analysis: fix getMinNrFluxes crash on all-non-negative scores, drop dead code

[edkerk]

Summary

Found while porting getMinNrFluxes to raven-toolbox (SysBioChalmers/raven-gecko-parity#42, SysBioChalmers/raven-toolbox#128): two issues worth fixing independently of the port itself.

Crash on an all-non-negative scores input. scores(scores>=0)=max(scores(scores<0)) evaluates the right-hand side to an empty array whenever nothing is negative. Unlike the literal [] MATLAB treats as element deletion, an empty array computed by max() doesn't delete anything — it just errors on the resulting size mismatch (scores has 3 elements selected, 0 provided), verified directly:

>> scores = [1;2;3];
>> scores(scores>=0) = max(scores(scores<0));
Unable to perform assignment because the left and right sides have a different number of elements.

Clamped to 0 in that case instead (every reaction becomes equally, un-weighted) — matching the choice made for the same edge case in the Python port.

Dead code. A fully commented-out Mosek-only branch, guarded by a stale TODO: modify for cobra/gurobi, could never execute (Mosek support was dropped from RAVEN entirely back in 2.3.0). Removed it along with the docstring's matching -2: optimization time out exit case, which was never actually reachable.

No change to the MILP formulation itself, and no change to any input that previously worked.

Test plan

• Verified the crash directly (isolated repro above) before and after the fix.
• tAnalysis test class: 23/25 passed; getMinNrFluxesReturnsFlux passes. The 2 failures (getMinimalMediumReturnsMedium, getMinimalMediumExplicitGrowth) are pre-existing and unrelated — a different function entirely, already confirmed unrelated in remove: followFluxes, dead code fully subsumed by printFluxes + followChanged #725/remove: exportToTabDelimited, dead fallback in exportToExcelFormat #727.
• SysBioChalmers/raven-gecko-parity's min_nr_fluxes_toy scenario (getMinNrFluxes.m vs raven-toolbox's get_min_nr_fluxes, via the scip solver): still MATCH after this change.

[github-actions]

Function test results

306 tests   279 ✅  1m 7s ⏱️
 25 suites   27 💤
  1 files      0 ❌

Results for commit 959b970.