ruff fixes + type annotations (#156)

* ruff auto fixes

* fix ruff FBT001 FBT002

* ruff select = ["ALL"] and fix legacy errors

* fix TypeError: unhashable type

'list'chgnet/model/functions.py:71: in __init__
    if hidden_dim in {None, 0}:

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.4.4
     hooks:
       - id: ruff
         args: [--fix]
@@ -46,7 +46,7 @@ repos:
           - svelte
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v9.2.0
+    rev: v9.3.0
     hooks:
       - id: eslint
         types: [file]

chgnet/data/dataset.py

@@ -33,6 +33,7 @@ def __init__(
         structures: list[Structure],
         energies: list[float],
         forces: list[Sequence[Sequence[float]]],
+        *,
         stresses: list[Sequence[Sequence[float]]] | None = None,
         magmoms: list[Sequence[Sequence[float]]] | None = None,
         structure_ids: list | None = None,
@@ -63,7 +64,7 @@ def __init__(
         """
         for idx, struct in enumerate(structures):
             if not isinstance(struct, Structure):
-                raise ValueError(f"{idx} is not a pymatgen Structure object: {struct}")
+                raise TypeError(f"{idx} is not a pymatgen Structure object: {struct}")
         for name in "energies forces stresses magmoms structure_ids".split():
             labels = locals()[name]
             if labels is not None and len(labels) != len(structures):
@@ -80,7 +81,7 @@ def __init__(
         self.keys = np.arange(len(structures))
         if shuffle:
             random.shuffle(self.keys)
-        print(f"{len(structures)} structures imported")
+        print(f"{type(self).__name__} imported {len(structures):,} structures")
         self.graph_converter = graph_converter or CrystalGraphConverter(
             atom_graph_cutoff=6, bond_graph_cutoff=3
         )
@@ -91,11 +92,12 @@ def __init__(
     def from_vasp(
         cls,
         file_root: str,
+        *,
         check_electronic_convergence: bool = True,
         save_path: str | None = None,
         graph_converter: CrystalGraphConverter | None = None,
         shuffle: bool = True,
-    ):
+    ) -> StructureData:
         """Parse VASP output files into structures and labels and feed into the dataset.
 
         Args:
@@ -196,6 +198,7 @@ class CIFData(Dataset):
     def __init__(
         self,
         cif_path: str,
+        *,
         labels: str | dict = "labels.json",
         targets: TrainTask = "efsm",
         graph_converter: CrystalGraphConverter | None = None,
@@ -311,6 +314,7 @@ class GraphData(Dataset):
     def __init__(
         self,
         graph_path: str,
+        *,
         labels: str | dict = "labels.json",
         targets: TrainTask = "efsm",
         exclude: str | list | None = None,
@@ -429,6 +433,7 @@ def get_train_val_test_loader(
         self,
         train_ratio: float = 0.8,
         val_ratio: float = 0.1,
+        *,
         train_key: list[str] | None = None,
         val_key: list[str] | None = None,
         test_key: list[str] | None = None,
@@ -541,6 +546,7 @@ def __init__(
         self,
         data: str | dict,
         graph_converter: CrystalGraphConverter,
+        *,
         targets: TrainTask = "efsm",
         energy_key: str = "energy_per_atom",
         force_key: str = "force",
@@ -580,14 +586,14 @@ def __init__(
         elif isinstance(data, dict):
             self.data = data
         else:
-            raise ValueError(f"data must be JSON path or dictionary, got {type(data)}")
+            raise TypeError(f"data must be JSON path or dictionary, got {type(data)}")
 
         self.keys = [
             (mp_id, graph_id) for mp_id, dct in self.data.items() for graph_id in dct
         ]
         if shuffle:
             random.shuffle(self.keys)
-        print(f"{len(self.data)} mp_ids, {len(self)} structures imported")
+        print(f"{len(self.data)} MP IDs, {len(self)} structures imported")
         self.graph_converter = graph_converter
         self.energy_key = energy_key
         self.force_key = force_key
@@ -602,7 +608,7 @@ def __len__(self) -> int:
         return len(self.keys)
 
     @functools.cache  # Cache loaded structures
-    def __getitem__(self, idx):
+    def __getitem__(self, idx: int) -> tuple[CrystalGraph, dict[str, Tensor]]:
         """Get one item in the dataset.
 
         Returns:
@@ -654,6 +660,7 @@ def get_train_val_test_loader(
         self,
         train_ratio: float = 0.8,
         val_ratio: float = 0.1,
+        *,
         train_key: list[str] | None = None,
         val_key: list[str] | None = None,
         test_key: list[str] | None = None,
@@ -747,7 +754,7 @@ def get_train_val_test_loader(
         return train_loader, val_loader, test_loader
 
 
-def collate_graphs(batch_data: list):
+def collate_graphs(batch_data: list) -> tuple[list[CrystalGraph], dict[str, Tensor]]:
     """Collate of list of (graph, target) into batch data.
 
