ruff fixes (#946)

Author: janosh

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.5.2
+  rev: v0.5.6
   hooks:
   - id: ruff
     args: [--fix]
@@ -30,7 +30,7 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.10.1
+  rev: v1.11.1
   hooks:
   - id: mypy
     files: ^src/
@@ -48,8 +48,7 @@ repos:
   rev: 0.7.1
   hooks:
     - id: nbstripout
-      args: [
-        --drop-empty-cells,
-        --strip-init-cells,
-        --extra-keys=metadata.kernelspec,
-        ]
+      args:
+        - --drop-empty-cells
+        - --strip-init-cells
+        - --extra-keys=metadata.kernelspec

pyproject.toml

@@ -54,10 +54,9 @@ forcefields = [
     "calorine<=2.2.1",
     "chgnet>=0.2.2",
     "mace-torch>=0.3.3",
-    "matgl>=1.1.1",
+    "matgl>=1.1.3",
     "quippy-ase>=0.9.14",
     "sevenn>=0.9.3",
-    "torch<=2.2.1",       # incompatibility with dgl if newer versions are used
 ]
 docs = [
     "FireWorks==2.0.3",
@@ -93,7 +92,7 @@ strict = [
     "jobflow==0.1.18",
     "lobsterpy==0.4.5",
     "mace-torch>=0.3.3",
-    "matgl==1.1.2",
+    "matgl==1.1.3",
     "monty==2024.7.30",
     "mp-api==0.41.2",
     "numpy",
@@ -198,7 +197,7 @@ ignore = [
     "S324",    # use of insecure hash function
     "S507",    # paramiko auto trust
     "S603",    # use of insecure subprocess
-    "TD",      # TODOs
+    "TD",      # todos
     "TRY003",  # long message outside exception class
 ]
 pydocstyle.convention = "numpy"

src/atomate2/abinit/sets/base.py

@@ -387,8 +387,9 @@ def get_input_set(
             link_files=True,
         )
 
+    @staticmethod
     def check_format_prev_dirs(
-        self, prev_dirs: str | tuple | list | Path | None
+        prev_dirs: str | tuple | list | Path | None,
     ) -> list[str] | None:
         """Check and format the prev_dirs (restart or dependency)."""
         if prev_dirs is None:
@@ -437,9 +438,9 @@ def resolve_prev_inputs(
         abinit_inputs = {}
         for prev_dir in prev_dirs:
             abinit_input = load_abinit_input(prev_dir)
-            for var_name, runlevels in prev_inputs_kwargs.items():
+            for var_name, run_levels in prev_inputs_kwargs.items():
                 if abinit_input.runlevel and abinit_input.runlevel.intersection(
-                    runlevels
+                    run_levels
                 ):
                     if var_name in abinit_inputs:
                         msg = (

src/atomate2/common/flows/gruneisen.py

@@ -201,7 +201,7 @@ def prev_calc_dir_argname(self) -> str | None:
         """
 
     def __post_init__(self) -> None:
-        """Test settings during the initialisation."""
+        """Test settings during the initialization."""
         if self.phonon_maker.bulk_relax_maker is not None:
             warnings.warn(
                 "An additional bulk_relax_maker has been added "
@@ -218,6 +218,6 @@ def __post_init__(self) -> None:
             )
         if self.phonon_maker.static_energy_maker is not None:
             warnings.warn(
-                "The static energy maker " "is not needed for " "this workflow.",
+                "The static energy maker is not needed for this workflow.",
                 stacklevel=2,
             )

src/atomate2/common/jobs/phonons.py

@@ -74,11 +74,11 @@ def get_supercell_size(
         Additional parameters that can be set.
     """
     kwargs.setdefault("force_diagonal", False)
-    common_kwds = dict(
-        min_length=min_length,
-        min_atoms=kwargs.get("min_atoms"),
-        force_diagonal=kwargs["force_diagonal"],
-    )
+    common_kwds = {
+        "min_length": min_length,
+        "min_atoms": kwargs.get("min_atoms"),
+        "force_diagonal": kwargs["force_diagonal"],
+    }
 
     if not prefer_90_degrees:
         transformation = CubicSupercellTransformation(

