Feat: set OptSolvX as default LP backend; add SBML-FBC→LP bridge

README.md

@@ -81,6 +81,57 @@ Further examples can be found directly within this repository in the [Examples P
 * How to run a [stochastic simulation](https://github.com/draeger-lab/SBSCL/blob/master/src/main/java/fern/Start.java)
 
 
+## Using OptSolvX (LP) in SBSCL
+
+SBSCL integrates the OptSolvX linear programming abstraction layer [OptSolvX Repo](https://github.com/draeger-lab/OptSolvX).
+
+### OptSolvX dependency (temporary)
+
+OptSolvX is not yet available on Maven Central and must be installed locally.
+
+To build SBSCL with OptSolvX support:
+1. Build OptSolvX locally in the **OptSolvX repo**:
+   ```bash 
+   mvn -P compat8 -DskipTests clean package
+   ```
+2. Activate the profile in the SBSCL repo:
+    ```bash 
+   mvn -DskipTests clean package
+    ```
+3. SBSCL resolves `org.optsolvx:optsolvx:0.1.0-SNAPSHOT:jar:jdk8` from the local Maven repository.
+
+### Run the OptSolvX demo
+
+* In your IDE, run: `org.simulator.optsolvx.OptSolvXDemo`.
+* The demo builds a tiny LP and solves it via OptSolvX (backend selectable via `-Doptsolvx.solver=commons-math|ojalgo`).
+* Make sure the OptSolvX **jdk8** artifact is on the classpath (declared in SBSCL’s `pom.xml`).
+
+*Note:* FBA in SBSCL now uses OptSolvX by default.
+
+### Enable debug logs
+
+Create the adapter with `debug = true`:
+
+```java
+LPSolverAdapter backend =
+        OptSolvXConfig.resolve(lpModel, System.getProperty("optsolvx.solver"));
+LPSolverAdapter solver =
+        new OptSolvXSolverAdapter(backend, true);
+```
+
+**Solver selection behavior**
+
+* You can pick a backend via `-Doptsolvx.solver=ojalgo` or env `OPTSOLVX_SOLVER=ojalgo`.
+* If an explicit solver name is provided and unknown, OptSolvX fails fast with an
+`IllegalArgumentException`.  
+* If no solver is specified, `commons-math` is used as the default backend.
+
+#### SBML/FBC → LP bridge (initial)
+
+`FbaToOptSolvX` implements a minimal SBML/FBC → LP mapping used by FBA.
+Advanced SBML features are intentionally out of scope.
+
+
 ### Comparison to Similar Libraries
 
 To compare SBSCL to other simulation engines and to benchmark its predictions and results, a separate project, [SBSCL simulator comparison](https://github.com/matthiaskoenig/sbscl-simulator-comparison), is available.
@@ -117,6 +168,11 @@ The package structure in more detail:
 
 Please e-mail any bugs, problems, suggestions, or issues regarding this library to the bug tracker at https://github.com/draeger-lab/SBSCL/issues
 
+### Note on XML parsers (JDK ≥ 17)
+
+SBSCL excludes legacy `xercesImpl`, `xml-apis`, and `xalan` (pulled transitively by `jlibsedml`) to avoid JAXP compatibility issues on modern JDKs (e.g., an `AbstractMethodError` during Log4j2 XML configuration).  
+If you rely on specific Xerces/Xalan features, please open an issue so we can provide an opt-in solution
+
 ## Licensing terms
 
 This file is part of Simulation Core Library, a Java-based library for efficient numerical simulation of biological models.

