Update pyproject.toml to resolve pip install issue

notebooks/direct/Example1_MPF2021.2.8.all.ipynb

@@ -205,7 +205,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "manual_selection_index = [i for i, l in enumerate(MPF_2021_2_8_All_feature_data[\"relax_label\"]) if l]"
+    "manual_selection_index = [i for i, j in enumerate(MPF_2021_2_8_All_feature_data[\"relax_label\"]) if j]"
    ]
   },
   {

notebooks/direct/Example2_Ti-H.ipynb

@@ -65,9 +65,7 @@
     "\n",
     "\n",
     "def load_ase_MD_traj(filename: str):\n",
-    "    \"\"\"\n",
-    "    Load .traj to pymatgen structures\n",
-    "    \"\"\"\n",
+    "    \"\"\"Load .traj to pymatgen structures.\"\"\"\n",
     "    traj = Trajectory(filename)\n",
     "    structures = [AseAtomsAdaptor.get_structure(tra) for tra in traj]\n",
     "    return structures"

notebooks/gbe/GB energy model.ipynb

@@ -123,8 +123,7 @@
    "source": [
     "\"\"\"\n",
     "Generate features for db entries\n",
-    "The dataframe containing all features and labels for all 361 data \n",
-    "is located at maml/apps/gbe/data/features.pickle\n",
+    "The dataframe containing all features and labels for all 361 data is located at maml/apps/gbe/data/features.pickle\n",
     "\"\"\"\n",
     "\n",
     "describer = GBDescriber()\n",
@@ -148,13 +147,13 @@
     }
    ],
    "source": [
+    "\n",
+    "import sklearn\n",
+    "\n",
     "\"\"\"\n",
     "Make prediction\n",
     "The model is a sklearn(0.24.2) pipeline object\n",
     "\"\"\"\n",
-    "\n",
-    "import sklearn\n",
-    "\n",
     "if sklearn.__version__ == \"0.24.2\":\n",
     "    features = [\"d_gb\", \"cos(theta)\", \"mean_delta_bl\", \"mean_bl\"]\n",
     "    module_dir = os.path.dirname(gbe.__file__)\n",

notebooks/model/garnet_formation_energy.ipynb

@@ -190,7 +190,7 @@
     "\n",
     "structures = []\n",
     "targets = []\n",
-    "for i, j in df.iterrows():\n",
+    "for _i, j in df.iterrows():\n",
     "    s = parent.copy()\n",
     "    for k, indices in mapping.items():\n",
     "        for index in indices:\n",

notebooks/pes/data/process_vasprun_to_mliap.ipynb

@@ -17,7 +17,7 @@
     "\n",
     "def get_document(vrun) -> dict:\n",
     "    \"\"\"\n",
-    "    Parse the vasprun into a dictionary\n",
+    "    Parse the vasprun into a dictionary.\n",
     "\n",
     "    Args:\n",
     "        vrun (Vasprun object): the vasprun object from pymatgen\n",

pyproject.toml

@@ -68,14 +68,15 @@ where = ["src"]
             "apps/pes/params/*.*",
             "describers/data/megnet_models/*",
             "describers/data/m3gnet_models/matbench_mp_e_form/0/m3gnet/*",
+            "apps/pes/params/*.json",
         ]
 
 [tool.black]
 line-length = 120
 
 [tool.ruff]
 target-version = "py311"
-line-length = 120
+line-length = 160
 lint.select = [
   "B",    # flake8-bugbear
   "C4",   # flake8-comprehensions
@@ -112,6 +113,7 @@ lint.ignore = [
   "B028",    # No explicit stacklevel keyword argument found
   "B904",    # Within an except clause, raise exceptions with ...
   "C408",    # unnecessary-collection-call
+  "D103",    # docstring is missing
   "D105",    # Missing docstring in magic method
   "D205",    # 1 blank line required between summary line and description
   "D212",    # Multi-line docstring summary should start at the first line
@@ -121,8 +123,10 @@ lint.ignore = [
   "PLR",     # pylint refactor
   "PLW2901", # Outer for loop variable overwritten by inner assignment target
   "PT013",   # pytest-incorrect-pytest-import
+  "RET504",  # assignment before `return` statement
   "RUF012",  # Disable checks for mutable class args. This is a non-problem.
   "SIM105",  # Use contextlib.suppress(OSError) instead of try-except-pass
+  "SIM108",  # Use ternary operator instead of `if`-`else`-block
 ]
 lint.pydocstyle.convention = "google"
 lint.isort.required-imports = ["from __future__ import annotations"]

src/maml/apps/pes/_gap.py

@@ -58,8 +58,7 @@ def _line_up(structure, energy, forces, virial_stress):
             virial_stress (list): stress should has 6 distinct
                 elements arranged in order [xx, yy, zz, xy, yz, xz].
 
-        Returns:
-            outputs: a proper format storing structure, energy, forces, virial_stress.
+        Returns: a proper format storing structure, energy, forces, virial_stress.
         """
         full_virial_stress = [
             virial_stress[0],

src/maml/describers/_m3gnet.py

@@ -134,6 +134,6 @@ def transform_one(self, structure: Structure | Molecule):
             g = self.describer_model.graph_layers[i](g)
             atom_fea[f"gc_{i + 1}"] = g[Index.ATOMS]
         atom_fea_dict = {k: v for k, v in atom_fea.items() if k in self.output_layers}
-        if isinstance(self.return_type, dict):
+        if self.return_type is dict:
             return atom_fea_dict
         return pd.DataFrame(np.concatenate(list(atom_fea_dict.values()), axis=1))