Support pip install of PETSc/SLEPc; drop mpi4py from petsc extra

[Marius1311]

Changes

• Drop mpi4py from the petsc extra (optional-dependencies.petsc = [ "petsc4py", "slepc4py" ]). pyGPCCA runs serially and never needs mpi4py; pinning it forced a system-MPI source build that made pip install "cellrank[petsc]" fail on any machine without a system MPI library (e.g. stock macOS, minimal Linux). Users who genuinely want a distributed MPI build can still install a system MPI and add mpi4py themselves.
• Document the pip install path for PETSc/SLEPc in docs/installation.md: a new "PETSc and SLEPc (faster large-scale solvers)" subsection covering pip install "cellrank[petsc]", the from-source compilation caveat, and the C-only PETSC_CONFIGURE_OPTIONS recipe for systems without a Fortran/MPI toolchain.

Bug fixes

• Correct the inaccurate "conda-only" framing. The docs previously called PETSc/SLEPc "conda-only packages" and implied conda was the only way to get them. They are pip-installable from PyPI sdists; the conda section is reframed as the pre-built, no-compilation option, cross-linked with the new pip instructions.

Context

petsc4py/slepc4py enable pyGPCCA's fast method='krylov' solver for macrostates and fate probabilities. Without them, pyGPCCA falls back to method='brandts', which densifies the transition matrix and emits warnings (Unable to import petsc4py or slepc4py ... / Densifying). conda ships prebuilt binaries, but pip-from-source is viable and only needs a C compiler — no Fortran or MPI — once mpi4py is out of the way.

Verified

• petsc 3.25.2 + slepc 3.25.1 compile from PyPI sdists on macOS arm64 with a C compiler only, using PETSC_CONFIGURE_OPTIONS="--with-fc=0 --with-mpi=0 --with-debugging=0 --with-shared-libraries=1" (no Fortran, MPI, or system libs).
• petsc4py/slepc4py import and report versions.
• pyGPCCA GPCCA(..., method='krylov').optimize() runs under warnings.simplefilter('error') — i.e. the brandts/densify fallback is gone — without mpi4py installed.
• cellrank[petsc] resolves to petsc/petsc4py/slepc/slepc4py with no mpi4py.
• pre-commit passes on the changed files.

Notes for reviewers

• The from-source build was validated on macOS arm64; the configure flags are platform-agnostic, but a Linux CI confirmation would be a nice follow-up. The Windows note in installation.md is intentionally unchanged (PETSc on Windows remains hard; WSL is still the recommendation).
• No mpi4py is bundled anymore — if any downstream tooling assumed cellrank[petsc] pulled in mpi4py, that is the one behavior change here.

Related issues

Closes #

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