pom.xml

@@ -458,20 +458,44 @@
         </exclusion>
       </exclusions>
     </dependency>
+
+    <!--
+      Exclude legacy XML parser stack for compatibility with modern JDKs.
+      Reason: xercesImpl/xml-apis/xalan can shadow the JDK's JAXP on JDK 17/22
+              and trigger AbstractMethodError during Log4j2 XML configuration.
+      If anyone needs explicit Xerces/Xalan features, please open an issue.
+      (See SBSCL issue #91)
+    -->
     <dependency>
       <groupId>org.jlibsedml</groupId>
       <artifactId>jlibsedml</artifactId>
       <version>2.2.3</version>
+      <exclusions>
+        <exclusion>
+          <groupId>xerces</groupId>
+          <artifactId>xercesImpl</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>xml-apis</groupId>
+          <artifactId>xml-apis</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>xalan</groupId>
+          <artifactId>xalan</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
-      <artifactId>commons-math</artifactId>
-      <version>2.2</version>
+      <artifactId>commons-lang3</artifactId>
+      <version>3.18.0</version>
     </dependency>
+
+    <!-- Commons Math 2.x (ODE API used under org.apache.commons.math.ode.*) -->
     <dependency>
       <groupId>org.apache.commons</groupId>
-      <artifactId>commons-lang3</artifactId>
-      <version>3.18.0</version>
+      <artifactId>commons-math</artifactId>
+      <version>2.2</version>
     </dependency>
 
     <dependency>
@@ -486,26 +510,12 @@
     </dependency>
 
     <!-- LP solvers -->
-    <dependency>
-      <groupId>scpsolver</groupId>
-      <artifactId>SCPSolver</artifactId>
-      <version>1.0v2</version>
-    </dependency>
-    <dependency>
-      <groupId>scpsolver</groupId>
-      <artifactId>GLPKSolverPack</artifactId>
-      <version>4.35v2</version>
-    </dependency>
-    <dependency>
-      <groupId>scpsolver</groupId>
-      <artifactId>LPSOLVESolverPack</artifactId>
-      <version>5.5.2.5</version>
-    </dependency>
     <dependency>
       <groupId>kisao</groupId>
       <artifactId>libkisao</artifactId>
       <version>1.0.3.1-rc</version>
     </dependency>
+
     <!-- OMEX archive -->
     <dependency>
       <groupId>de.uni-rostock.sbi</groupId>
@@ -518,6 +528,14 @@
         </exclusion>
       </exclusions>
     </dependency>
+
+    <!-- OptSolvX -->
+    <dependency>
+      <groupId>org.optsolvx</groupId>
+      <artifactId>optsolvx</artifactId>
+      <version>0.1.0-SNAPSHOT</version>
+      <classifier>jdk8</classifier>
+    </dependency>
   </dependencies>
 
 
@@ -796,6 +814,17 @@
         <javadoc.opts>-Xdoclint:none</javadoc.opts>
       </properties>
     </profile>
+
+  <!--  Local OptSolvX call  -->
+    <profile>
+        <id>local-optsolvx</id>
+        <repositories>
+            <repository>
+                <id>local-optsolvx</id>
+                <url>file:${project.basedir}/lib/maven</url>
+            </repository>
+        </repositories>
+    </profile>
   </profiles>
 
   <!-- =================================================================== -->

src/lib/register_maven_jars.sh

@@ -11,7 +11,4 @@
 LIB_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
 # register
-mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=scpsolver -DartifactId=SCPSolver -Dversion=1.0v2 -Dfile=nmi/scpsolver/1.0/SCPSolver-1.0v2.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true
-mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=scpsolver -DartifactId=GLPKSolverPack -Dversion=4.35v2 -Dfile=nmi/scpsolver/1.0/GLPKSolverPack-4.35v2.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true
-mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=scpsolver -DartifactId=LPSOLVESolverPack -Dversion=5.5.2.5 -Dfile=nmi/scpsolver/1.0/LPSOLVESolverPack-5.5.2.5.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true
 mvn org.apache.maven.plugins:maven-install-plugin:2.5.2:install-file -DgroupId=kisao -DartifactId=libkisao -Dversion=1.0.3.1-rc -Dfile=kisao/LibKiSAO/1.0.3.1/libkisao-1.0.3.1-rc.jar -DlocalRepositoryPath=${LIB_DIR}/maven -Dpackaging=jar -DgeneratePom=true -DcreateChecksum=true