     Args:
@@ -777,13 +784,14 @@ def collate_graphs(batch_data: list):
 
 def get_train_val_test_loader(
     dataset: Dataset,
+    *,
     batch_size: int = 64,
     train_ratio: float = 0.8,
     val_ratio: float = 0.1,
     return_test: bool = True,
     num_workers: int = 0,
     pin_memory: bool = True,
-):
+) -> tuple[DataLoader, DataLoader, DataLoader]:
     """Randomly partition a dataset into train, val, test loaders.
 
     Args:
@@ -842,7 +850,9 @@ def get_train_val_test_loader(
     return train_loader, val_loader
 
 
-def get_loader(dataset, batch_size=64, num_workers=0, pin_memory=True):
+def get_loader(
+    dataset, *, batch_size: int = 64, num_workers: int = 0, pin_memory: bool = True
+) -> DataLoader:
     """Get a dataloader from a dataset.
 
     Args:

chgnet/graph/converter.py

@@ -33,6 +33,7 @@ class CrystalGraphConverter(nn.Module):
 
     def __init__(
         self,
+        *,
         atom_graph_cutoff: float = 6,
         bond_graph_cutoff: float = 3,
         algorithm: Literal["legacy", "fast"] = "fast",
@@ -274,7 +275,6 @@ def set_isolated_atom_response(
             None
         """
         self.on_isolated_atoms = on_isolated_atoms
-        return
 
     def as_dict(self) -> dict[str, str | float]:
         """Save the args of the graph converter."""

chgnet/graph/crystalgraph.py

@@ -183,7 +183,7 @@ def __repr__(self) -> str:
         )
 
     @property
-    def num_isolated_atoms(self):
+    def num_isolated_atoms(self) -> int:
         """Number of isolated atoms given the atom graph cutoff
         Isolated atoms are disconnected nodes in the atom graph
         that will not get updated in CHGNet.

chgnet/graph/graph.py

@@ -66,7 +66,7 @@ class UndirectedEdge(Edge):
 
     __hash__ = Edge.__hash__
 
-    def __eq__(self, other):
+    def __eq__(self, other: object) -> bool:
         """Check if two undirected edges are equal."""
         return set(self.nodes) == set(other.nodes) and self.info == other.info
 
@@ -178,16 +178,16 @@ def add_edge(self, center_index, neighbor_index, image, distance) -> None:
                 ):
                     # There is an undirected edge with similar length and only one of
                     # the directed edges associated has been added
-                    added_DE = self.directed_edges_list[
+                    added_dir_edge = self.directed_edges_list[
                         undirected_edge.info["directed_edge_index"][0]
                     ]
 
                     # See if the DE that's associated to this UDE
                     # is the reverse of our DE
-                    if added_DE == this_directed_edge:
+                    if added_dir_edge == this_directed_edge:
                         # Add UDE index to this DE
                         this_directed_edge.info["undirected_edge_index"] = (
-                            added_DE.info["undirected_edge_index"]
+                            added_dir_edge.info["undirected_edge_index"]
                         )
 
                         # At the center node, draw edge with this DE
@@ -217,7 +217,7 @@ def add_edge(self, center_index, neighbor_index, image, distance) -> None:
             self.nodes[center_index].add_neighbor(neighbor_index, this_directed_edge)
             self.directed_edges_list.append(this_directed_edge)
 
-    def adjacency_list(self):
+    def adjacency_list(self) -> tuple[list[list[int]], list[int]]:
         """Get the adjacency list
         Return:
             graph: the adjacency list
@@ -240,7 +240,7 @@ def adjacency_list(self):
         ]
         return graph, directed2undirected
 
-    def line_graph_adjacency_list(self, cutoff):
+    def line_graph_adjacency_list(self, cutoff) -> tuple[list[list[int]], list[int]]:
         """Get the line graph adjacency list.
 
