BIOMD0000001065 flaps between PASS and SOLVER_FAILURE: investigate the fractional-pow-through-zero, and add an INTERMITTENT test status

Start in vcell-core/.../sedml/testsupport/OmexTestCase.java where Status is defined, then read the FAIL branch in OmexTestReport that compares known_failure_type against execSummary.failure_type; add INTERMITTENT as a fourth value with a parallel branch that accepts either a pass or a matching failure type. For the mechanism, locate the fractional-pow domain guard in SundialsSolverStandalone and print the base with %.17g or check signbit to separate -0.0 from genuine negative drift. Done when BIOMD0000001065 passing or failing with SOLVER_FAILURE is green, while a different failure type still turns the nightly red.

Summary

BIOMD0000001065 (von Dassow 2000 segment polarity, 148 species) flaps between PASSED and
FAILED (SOLVER_FAILURE). It failed on essentially every nightly from 2026-06-09 to 2026-08-17,
passed once in run 32094317081
(2026-08-18 03:07 UTC), and has failed on every run since.

That single pass was baselined by 52cf62cbc3, which is why the nightly has been red ever since —
full forensics in #2000. This issue is about the model and the mechanism, not that incident.

Is there already a way to mark a flapping test? Half of it exists.

OmexTestCase.Status is a closed enum with exactly three values
(vcell-core/.../sedml/testsupport/OmexTestCase.java:5):

public enum Status { PASS, FAIL, SKIP }

The failure-signature check already exists and works. In OmexTestReport the comparison is not
just pass/fail — for a case documented FAIL, a run that also fails is a change only if the
failure type differs:

} else if (matchingTestCase.known_status == OmexTestCase.Status.FAIL) {
    if (matchingTestCase.known_failure_type == null
            || !matchingTestCase.known_failure_type.equals(execSummary.failure_type)) {
        // ... recorded as a change

So known_failure_type is exactly the "confirm it failed the way we expect" mechanism. Note also
that known_failure_desc is stored but not compared — correct, since it embeds a per-run temp
path (/tmp/VCell_CLI_<random>/…) and would otherwise differ every night.

What does not exist is a status that tolerates either outcome. Today both directions are
regressions:

baseline	run passes	run fails
PASS	green	red
FAIL + type	red	green if the failure type matches
SKIP	red	red (recorded, stays SKIP)

So for a genuinely intermittent model there is no setting that is green both ways.

Why the obvious workarounds are not good enough

• Restore FAIL / SOLVER_FAILURE (the state it held for two months) — correct today and the
  right immediate action, but the gate goes red again the next time it passes: "Test case marked
  as FAIL … but passed". A stopgap that is guaranteed to flap.
• Mark it SKIP — silences it, but SKIP means not run at all (the model list is also
  hard-coded in NightlyBMDB_CLI.yml, the case $number in 235|255|… block). Total coverage loss:
  we would never learn that it started passing reliably, and never notice if it began failing in a
  new way, which is precisely the signal worth keeping.

Proposed: a fourth status

public enum Status { PASS, FAIL, SKIP, INTERMITTENT }

with the semantics "either outcome is acceptable, but a failure must look like the documented
one":

run result	INTERMITTENT verdict
passes	accepted — no change
fails with known_failure_type	accepted — no change
fails with a different failure type	change → red

That keeps the model executing and keeps the failure-signature check, while not gating on the coin
flip. It is a small change — one enum value plus a branch in OmexTestReport, alongside the
existing FAIL branch that already does the type comparison.

The mechanism generalises beyond this model; splitting it into its own issue is reasonable if it
grows.

The actual question about this model

Marking it intermittent manages the symptom. Why it is intermittent is the interesting part, and
#2000 has narrowed it considerably:

• The generated MathDescription is byte-identical across the shas either side of the flip
  (verified, with a negative control) — no VCell model-processing change is involved.
• The solver binary is unchanged (v0.0.44-dev4, asset last uploaded 2024-02-11).
• The corpus is unchanged (and now pinned by #2003).

The failure is a Hill term raising a species to a fractional power as it passes through zero:

pow(u,v) and u=-0.000000<0 and v=2.619640 not an integer
  where: EN_0_0 = -0.000000

Two candidate explanations, with different fixes:

1. The guard is wrong. If EN_0_0 is true IEEE -0.0, then -0.0 < 0 is false and C99
   §F.9.4.4 gives pow(-0.0, 2.61964) = +0.0. The C++ guard in SundialsSolverStandalone would be
   rejecting a legal input — and this becomes an instance of #1646, currently marked Done on the
   board. If so, fixing it may make this model pass reliably, which would be the real fix and
   would explain the intermittency as "sometimes the drift lands exactly on -0.0, sometimes a
   hair below".
2. It is drift, and the model is simply marginal. A stiff 148-species model whose integrator
   undershoots zero into a fractional power will hit this eventually; whether it does depends on
   last-ulp differences, which vary with the runner's CPU (glibc pow dispatches differently with
   and without FMA). Then the question is whether VCell should clamp a negative concentration to
   zero before a fractional pow — a modelling decision, not just a guard fix.

Distinguishing them is cheap: print the base with %.17g, or test signbit, at the guard.

Suggested work

1. Settle (1) vs (2) — one print statement in the solver's domain guard.
2. Restore 1065 to FAIL / SOLVER_FAILURE so the nightly is honest in the meantime (#2000).
3. Add INTERMITTENT, and apply it here.
4. If it turns out to be (1), fix the guard and check whether this model — and any others using
   fractional powers of concentrations — become reliable.

Worth grepping the corpus for other models with fractional exponents on species; if the guard is
wrong, 1065 is unlikely to be the only one sitting near the edge.

Refs #2000, #1646, #1901