Add OptSolvX adapter, demo, tests, and docs (initial SBSCL integration)

[xts-Michi]

Not ready to merge yet — updated scope below 👇

Summary

Wires SBSCL ↔ OptSolvX via a small solver adapter and adds a first SBML/FBC → LP bridge skeleton. Includes a runnable demo, unit tests, and short docs. No existing code paths are changed; OptSolvX stays Java-8 compatible (jdk8 classifier).

Changes

Adapter

• org.simulator.optsolvx.OptSolvXSolverAdapter

  • Validates input (null + build()), delegates to CommonsMathSolver.
  • Small hardening (final fields, clearer errors, simple runtime timer), optional debug logs.

SBML/FBC → LP bridge (new)

• org.simulator.optsolvx.FbaToOptSolvX (skeleton)

  • Minimal mapping from SBML/FBC: reactions → variables, bounds → variable bounds, objective (direction + coeffs), first equality constraint(s).
  • Logs a short summary (vars/cons/objective/dir) to aid debugging.

Tests

• org.simulator.optsolvx.OptSolvXSolverAdapterTest

  • solve_requires_non_null_model (IAE)
  • solve_requires_build (ISE)
  • smoke_minimize_with_eq_and_bounds (min 2x+y, x+y=5 → x=0,y=5,obj=5)

• Bridge tests (new):

  • org.simulator.optsolvx.BridgeSmokeTest
  • org.simulator.optsolvx.BridgeObjectiveTest
  • Assert that the SBML mini-model maps to a solvable LP with the expected objective setup.

Docs

• README: “Using OptSolvX (LP) in SBSCL” — how to run the demo, enable debug, and what’s validated.

How to run

• Demo (IDE): org.simulator.optsolvx.OptSolvXDemo

• Tests (Maven):

  • Adapter only:
    mvn -q -Dtest=org.simulator.optsolvx.OptSolvXSolverAdapterTest test
  • Bridge tests:
    mvn -q -Dtest=org.simulator.optsolvx.BridgeSmokeTest,org.simulator.optsolvx.BridgeObjectiveTest test
  • All OptSolvX tests:
    mvn -q -Dtest=org.simulator.optsolvx.* test

Open items / Next

• Complete FbaToOptSolvX mapping (full stoichiometry constraints, reversible flux handling, edge cases).
• Decide logging config format (XML vs YAML/JSON) and add a Maven Enforcer rule to keep legacy XML parsers off the classpath.
• Discuss adapter placement and optional backend selection (factory/flag).
• Extend tests with real SBML/FBC fixtures and numerical assertions.

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[matthiaskoenig]

Looks good

[draeger]

Please coordinate with Ayush that all tests from the SBML test suite run smoothly, including fbc tests.