src/atomate2/common/schemas/gruneisen.py

@@ -213,7 +213,7 @@ def from_phonon_yamls(
         kpath_dict, kpath_concrete = PhononBSDOSDoc.get_kpath(
             structure=structure, kpath_scheme=kpath_scheme, symprec=symprec
         )
-        qpoints, connections = get_band_qpoints_and_path_connections(
+        qpoints, _connections = get_band_qpoints_and_path_connections(
             kpath_concrete,
             npoints=compute_gruneisen_param_kwargs.get("npoints_band", 101),
         )

src/atomate2/cp2k/flows/core.py

@@ -251,7 +251,7 @@ def __post_init__(self) -> None:
         }
         if self.initialize_with_pbe:
             updates["activate_hybrid"].update(
-                {"screen_on_initial_p": True, "screen_p_forces": True}
+                screen_on_initial_p=True, screen_p_forces=True
             )
         self.hybrid_maker.input_set_generator.user_input_settings = recursive_update(
             updates, self.hybrid_maker.input_set_generator.user_input_settings

src/atomate2/forcefields/schemas.py

@@ -255,11 +255,9 @@ def from_ase_compatible_result(
             # include "magmoms" in :obj:`ionic_step` if the trajectory has "magmoms"
             if "magmoms" in trajectory.frame_properties[idx]:
                 _ionic_step_data.update(
-                    {
-                        "magmoms": trajectory.frame_properties[idx]["magmoms"]
-                        if "magmoms" in ionic_step_data
-                        else None
-                    }
+                    magmoms=trajectory.frame_properties[idx]["magmoms"]
+                    if "magmoms" in ionic_step_data
+                    else None
                 )
 
             ionic_step = IonicStep(
@@ -287,17 +285,14 @@ def from_ase_compatible_result(
         )
 
         # map force field name to its package name
-        pkg_names = {
-            str(k): v
-            for k, v in {
-                MLFF.M3GNet: "matgl",
-                MLFF.CHGNet: "chgnet",
-                MLFF.MACE: "mace-torch",
-                MLFF.GAP: "quippy-ase",
-                MLFF.Nequip: "nequip",
-            }.items()
+        model_to_pkg_map = {
+            MLFF.M3GNet: "matgl",
+            MLFF.CHGNet: "chgnet",
+            MLFF.MACE: "mace-torch",
+            MLFF.GAP: "quippy-ase",
+            MLFF.Nequip: "nequip",
         }
-        pkg_name = pkg_names.get(forcefield_name)
+        pkg_name = {str(k): v for k, v in model_to_pkg_map.items()}.get(forcefield_name)
         if pkg_name:
             import importlib.metadata
 

src/atomate2/forcefields/utils.py

@@ -446,7 +446,6 @@ def ase_calculator(calculator_meta: str | dict, **kwargs: Any) -> Calculator | N
             calculator = NequIPCalculator.from_deployed_model(**kwargs)
 
         elif calculator_name == MLFF.SevenNet:
-            # pip install git+https://github.com/MDIL-SNU/SevenNet
             from sevenn.sevennet_calculator import SevenNetCalculator
 
             calculator = SevenNetCalculator(**{"model": "7net-0"} | kwargs)

src/atomate2/lobster/schemas.py

@@ -1302,7 +1302,7 @@ def _get_strong_bonds(
     else:
         prop = "icohp"
 
-    bond_dict = {}
+    bond_dict: dict[str, dict[str, Union[float, str]]] = {}
     for idx, lab in enumerate(bond_labels_unique):
         label = lab.split("-")
         label.sort()
@@ -1312,24 +1312,20 @@ def _get_strong_bonds(
             if label == rel_bnd_list:
                 if prop == "icohp":
                     index = np.argmin(sep_icohp[idx])
-                    bond_dict.update(
-                        {
-                            rel_bnd: {
-                                "bond_strength": min(sep_icohp[idx]),
-                                "length": sep_lengths[idx][index],
-                            }
+                    bond_dict |= {
+                        rel_bnd: {
+                            "bond_strength": min(sep_icohp[idx]),
+                            "length": sep_lengths[idx][index],
                         }
-                    )
+                    }
                 else:
                     index = np.argmax(sep_icohp[idx])
-                    bond_dict.update(
-                        {
-                            rel_bnd: {
-                                "bond_strength": max(sep_icohp[idx]),
-                                "length": sep_lengths[idx][index],
-                            }
+                    bond_dict |= {
+                        rel_bnd: {
+                            "bond_strength": max(sep_icohp[idx]),
+                            "length": sep_lengths[idx][index],
                         }
-                    )
+                    }
     return bond_dict