
@@ -79,84 +81,71 @@ runs:
       id: setup-jextract-windows
       if: runner.os == 'Windows'
       shell: pwsh
+      env:
+        INPUT_JAVA_VERSION: ${{ inputs.java-version }}
       run: |
-        Write-Host "Installing jextract for Windows..."
+        Write-Host "Installing jextract 25 for Windows..."
+
+        if ($env:INPUT_JAVA_VERSION -ne "25") {
+          Write-Host "ERROR: Only jextract 25 is supported (requested: $env:INPUT_JAVA_VERSION)"
+          exit 1
+        }
 
-        # Try multiple jextract versions (latest to older)
-        # Windows now uses .tar.gz format
-        $JextractUrls = @(
-          "https://download.java.net/java/early_access/jextract/22/6/openjdk-22-jextract+6-47_windows-x64_bin.tar.gz",
-          "https://download.java.net/java/early_access/jextract/21/5/openjdk-21-jextract+5-31_windows-x64_bin.tar.gz",
-          "https://download.java.net/java/early_access/jextract/20/1/openjdk-20-jextract+1-2_windows-x64_bin.tar.gz"
-        )
+        # Use fixed jextract 25 version
+        $JextractUrl = "https://download.java.net/java/early_access/jextract/25/2/openjdk-25-jextract+2-4_windows-x64_bin.tar.gz"
+        Write-Host "Downloading jextract 25 from: $JextractUrl"
 
         $JextractHome = "$env:USERPROFILE\jextract"
         New-Item -ItemType Directory -Force -Path $JextractHome | Out-Null
+        $TarPath = "$JextractHome\jextract.tar.gz"
 
-        $Success = $false
-        foreach ($Url in $JextractUrls) {
-          Write-Host "Trying to download from: $Url"
-          $TarPath = "$JextractHome\jextract.tar.gz"
-
-          try {
-            Invoke-WebRequest -Uri $Url -OutFile $TarPath -ErrorAction Stop
-            Write-Host "✓ Download successful from $Url"
-
-            # Extract using tar (available in Windows 10+)
-            $TempExtract = "$JextractHome\temp"
-            New-Item -ItemType Directory -Force -Path $TempExtract | Out-Null
-            tar -xzf "$TarPath" -C "$TempExtract" 2>&1 | Out-Null
-
-            # Find jextract.bat
-            $JextractBat = Get-ChildItem -Path $TempExtract -Filter "jextract.bat" -Recurse -ErrorAction SilentlyContinue | Select-Object -First 1
-
-            if ($JextractBat) {
-              Write-Host "Found jextract.bat at: $($JextractBat.FullName)"
-
-              # Move contents to JextractHome
-              $JextractRoot = $JextractBat.Directory.Parent.FullName
-              Get-ChildItem -Path $JextractRoot | ForEach-Object {
-                Move-Item -Path $_.FullName -Destination $JextractHome -Force
-              }
-
-              # Clean up
-              Remove-Item -Path $TempExtract -Recurse -Force
-              Remove-Item -Path $TarPath -Force
-
-              # Verify
-              if (Test-Path "$JextractHome\bin\jextract.bat") {
-                Write-Host "✓ jextract extracted successfully to $JextractHome"
-                $Success = $true
-                break
-              }
-            } else {
-              Write-Host "✗ Could not find jextract.bat in extracted files"
-              Remove-Item -Path $TempExtract -Recurse -Force -ErrorAction SilentlyContinue
-            }
-          }
-          catch {
-            Write-Host "✗ Failed to download or extract from $Url"
-            Write-Host "Error: $_"
-          }
+        try {
+          Invoke-WebRequest -Uri $JextractUrl -OutFile $TarPath -ErrorAction Stop
+        }
+        catch {
+          Write-Host "ERROR: Failed to download jextract 25 from $JextractUrl"
+          Write-Host "See https://jdk.java.net/jextract/25/ for available builds"
+          Write-Host "Error: $_"
+          exit 1
+        }
+
+        # Extract using tar (available in Windows 10+)
+        $TempExtract = "$JextractHome\temp"
+        New-Item -ItemType Directory -Force -Path $TempExtract | Out-Null
+        tar -xzf "$TarPath" -C "$TempExtract" 2>&1 | Out-Null
+
+        # Find jextract.bat
+        $JextractBat = Get-ChildItem -Path $TempExtract -Filter "jextract.bat" -Recurse -ErrorAction SilentlyContinue | Select-Object -First 1
+        if (-not $JextractBat) {
+          Write-Host "ERROR: jextract.bat not found in downloaded jextract 25 archive"
+          exit 1
+        }
+
+        $JextractRoot = $JextractBat.Directory.Parent.FullName
+        Get-ChildItem -Path $JextractRoot | ForEach-Object {
+          Move-Item -Path $_.FullName -Destination $JextractHome -Force
         }
 
-        if (-not $Success) {
-          Write-Host "ERROR: Failed to download jextract from any known source"
-          Write-Host "Please check https://jdk.java.net/jextract/ for available builds"
+        # Clean up
+        Remove-Item -Path $TempExtract -Recurse -Force
+        Remove-Item -Path $TarPath -Force
+
+        # Verify
+        if (-not (Test-Path "$JextractHome\bin\jextract.bat")) {
+          Write-Host "ERROR: jextract 25 install incomplete (missing bin\jextract.bat)"
           exit 1
         }
 
         # Set outputs
         echo "jextract-home=$JextractHome" >> $env:GITHUB_OUTPUT
 
         # Verify installation
-        try {
-          $Version = & "$JextractHome\bin\jextract.bat" --version 2>&1 | Select-Object -First 1
-          echo "jextract-version=$Version" >> $env:GITHUB_OUTPUT
-          Write-Host "✓ jextract installed successfully: $Version"
-        } catch {
-          echo "jextract-version=unknown" >> $env:GITHUB_OUTPUT
-          Write-Host "✓ jextract installed (version check not supported)"
+        $Version = & "$JextractHome\bin\jextract.bat" --version 2>&1 | Select-Object -First 1
+        echo "jextract-version=$Version" >> $env:GITHUB_OUTPUT
+        Write-Host "✓ jextract installed successfully: $Version"
+        if ($Version -notlike "jextract 25*") {
+          Write-Host "ERROR: Expected jextract 25, got: $Version"
+          exit 1
         }
 
     - name: Set environment variables