         Args:
@@ -264,11 +264,12 @@ def line_graph_adjacency_list(self, cutoff):
                 a list of length = num_undirected_edge that
                 maps the undirected edge index to one of its directed edges indices
         """
-        assert len(self.directed_edges_list) == 2 * len(self.undirected_edges_list), (
-            f"Error: number of directed edges={len(self.directed_edges_list)} != 2 * "
-            f"number of undirected edges={len(self.directed_edges_list)}!"
-            f"This indicates directed edges are not complete"
-        )
+        if len(self.directed_edges_list) != 2 * len(self.undirected_edges_list):
+            raise ValueError(
+                f"Error: number of directed edges={len(self.directed_edges_list)} != 2 "
+                f"* number of undirected edges={len(self.directed_edges_list)}!"
+                f"This indicates directed edges are not complete"
+            )
         line_graph = []
         undirected2directed = []
 
@@ -285,39 +286,42 @@ def line_graph_adjacency_list(self, cutoff):
             # if encountered exception,
             # it means after Atom_Graph creation, the UDE has only 1 DE associated
             # This exception is not encountered from the develop team's experience
-            assert len(u_edge.info["directed_edge_index"]) == 2, (
-                "Did not find 2 Directed_edges !!!"
-                f"undirected edge {u_edge} has:"
-                f"edge.info['directed_edge_index'] = "
-                f"{u_edge.info['directed_edge_index']}"
-                f"len directed_edges_list = {len(self.directed_edges_list)}"
-                f"len undirected_edges_list = {len(self.undirected_edges_list)}"
-            )
+            if len(u_edge.info["directed_edge_index"]) != 2:
+                raise ValueError(
+                    "Did not find 2 Directed_edges !!!"
+                    f"undirected edge {u_edge} has:"
+                    f"edge.info['directed_edge_index'] = "
+                    f"{u_edge.info['directed_edge_index']}"
+                    f"len directed_edges_list = {len(self.directed_edges_list)}"
+                    f"len undirected_edges_list = {len(self.undirected_edges_list)}"
+                )
 
             # This UDE is valid to be considered as a node in Bond_Graph
 
             # Get the two ends (centers) and the two DE associated with this UDE
             # DE1 should have center=center1 and DE2 should have center=center2
             # We will need to find directed edges with center = center1
             # and create angles with DE1, then do the same for center2 and DE2
-            for center, DE in zip(u_edge.nodes, u_edge.info["directed_edge_index"]):
+            for center, dir_edge in zip(
+                u_edge.nodes, u_edge.info["directed_edge_index"]
+            ):
                 for directed_edges in self.nodes[center].neighbors.values():
                     for directed_edge in directed_edges:
-                        if directed_edge.index == DE:
+                        if directed_edge.index == dir_edge:
                             continue
                         if directed_edge.info["distance"] < cutoff:
                             line_graph.append(
                                 [
                                     center,
                                     u_edge.index,
-                                    DE,
+                                    dir_edge,
                                     directed_edge.info["undirected_edge_index"],
                                     directed_edge.index,
                                 ]
                             )
         return line_graph, undirected2directed
 
-    def undirected2directed(self):
+    def undirected2directed(self) -> list[int]:
         """The index map from undirected_edge index to one of its directed_edge
         index.
         """
@@ -326,7 +330,7 @@ def undirected2directed(self):
             for undirected_edge in self.undirected_edges_list
         ]
 
-    def as_dict(self):
+    def as_dict(self) -> dict:
         """Return dictionary serialization of a Graph."""
         return {
             "nodes": self.nodes,

chgnet/model/basis.py

@@ -8,7 +8,7 @@
 class Fourier(nn.Module):
     """Fourier Expansion for angle features."""
 
-    def __init__(self, order: int = 5, learnable: bool = False) -> None:
+    def __init__(self, *, order: int = 5, learnable: bool = False) -> None:
         """Initialize the Fourier expansion.
 
         Args:
@@ -47,6 +47,7 @@ class RadialBessel(torch.nn.Module):
 
     def __init__(
         self,
+        *,
         num_radial: int = 9,
         cutoff: float = 5,
         learnable: bool = False,
@@ -90,7 +91,7 @@ def __init__(
             self.smooth_cutoff = None
 
     def forward(
-        self, dist: Tensor, return_smooth_factor: bool = False
+        self, dist: Tensor, *, return_smooth_factor: bool = False
     ) -> Tensor | tuple[Tensor, Tensor]:
         """Apply Bessel expansion to a feature Tensor.
 
@@ -122,8 +123,8 @@ class GaussianExpansion(nn.Module):
 
     def __init__(
         self,
-        min: float = 0,
-        max: float = 5,
+        min: float = 0,  # noqa: A002
+        max: float = 5,  # noqa: A002
         step: float = 0.5,
         var: float | None = None,
     ) -> None:
@@ -137,8 +138,10 @@ def __init__(
             var (float): variance in gaussian filter, default to step
         """
         super().__init__()
-        assert min < max
-        assert max - min > step
+        if min >= max:
+            raise ValueError(f"{min=} must be less than {max=}")
+        if max - min <= step:
+            raise ValueError(f"{max - min=} must be greater than {step=}")
         self.register_buffer("gaussian_centers", torch.arange(min, max + step, step))
         self.var = var or step
         if self.var <= 0: