fix flake8 errors

.github/workflows/Lint.yaml

@@ -20,7 +20,7 @@ jobs:
       - name: Install lint
         shell: bash
         run: |
-          pip install black isort flake8
+          pip install black isort Flake8-pyproject
 
       - name: Run black
         shell: bash

naglmbis/__init__.py

@@ -7,3 +7,5 @@
 __version__ = _version.get_versions()["version"]
 # make sure all custom features are loaded
 import naglmbis.features
+
+__all__ = [naglmbis.features]

naglmbis/features/__init__.py

@@ -13,3 +13,19 @@
     TotalValence,
     VDWRadius,
 )
+
+__all__ = [
+    AtomicMass,
+    AtomicPolarisability,
+    AtomInRingOfSize,
+    ExplicitValence,
+    Hybridization,
+    HydrogenAtoms,
+    LipinskiAcceptor,
+    LipinskiDonor,
+    PaulingElectronegativity,
+    SandersonElectronegativity,
+    TotalDegree,
+    TotalValence,
+    VDWRadius,
+]

naglmbis/features/atom.py

@@ -1,8 +1,7 @@
-from typing import Literal, Optional
+from typing import Literal
 
 import torch
 from nagl.features import AtomFeature, one_hot_encode, register_atom_feature
-from openff.toolkit.topology import Molecule
 from pydantic import Extra, Field, dataclasses
 from rdkit import Chem
 

naglmbis/models/__init__.py

@@ -1,2 +1,4 @@
 from naglmbis.models.base_model import MBISGraphModel
 from naglmbis.models.models import CHARGE_MODELS, load_charge_model
+
+__all__ = [MBISGraphModel, CHARGE_MODELS, load_charge_model]

naglmbis/models/base_model.py

@@ -1,8 +1,5 @@
 # models for the nagl run
 
-import abc
-from typing import Dict, List, Literal, Optional
-
 import torch
 from nagl.molecules import DGLMolecule
 from nagl.training import DGLMoleculeLightningModel
@@ -12,7 +9,7 @@
 class MBISGraphModel(DGLMoleculeLightningModel):
     "A wrapper to make it easy to load and evaluate models"
 
-    def compute_properties(self, molecule: Chem.Mol) -> Dict[str, torch.Tensor]:
+    def compute_properties(self, molecule: Chem.Mol) -> dict[str, torch.Tensor]:
         dgl_molecule = DGLMolecule.from_rdkit(
             molecule, self.config.model.atom_features, self.config.model.bond_features
         )

naglmbis/models/models.py

@@ -1,4 +1,3 @@
-import pathlib
 from typing import Literal
 
 import torch

naglmbis/plugins/__init__.py

@@ -1,2 +1,4 @@
 from naglmbis.plugins.plugins import NAGLMBISHandler
 from naglmbis.plugins.utils import modify_force_field
+
+__all__ = [NAGLMBISHandler, modify_force_field]

naglmbis/tests/test_atom_features.py

@@ -1,5 +1,4 @@
 import numpy as np
-from nagl.features import AtomConnectivity
 
 from naglmbis.features import (
     AtomicMass,