remove mypy rdkit pin

.github/workflows/mypy.yaml

@@ -36,9 +36,7 @@ jobs:
           cache-downloads-key: downloads-${{ steps.date.outputs.date }}
           create-args: >-
             python=3.12
-            rdkit=2023.09.5
             mypy>=1.17.0
-            types-setuptools
 
           init-shell: bash
 

openfe/tests/conftest.py

@@ -117,7 +117,7 @@ def pytest_configure(config):
 
 def mol_from_smiles(smiles: str) -> Chem.Mol:
     m = Chem.MolFromSmiles(smiles)
-    AllChem.Compute2DCoords(m)
+    AllChem.Compute2DCoords(m)  # type: ignore[attr-defined]
 
     return m
 

openfe/tests/dev/serialization_test_templates.py

@@ -27,7 +27,7 @@
 
 def mol_from_smiles(smiles: str) -> Chem.Mol:
     m = Chem.MolFromSmiles(smiles)
-    AllChem.Compute2DCoords(m)
+    AllChem.Compute2DCoords(m)  # type: ignore[attr-defined]
 
     return m
 

openfe/tests/setup/atom_mapping/test_lomap_scorers.py

@@ -9,7 +9,7 @@
 import pytest
 from numpy.testing import assert_allclose
 from rdkit import Chem
-from rdkit.Chem.AllChem import Compute2DCoords
+from rdkit.Chem.AllChem import Compute2DCoords  # type: ignore[attr-defined]
 
 import openfe
 from openfe.setup import LigandAtomMapping, lomap_scorers

openfe/utils/atommapping_network_plotting.py

@@ -42,7 +42,7 @@ def _draw_mapped_molecule(
         molA_to_molB: Dict[int, int],
     ):
         # create the image in a format matplotlib can handle
-        d2d = Chem.Draw.rdMolDraw2D.MolDraw2DCairo(300, 300, 300, 300)
+        d2d = Chem.Draw.rdMolDraw2D.MolDraw2DCairo(300, 300, 300, 300)  # type: ignore[attr-defined]
         d2d.drawOptions().setBackgroundColour((1, 1, 1, 0.7))
         # TODO: use a custom draw2d object; figure size from transforms
         img_bytes = draw_one_molecule_mapping(