Summary

Now that cellrank 2.3.1 ships an mpi4py-free [petsc] extra (scverse/cellrank#1362), the gpcca-fast dependency group delegates petsc4py/slepc4py to cellrank[petsc]>=2.3.1 instead of hardcoding the package list — CellRank owns it. This is the follow-up to #81 (which dropped Python 3.11 so the graph could resolve cellrank ≥2.1).

 gpcca-fast = [
-  "petsc",
-  "petsc4py",
-  "slepc",
-  "slepc4py",
+  "cellrank[petsc]>=2.3.1",
+  "slepc>=3.25",
 ]

Behavior Or Invariants Changed

• gpcca-fast no longer hardcodes petsc/petsc4py/slepc4py; they come transitively from cellrank[petsc]. The fast pyGPCCA method='krylov' path is unchanged.
• The opt-in mechanics are unchanged: still a PEP 735 group (not in --all-extras), still needs PETSC_CONFIGURE_OPTIONS for the C-only source build.

Why slepc is still listed explicitly

cellrank[petsc] alone is not sufficient: slepc4py's published sdist metadata lists only [numpy, petsc4py] — it adds its slepc runtime dependency dynamically at build time, so uv's resolver never installs the slepc library package. Result: import slepc4py → ImportError: Library not loaded: @rpath/libslepc.3.25.dylib. petsc4py declares petsc correctly (static metadata), so only slepc needs the workaround. Drop it once slepc4py — or cellrank's petsc extra — declares slepc.

Tests Run

• uv lock (with PETSC_CONFIGURE_OPTIONS set) → resolves cellrank 2.3.1 + petsc 3.25.2 + petsc4py 3.25.2 + slepc 3.25.1 + slepc4py 3.25.1, and no mpi4py.
• Throwaway-venv proof of the slepc gap: installing slepc4py via cellrank[petsc] semantics (no explicit slepc) → slepc absent, import fails with the dlopen error; adding slepc>=3.25 → slepc4py import OK (3, 25, 1).
• pre-commit passes on the changed files.

Reviewer Focus

pyproject.toml [dependency-groups].gpcca-fast and its comment block (documents the slepc4py workaround and the env-var build recipe). No code changes.

Open Questions Or Follow-Ups

• Changelog {pr} placeholder will be updated to this PR's number.
• Upstream cleanup worth considering: have cellrank's [petsc] extra include slepc/petsc (the lib packages), or fix slepc4py to declare slepc statically — either would let CellMapper drop the explicit slepc line entirely.

🤖 Generated with Claude Code