Update Boilerplate scripts

Author: tferr

src/main/java/sc/fiji/snt/gui/ScriptInstaller.java

@@ -44,6 +44,7 @@
 import java.util.List;
 import java.util.*;
 import java.util.concurrent.Future;
+import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
@@ -54,6 +55,10 @@
  */
 public class ScriptInstaller implements MenuKeyListener {
 
+	/** Matches requireVersion("x.y.z") calls (any quoted version string) in boilerplate scripts. */
+	private static final Pattern REQUIRE_VERSION_PATTERN = Pattern
+			.compile("(requireVersion\\(\\s*\")[^\"]*(\"\\s*\\))");
+
 	@Parameter
 	private Context context;
 
@@ -541,7 +546,16 @@ public static String getBoilerplateScript(final String extension) {
 		final InputStream is = classloader.getResourceAsStream("script_templates/Neuroanatomy/Boilerplate/"
 				+ getBoilerPlateFile(extension));
         assert is != null;
-        return  new BufferedReader(new InputStreamReader(is)).lines().collect(Collectors.joining("\n"));
+        final String script = new BufferedReader(new InputStreamReader(is)).lines().collect(Collectors.joining("\n"));
+        // Boilerplate files have a hardwired requireVersion() call: inject the running SNT version so templates don't
+		// lag behind the release they were generated from
+        final Matcher matcher = REQUIRE_VERSION_PATTERN.matcher(script);
+        final StringBuilder sb = new StringBuilder();
+        while (matcher.find()) {
+            matcher.appendReplacement(sb, Matcher.quoteReplacement(matcher.group(1) + SNTUtils.VERSION + matcher.group(2)));
+        }
+        matcher.appendTail(sb);
+        return sb.toString();
 	}
 
 	public static boolean runScript(final String dir, final String file, final Map<String, Object> inputMap) {

src/main/resources/script_templates/Neuroanatomy/Boilerplate/BSH.bsh

@@ -21,6 +21,7 @@ import sc.fiji.snt.analysis.sholl.*;
 import sc.fiji.snt.annotation.*;
 import sc.fiji.snt.io.*;
 import sc.fiji.snt.plugin.*;
+import sc.fiji.snt.tracing.auto.*;
 import sc.fiji.snt.util.*;
 import sc.fiji.snt.viewer.*;
 

src/main/resources/script_templates/Neuroanatomy/Boilerplate/GVY.groovy

@@ -21,6 +21,7 @@ import sc.fiji.snt.analysis.sholl.*
 import sc.fiji.snt.annotation.*
 import sc.fiji.snt.io.*
 import sc.fiji.snt.plugin.*
+import sc.fiji.snt.tracing.auto.*
 import sc.fiji.snt.util.*
 import sc.fiji.snt.viewer.*
 

src/main/resources/script_templates/Neuroanatomy/Boilerplate/PY.py

@@ -18,7 +18,8 @@
 from sc.fiji.snt.analysis import GroupedTreeStatistics, MultiTreeStatistics, NodeStatistics, TreeStatistics,\
             ConvexHullAnalyzer, PersistenceAnalyzer, ShollAnalyzer, StrahlerAnalyzer, NodeColorMapper,\
             TreeColorMapper, PathProfiler, PathStraightener, RoiConverter, SNTChart, SNTTable
-from sc.fiji.snt.tracing.auto import BinaryTracer
+from sc.fiji.snt.tracing.auto import AutoTraceConfig, AutoTracer, BinaryTracer, ComponentReconnector,\
+            DiskBackedGWDTTracer, GWDTTracer, GWDTTracerFactory, SomaUtils, SparseGWDTTracer
 from sc.fiji.snt.analysis.graph import DirectedWeightedGraph
 from sc.fiji.snt.analysis.sholl.parsers import TreeParser
 from sc.fiji.snt.annotation import AllenCompartment, AllenUtils, VFBUtils, ZBAtlasUtils