[DRAFT] chore: move h5py from base deps to [benchmarks] extra

[speckhard]

Summary

h5py>=3.10 was a runtime dep but only used by 2 comparison benchmark scripts under atompack-py/benchmarks/. Move to a new [benchmarks] extra so the base wheel doesn't pull ~50 MB of HDF5 binaries unnecessarily.

What changes

• pyproject.toml — h5py>=3.10 moves from [project] dependencies to [project.optional-dependencies] benchmarks.
• uv.lock — regenerated; h5py is still locked, just under the benchmarks extra now.
• atompack-py/benchmarks/README.md — two stale claims about h5py being part of the base benchmark environment are updated to point users at pip install atompack-db[benchmarks].
• Makefile py-test-benchmarks target — now passes --extra benchmarks alongside --extra dev so the benchmark suite continues to actually exercise h5py paths instead of silently skipping them.

Users running comparison benchmarks now install with:

pip install atompack-db[benchmarks]

Test plan

• After resync, h5py absent from base dev env:

$ uv run python -c "import h5py"
ModuleNotFoundError: No module named 'h5py'

• Full pytest suite green; h5py-gated tests skip cleanly via existing pytest.importorskip("h5py") calls:

$ uv run --extra dev --locked pytest tests/ -q
118 passed, 8 skipped in 2.15s

• make py-test-benchmarks (now --extra dev --extra benchmarks) actually runs the h5py tests instead of skipping them — verified directly:

$ uv run --extra dev --extra benchmarks --locked pytest tests/benchmarks -q
52 passed, 4 skipped in 6.88s

Backward compat

• Existing users running python atompack-py/benchmarks/atom_hdf5_soa.py without re-installing will see ImportError: No module named 'h5py'. They should pip install atompack-db[benchmarks].
• Production users of the atompack Python package never imported h5py, so they're unaffected.
• No on-disk format change. No API change.

Considered alternatives

• Keep h5py in [dev]: rejected — most contributors don't run the HDF5 benchmark and shouldn't pay the install cost.
• Have dev include benchmarks (nested extras): no precedent for nested extras in this repo. Just updated the Makefile target to pass both.