CLI write path fails on anndata >= 0.11: allow_write_nullable_strings is False #23

Surfaced while running the full suite for #22 (settylab/dotto-nexus#310 work); not caused by
that branch — it reproduces at 19ee1a1 in a clean worktree. Filing rather than working around
it, per the lab-tool routing contract.

Symptom

49 tests fail in tests/test_cli.py, tests/test_cli_compute_config.py,
tests/test_cli_dm_coverage.py and tests/test_cli_smooth.py, all with the same error:

RuntimeError: `anndata.settings.allow_write_nullable_strings` is False, because writing of
`pd.arrays.StringArray` is new and not supported in anndata < 0.11, still use by many people.
Opt-in to writing these arrays by toggling the setting to True.

Minimal repro:

python -m pytest tests/test_cli_smooth.py::TestCLISmooth::test_smooth_basic

Scope

Environment: anndata 0.12.6, kompot 0.8.0 @19ee1a1, Python 3.13.5. The rest of the suite is
green (2,021 passed, 32 skipped) — this is confined to the CLI's .h5ad write path.

The CLI writes a var/obs column backed by a pandas StringArray, which anndata refuses to
write unless the caller opts in. Because it is the writing side, the failure only shows up in
the CLI tests; the library API paths never hit it.

Why it matters beyond the tests

If the CLI genuinely cannot write its output under a current anndata, kompot de / kompot da /
kompot smooth are broken for anyone on anndata >= 0.11 with default settings, not just in CI.
Worth confirming against a real invocation before deciding whether this is a test-fixture issue or
a user-facing one — I have not done that, since it is outside the scope of the work that surfaced
it.

Likely fixes

Either coerce the offending column to object/category before writing, or set
anndata.settings.allow_write_nullable_strings = True at the CLI's write site (narrow, explicit)
rather than globally at import.