From ba1f4dcde243fdfa844a98ae38732dc46cc044e1 Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Thu, 10 Apr 2025 01:10:15 -0400
Subject: [PATCH 1/3] update vcell-submodule to remove most serialization in
 vcell-core

---
 vcell_submodule | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcell_submodule b/vcell_submodule
index 0c860b5..745e4ce 160000
--- a/vcell_submodule
+++ b/vcell_submodule
@@ -1 +1 @@
-Subproject commit 0c860b574b260cf14d31f19b448c6dc5b240d0e7
+Subproject commit 745e4cefe8e9eabfa9ef122ea06105e33ff43a83

From 0d89adff423b92328711374a6faad833a11ddbd0 Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Thu, 10 Apr 2025 01:12:52 -0400
Subject: [PATCH 2/3] set XmlHelper.cloneUsingXML from libvcell, still errors
 in VCell Tests

---
 vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java | 3 +++
 .../src/main/java/org/vcell/libvcell/SolverUtils.java         | 4 ++++
 2 files changed, 7 insertions(+)

diff --git a/vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java b/vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java
index 942ae16..fb79f14 100644
--- a/vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java
+++ b/vcell-native/src/main/java/org/vcell/libvcell/ModelUtils.java
@@ -35,6 +35,7 @@ public static void sbml_to_vcml(String sbml_content, Path vcmlPath)
 
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
 
         record LoggerMessage(VCLogger.Priority priority, VCLogger.ErrorType errorType, String message) {};
         final ArrayList<LoggerMessage> messages = new ArrayList<>();
@@ -76,6 +77,7 @@ public static void vcml_to_sbml(String vcml_content, String applicationName, Pat
             throws XmlParseException, IOException, XMLStreamException, SbmlException, MappingException, ImageException, GeometryException, ExpressionException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
 
         BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
         bioModel.updateAll(false);
@@ -115,6 +117,7 @@ public static void vcml_to_sbml(String vcml_content, String applicationName, Pat
     public static void vcml_to_vcml(String vcml_content, Path vcmlPath) throws XmlParseException, IOException, MappingException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
 
         BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml_content));
         bioModel.updateAll(false);
diff --git a/vcell-native/src/main/java/org/vcell/libvcell/SolverUtils.java b/vcell-native/src/main/java/org/vcell/libvcell/SolverUtils.java
index 95cf2bb..b141127 100644
--- a/vcell-native/src/main/java/org/vcell/libvcell/SolverUtils.java
+++ b/vcell-native/src/main/java/org/vcell/libvcell/SolverUtils.java
@@ -41,6 +41,8 @@ public class SolverUtils {
     public static void vcmlToFiniteVolumeInput(String vcml_content, String simulation_name, File parentDir, File outputDir) throws XmlParseException, MappingException, SolverException, ExpressionException, MathException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
+
         if (vcml_content.substring(0, 300).contains("<sbml xmlns=\"http://www.sbml.org/sbml")) {
             throw new IllegalArgumentException("expecting VCML content, not SBML");
         }
@@ -134,6 +136,8 @@ private static FieldDataIdentifierSpec[] getFieldDataIdentifierSpecs(Simulation
     public static void sbmlToFiniteVolumeInput(String sbml_content, File outputDir) throws MappingException, PropertyVetoException, SolverException, ExpressionException, VCLoggerException {
         GeometrySpec.avoidAWTImageCreation = true;
         VCMongoMessage.enabled = false;
+        XmlHelper.cloneUsingXML = true;
+
         SBMLExporter.MemoryVCLogger vcl = new SBMLExporter.MemoryVCLogger();
         boolean bValidateSBML = true;
         // input stream from sbml_content String

From f78c9779a09c67ce19cc2698ec5808bf522809c9 Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Thu, 10 Apr 2025 01:29:52 -0400
Subject: [PATCH 3/3] bump version to 0.0.13

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 53ac9c9..dc9f896 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "libvcell"
-version = "0.0.12"
+version = "0.0.13"
 description = "This is a python package which wraps a subset of VCell Java code as a native python package."
 authors = ["Jim Schaff <schaff@uchc.edu>", "Ezequiel Valencia <evalencia@uchc.edu>"]
 repository = "https://github.com/virtualcell/libvcell"