fix

CONTRIBUTING.md

@@ -34,7 +34,7 @@ Next verify the tests all pass:
 
 ```bash
 pip install pytest
-pytest src/  # or uv run pytest src/
+pytest tests/  # or uv run pytest tests/
 ```
 
 Then push your changes back to your fork of the repository:

pyproject.toml

@@ -36,7 +36,6 @@ requires-python = ">=3.9"
 
 [project.optional-dependencies]
 test = ["pytest", "pytest-cov"]
-dev = ["ruff", "sphinx-autobuild"]
 docs = [
     "sphinx",
     "furo",
@@ -130,3 +129,6 @@ filterwarnings = [
     "ignore:.*The TorchScript type system doesn't support instance-level annotations on empty non-base types.*",
 ]
 norecursedirs = "tests/helpers"
+
+[dependency-groups]
+dev = ["notebook>=7.3.2", "ruff", "sphinx-autobuild"]

src/graph_pes/atomic_graph.py

@@ -376,7 +376,9 @@ def from_ase(
         cell = torch.tensor(structure.cell.array, dtype=_float)
 
         # neighbour list
-        i, j, offsets = vesin.ase_neighbor_list("ijS", structure, cutoff)
+        i, j, offsets = vesin.ase_neighbor_list("ijS", structure, float(cutoff))
+        i = i.astype(np.int64)
+        j = j.astype(np.int64)
         neighbour_list = torch.tensor(np.vstack([i, j]), dtype=torch.long)
         neighbour_cell_offsets = torch.tensor(offsets, dtype=_float)