Align ODE dependencies (Commons Math 2.x vs. 3.x)

[xts-Michi]

Description

SBSCL’s ODE modules import org.apache.commons.math.ode.* (Commons Math 2.x).
With the OptSolvX integration we also require Commons Math 3.x (org.apache.commons.math3.*).
Because 2.x and 3.x use different package names and are not interchangeable, both must be present.

Current status

• pom.xml updated to include org.apache.commons:commons-math:2.2 alongside commons-math3:3.6.1.
• Build and demo run successfully.

Affected code

• org/simulator/math/odes/*
• org/simulator/sbml/SBMLinterpreter.java
• org/simulator/examples/*
  (ODE types like FirstOrderDifferentialEquations, DerivativeException, EventHandler come from 2.x.)

Steps to reproduce (failure case)

1. Remove commons-math:2.2 from pom.xml.
2. Reimport Maven / mvn -U clean package.
3. Compilation fails (package org.apache.commons.math.ode does not exist, missing ODE types).

Expected

Project compiles and runs with both libraries coexisting.

Acceptance criteria

• mvn -q dependency:tree -Dincludes=org.apache.commons:commons-math,org.apache.commons:commons-math3 lists both.
• mvn clean package succeeds on a fresh checkout.
• Demo: org.simulator.optsolvx.OptSolvXDemo runs without errors.

Follow-up

Migrate ODE code to the Commons Math 3 API (org.apache.commons.math3.ode.*) and then drop 2.x.

[dyrpsf]

Hi @xts-Michi @draeger ,
I’d like to work on this issue.

Plan:

• Inspect the current dependency tree for commons-math 2.x and 3.x.
• Ensure pom.xml declares both org.apache.commons:commons-math (2.x) and
  org.apache.commons:commons-math3 (3.x) as needed.
• Verify that the ODE modules and the OptSolvX demo compile and run with both
  libraries coexisting.
• Confirm the acceptance criteria (mvn dependency:tree shows both libs,
  mvn clean package succeeds, and org.simulator.optsolvx.OptSolvXDemo runs).

[dyrpsf]

Hi @xts-Michi & @draeger ,
I’ve opened a PR for this: #98.

It adds commons-math3:3.6.1 alongside the existing commons-math:2.2 to pom.xml, and the
project builds successfully. The dependency tree now shows both Commons Math 2.x and 3.x present.