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

Makefile

@@ -82,7 +82,7 @@ py-test: py-dev
 
 py-test-benchmarks: py-dev
 	@command -v $(UV) >/dev/null 2>&1 || (echo "uv not found; install from https://docs.astral.sh/uv/" && exit 1)
-	cd atompack-py && UV_CACHE_DIR=$(UV_CACHE_DIR) $(UV) run --extra dev --locked pytest tests/benchmarks
+	cd atompack-py && UV_CACHE_DIR=$(UV_CACHE_DIR) $(UV) run --extra dev --extra benchmarks --locked pytest tests/benchmarks
 
 docs-sync:
 	@command -v $(UV) >/dev/null 2>&1 || (echo "uv not found; install from https://docs.astral.sh/uv/" && exit 1)

atompack-py/benchmarks/README.md

@@ -64,7 +64,8 @@ Notes:
 - `get_molecules_flat(...)` remains the fastest tensor-batch path when the
   consumer can work with concatenated arrays directly.
 - `hdf5_soa` reflects the usual chunked-dataset HDF5 layout used for
-  fixed-shape materials data and is part of the default benchmark environment.
+  fixed-shape materials data; install with `pip install atompack-db[benchmarks]`
+  to pull in the `h5py` dependency.
 - `lmdb_packed` now participates in the synthetic custom-property variants in
   this suite too; `lmdb_soa` remains the builtins-only helper baseline.
 - In this suite, `hdf5_soa` is intentionally read one molecule at a time so it
@@ -330,8 +331,9 @@ tuning that matters most for dataloader-like access:
 - reader-side raw chunk cache sizing through `h5py` open options
 - batch reads that regroup requested indices by chunk before rebuilding payloads
 
-This backend is included in the default benchmark environment through the base
-project dependencies.
+This backend depends on `h5py`, which is shipped as the `[benchmarks]` extra:
+install with `pip install atompack-db[benchmarks]` (or `make py-test-benchmarks`
+which now uses both the `dev` and `benchmarks` extras).
 
 ### `atom_lmdb_soa.py`
 

atompack-py/pyproject.toml

@@ -32,7 +32,6 @@ classifiers = [
     "Programming Language :: Python :: 3.14",
 ]
 dependencies = [
-    "h5py>=3.10",
     "huggingface_hub>=0.24",
     "numpy>=1.20",
 ]
@@ -51,6 +50,12 @@ dev = [
     "mypy",
     "ruff",
 ]
+# Used only by the comparison scripts under atompack-py/benchmarks/. Not
+# imported anywhere under python/atompack/, so it has no business in the
+# base wheel — pulls ~50 MB of HDF5 binaries onto every install.
+benchmarks = [
+    "h5py>=3.10",
+]
 
 [tool.maturin]
 python-source = "python"