Remove viz deps + run pyupgrade 3.11 (#155)

* Remove viz deps + run pyupgrade 3.11

* Add missing dep to highlight the notebooks

* need optinal deps to test notebook

* fix dep name

Author: mikemhenry

docs/environment.yml

@@ -19,9 +19,7 @@ dependencies:
   - myst-parser
   - pydata-sphinx-theme
   - nbsphinx-link
-  # vis
-  - ipywidgets
-  - py3Dmol
+  - ipython_pygments_lexers
   # docs
   - pip:
     - git+https://github.com/OpenFreeEnergy/ofe-sphinx-theme@a45f3edd5bc3e973c1a01b577c71efa1b62a65d6

environment.yml

@@ -26,7 +26,7 @@ dependencies:
   - myst-parser
   - pydata-sphinx-theme
   - nbsphinx-link
-  # vis
+  # opt
   - ipywidgets
   - py3Dmol
   # docs

src/kartograf/tests/conftest.py

@@ -133,7 +133,7 @@ def fused_ring_mols() -> tuple[SmallMoleculeComponent, SmallMoleculeComponent]:
     atom ordering."""
     d = resources.files("kartograf.tests.data")
     rd_mols = [Chem.MolFromMolFile(str(f), removeHs=False) for f in [d / "biphenyl.sdf", d / "biaryl-indene.sdf"]]
-    mol_a, mol_b = [SmallMoleculeComponent.from_rdkit(m) for m in rd_mols]
+    mol_a, mol_b = (SmallMoleculeComponent.from_rdkit(m) for m in rd_mols)
     mol_b_to_a = align_mol_shape(mol_b, ref_mol=mol_a)
     return mol_a, mol_b_to_a