Remove GPJax dependency from the test suite#37
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Replace the GPJax reference comparisons with self-contained correctness checks so the suite no longer breaks on GPJax API changes (e.g. the 0.15 gram-operator change that required pinning gpjax==0.13.6). - Kernels: compare ExpQuad/Matern52/32 against closed-form analytic references in numpy. Matern uses a looser tolerance to absorb the float32 sqrt(5)/sqrt(3) constant pytensor evaluates in floatX. - Gaussian likelihood: closed-form variational expectation. - Bernoulli likelihood: independent numpy Gauss-Hermite quadrature. - SVGP Bernoulli/Poisson ELBO: reuse the numpy+scipy reference machinery (factored into tests/_svgp_ref.py and shared with the StudentT/NegBinom tests), as the scipy-ref module already anticipated. - Drop gpjax from conda_envs/environment-test.yaml. Closes #36.
… env - Matern52/32 used pt.sqrt(5.0)/pt.sqrt(3.0), which autocasts the literal to float32 regardless of config.floatX, injecting ~1e-7 error into an otherwise float64 kernel. Use pt.constant(..., dtype=config.floatX) so the constant follows the backend's precision; Matern now matches the analytic reference to ~3e-15 in float64. Tighten the kernel test tolerance accordingly. - ptgp, and the test suite after the GPJax removal, never import jax/optax, so drop jax/jaxlib/optax from conda_envs/environment-test.yaml.
jessegrabowski
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Jun 12, 2026
jessegrabowski
added
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Closes #36.
Replaces the GPJax reference comparisons with self-contained correctness checks, so the suite no longer breaks on GPJax API changes (the reason #35 had to pin
gpjax==0.13.6).What changed
test_stationary.py): compared against closed-form analytic references in NumPy.test_svgp.py): reuse the numpy+scipy reference that already backs the StudentT/NegBinom tests, factored intotests/_svgp_ref.py.stationary.py): Matern52/32 usedpt.sqrt(5.0), which autocasts the literal to float32 regardless offloatX. Typed viapt.constant(..., dtype=floatX)so it follows the backend; Matern now matches the reference to ~3e-15. Other kernel literals are float32-exact, so no other changes.gpjax(plus now-unusedjax/jaxlib/optax).Test plan
pytest tests/— 265 passedpre-commit run --all-filescleanscripts/run_mypy.py— 37/37 pass