Test suite fails with jax >= 0.10: spurious FutureWarning from jax's internal `cho_solve` dispatch, escalated by `filterwarnings = ["error"]`

Start in pyproject.toml at the filterwarnings configuration and review the existing h5py precedent and the proposed JAX warning pattern. Run the affected tests, including test_phase_link_core, test_phase_link_compress, and workflow tests, with JAX 0.10.x; done means the spurious FutureWarning no longer turns these tests into failures.

Summary

With jax/jaxlib 0.10.x (conda-forge currently serves 0.10.2), 44 tests fail on an unmodified checkout of main (c2f7c24). This is not a dolphin regression: jax 0.10.0 added a deprecation warning that jax.scipy.linalg.solve(assume_a="pos") trips internally, and dolphin's pytest config (filterwarnings = ["error"]) escalates it to an error at trace time.

Evidence

CI run of unmodified main (c2f7c24) on my fork, same test-build-push.yml workflow: https://github.com/s-sasaki-earthsea-wizard/dolphin/actions/runs/31772307761

• 44 failed / 702 passed / 19 skipped (test_phase_link_core, test_phase_link_compress, workflow tests)
• Every failure's traceback ends the same way: _core.py:521 (process_coherence_matrices) → crlb.py:187 (_crlb_from_x) → jax/_src/scipy/linalg.py:170: FutureWarning

FutureWarning: jax.scipy.linalg.cho_solve: batched 1D solves with b.ndim > 1 are deprecated, and in the future will be treated as a batched 2D solve. Use cho_solve(c_and_lower, b[..., None]).squeeze(-1) to avoid this warning.

Any CI run whose environment resolves jax >= 0.10.0 will hit this (reproduced with 0.10.1 and 0.10.2); the last unaffected jax release is 0.9.2.

Root cause

crlb.py calls jax.scipy.linalg.solve(..., assume_a="pos") on batched matrices (crlb.py:187 on every CRLB computation; also crlb.py:178 when aps_variance > 0 and crlb.py:241 in compute_crlb_jax). Inside jax 0.10.x, _solve implements assume_a="pos" by vmapping an internal cho_solve(factors, x) over the RHS columns (linalg.py#L1196); the per-example rhs then has x.ndim == factors.ndim - 1, which is exactly the batched-1D dispatch that jax 0.10.0 deprecated (linalg.py#L164-L177) — so jax's own internal call emits the warning. User code never touches cho_solve; results are numerically correct; only the warning is spurious.

Dolphin's two direct cho_solve call sites are not affected (verified on 0.10.2): phase_link/_core.py:472 has equal-ndim c/b and takes the matrix branch; timeseries.py:1496 is vmapped with a per-pixel 1D rhs.

Options

1. Targeted warning ignore (smallest diff, my suggestion): add to pyproject.toml's filterwarnings, following the existing h5py precedent:

   # jax >= 0.10 solve(assume_a="pos") trips its own cho_solve deprecation
   # warning internally; remove once fixed upstream in jax:
   "ignore:jax.scipy.linalg.cho_solve. batched 1D solves.*:FutureWarning",
   

   Keeps CI on latest jax, no behavior change, self-documenting removal condition.

2. Avoid the warning at the source: replace the assume_a="pos" calls in crlb.py with explicit cho_factor + cho_solve on the matrix RHS (the non-deprecated branch). Numerically identical; would forgo custom_linear_solve's factorization reuse under differentiation, which the CRLB path doesn't appear to use.

3. Pin jax<0.10: least attractive — that walks back three minor releases and the warning is still present on jax main, so the pin would linger.

Happy to open the small PR for option 1 (or 2), and/or to file this upstream with jax as a minimal-repro issue — your call.

Disclosure: AI tools assisted with research, implementation, and drafting. I verified the technical claims and take responsibility for the proposal.