Updates for dependencies (especially RDKit and NumPy) (#33)

* Add adjustDegree = False to adjust query params

This fixes an issue that changed between RDKit 2024.9.6 and 2025.3.1.
Details in rdkit/rdkit#8592

* Update tests for NumPy 2.0+ compatibility

* Update pyproject.toml and poetry.lock for 2025-07

Author: dwhswenson

pdbeccdutils/core/depictions.py

@@ -174,6 +174,7 @@ def _load_template(self, path):
         p = Chem.AdjustQueryParameters()
         p.makeAtomsGeneric = True
         p.makeBondsGeneric = True
+        p.adjustDegree = False
 
         mol = Chem.AdjustQueryProperties(mol, p)
 

pdbeccdutils/tests/test_rdkit_fixtures.py

@@ -12,7 +12,7 @@ def test_conformer_is_broken_ion():
         mol.AddAtom(atom)
 
         conformer = rdkit.Chem.Conformer(1)
-        atom_position = rdkit.Chem.rdGeometry.Point3D(np.NaN, np.NaN, np.NaN)
+        atom_position = rdkit.Chem.rdGeometry.Point3D(np.nan, np.nan, np.nan)
         conformer.SetAtomPosition(0, atom_position)
         mol.AddConformer(conformer, assignId=True)
 
@@ -37,7 +37,7 @@ def test_conformer_has_broken_atom():
 
         conformer = rdkit.Chem.Conformer(1)
         o_position = rdkit.Chem.rdGeometry.Point3D(1, 2, 3)
-        h_position = rdkit.Chem.rdGeometry.Point3D(np.NaN, np.NaN, np.NaN)
+        h_position = rdkit.Chem.rdGeometry.Point3D(np.nan, np.nan, np.nan)
 
         conformer.SetAtomPosition(0, o_position)
         conformer.SetAtomPosition(1, h_position)