Drop Python 3.11 support (require >=3.12)

[Marius1311]

Summary

Bump CellMapper's minimum Python from 3.11 to 3.12. cellrank requires Python ≥3.12 since 2.1.0, so our requires-python = ">=3.11" floor forced uv's universal lock to hold the entire dependency graph — including the local kernel venv — back to the last cellrank that still supported 3.11 (2.0.7). Dropping 3.11 unpins the tutorials extra to cellrank 2.3.x (and modernizes scanpy → 1.12, scvi-tools → 1.4.3, etc.).

Behavior Or Invariants Changed

• Minimum Python is now 3.12. requires-python = ">=3.12", the :: 3.11 trove classifier is removed, and the hatch-test matrix moves from 3.11, 3.14 to 3.12, 3.14. No code/API changes.

Tests Run

• uv lock --dry-run with requires-python = ">=3.12" → resolves cleanly (302 packages), cellrank moves off 2.0.7. The same dry-run on the old >=3.11 floor with a cellrank>=2.3 probe fails with "cellrank==2.3.0 depends on Python>=3.12", confirming the root cause.
• pre-commit run --files pyproject.toml README.md AGENTS.md CHANGELOG.md → passes (pyproject-fmt etc.).
• Full hatch test matrix not run locally (CI will exercise 3.12/3.14).

Reviewer Focus

pyproject.toml — requires-python, classifiers, and the hatch-test matrix. Doc touch-ups in README.md and AGENTS.md. No ruff/mypy target-version pins exist (they infer from requires-python), so nothing else needed updating.

Context

This is step 1 of delegating the pyGPCCA fast backend to CellRank. Once a cellrank release ships the mpi4py-free [petsc] extra (scverse/cellrank#1362, merged to main), a follow-up will replace the hardcoded gpcca-fast group (petsc petsc4py slepc slepc4py) with cellrank[petsc]>=<that release>. That follow-up is blocked on the release and is intentionally not part of this PR.

Open Questions Or Follow-Ups

• Changelog entry references {pr} with a placeholder that will be updated to this PR's number.
• 3.11 is dropped for the whole package, not just the tutorials extra — intentional, per maintainer decision, and consistent with the broader scverse ecosystem moving to ≥3.12.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.37%. Comparing base (91ebb3c) to head (ee2f3ba).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #81   +/-   ##
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  Coverage   86.37%   86.37%           
=======================================
  Files          13       13           
  Lines        1387     1387           
=======================================
  Hits         1198     1198           
  Misses        189      189           

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