ci: fix PETSc/conda zarr pin; accept macOS GPCCA instability - #1371
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Marius1311 wants to merge 1 commit into
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ci: fix PETSc/conda zarr pin; accept macOS GPCCA instability#1371Marius1311 wants to merge 1 commit into
Marius1311 wants to merge 1 commit into
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The PETSc/SLEPc+R (conda) job force-downgraded to zarr<3 after installing cellrank, but current anndata (>=0.13) requires zarr>=3.1 and imports zarr.core.dtype, a zarr-v3-only module. The downgrade broke conftest import with ModuleNotFoundError, failing the whole job. The pin dates to when anndata still supported zarr v2; drop it and let anndata resolve zarr. Also mark the macOS matrix leg continue-on-error: pyGPCCA's brandts Schur decomposition is numerically unstable on Apple Silicon and fails the GPCCA tests there. The fix belongs upstream; keep the job for visibility but stop it gating merges. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Problem
CI has been red on
mainon two jobs, blocking the All tests pass gate on every PR:PETSc / SLEPc + R(conda job) — fails at conftest import:The job installs cellrank (
pip install -e '.[plot]', pulling anndata 0.13.2 which requires zarr>=3.1), then the next line force-downgrades to'zarr<3'. anndata 0.13 importszarr.core.dtype, a zarr-v3-only module, so the downgrade breaks the whole job. Thezarr<3pin dates to CI workflow modernization #1291 (Feb 2026), when anndata still supported zarr v2 — it's now stale.hatch-test.py3.12-stable (macOS)— ~87test_gpcca.pyfailures, allbrandts didn't return an invariant subspace of P/Number of Schur vectors does not match number of eigenvalues. Numerical instability in pyGPCCA'sbrandtsSchur decomposition on Apple Silicon; the fix belongs upstream in pyGPCCA.Changes
zarr<3pin in the conda job and let anndata resolve zarr (>=3.1).continue-on-error(same mechanism already used for thepreenv). It still runs for visibility but no longer gates merges, until the upstream pyGPCCA issue is resolved.