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

[xts-Michi]

Status: Not ready to merge yet - review welcome.

Summary

Switch FBA to OptSolvX by default, introduce an initial SBML-FBC→LP bridge, fix dependency/classpath issues for modern JDKs, and remove the legacy SCPSolver/GLPK backend.

What changed since the last review

• Removed NewGLPKSolver and SCPSolver test (SCPSolverIssue); no SCPSolver/GLPK deps remain in code or POM.
• Added constraint-level tests for the bridge (BridgeConstraintTests) and minor perf tidy-ups in the bridge (cached SBML lists, pre-sized maps).
• Restored getActiveObjective() in FBA for API/test compatibility.
• Aligned dependencies to include Commons Math 2.2 alongside Math3 for legacy ODE API.

Key changes

1) Default backend = OptSolvX

• FBA uses OptSolvX by default via OptSolvXSolverAdapter.
• The solver selection is currently limited to the CommonsMathSolver. Other solvers will follow!

2) SBML-FBC → LP bridge (prototype)

• FbaToOptSolvX maps:

  • variables = reactions (+ bounds from FBC v1/v2),
  • constraints = S·v = 0 with boundary species ignored,
  • objective = active FBC objective (v1/v2).

• Small perf pass: cache SBML lists, pre-size maps.

3) Dependency / classpath

• Add org.apache.commons:commons-math:2.2 for legacy ODE API (Math2) next to commons-math3:3.6.1.
• Exclude legacy XML stack (xercesImpl, xml-apis, xalan) to avoid JAXP conflicts with modern JDKs (Log4j2 config now clean).

4) Cleanup: remove SCPSolver/GLPK

• Delete legacy GLPK/SCPSolver backend (code + test).
• No more SCPSolver jars on the compile/test classpath.
• Note: A shell helper under src/test/scripts/** still references old GLPK jars only for the historic wrapper; it’s inert for Maven builds and can be pruned later.

5) Tests & layout

• Bridge smoke/objective: BridgeSmokeTest, BridgeObjectiveTest.

• New: BridgeConstraintTests checking S·v=0 at coefficient level:

  • counts per species,
  • sign/value for non-unit stoichiometry,
  • sum across reactions,
  • ignore boundary species,
  • ignore species with no participation,
  • multi-species (A,B) with different patterns.

• Tests live under src/test/java/org/simulator/optsolvx.

6) Docs / build hygiene

• README adds short “Using OptSolvX (LP) in SBSCL)” snippet & JDK notes.
• Ensured OptSolvX artifact remains Java 8 bytecode (major 52) for downstream users.

How to test

# E. coli core (unchanged public API)
mvn -q -Dtest=org.simulator.fba.FluxBalanceAnalysisTest#solveEColiCore test
mvn -q -Dtest=org.simulator.fba.FluxBalanceAnalysisTest#solveEColiCoreGZ test

# Bridge-focused
mvn -q -Dtest=org.simulator.optsolvx.BridgeSmokeTest test
mvn -q -Dtest=org.simulator.optsolvx.BridgeObjectiveTest test
mvn -q -Dtest=org.simulator.optsolvx.BridgeConstraintTests test

Typical runtime (E. coli core):

INFO: FbaToOptSolvX: built LP (vars=95, cons=72, objectiveVars=1, dir=MAXIMIZE)
INFO: FBA: built OptSolvX model (vars=95, cons=72)
INFO: OptSolvXSolverAdapter: result feasible=true, objective≈0.874

Compatibility

• No public API changes; only the default backend changed.
• getActiveObjective() restored; tests depending on it pass.
• Builds/runs on modern JDKs (tested with JDK 22); OptSolvX stays Java-8 compatible.

Follow-ups

• Decide how OptSolvX should be implemented into SBSCL

[draeger]

Please place a local lib file of OptSolvX and use a local dependency for the time being, until we have it in MavenCentral.