Fix warnings

src/stk/_internal/building_block.py

@@ -1,7 +1,6 @@
 import logging
 import os
 import typing
-import warnings
 from collections.abc import Collection, Iterable, Iterator
 from functools import partial
 
@@ -38,12 +37,6 @@ class BuildingBlock(Molecule):
     _init_funcs = {
         ".mol": partial(rdkit.MolFromMolFile, sanitize=False, removeHs=False),
         ".sdf": partial(rdkit.MolFromMolFile, sanitize=False, removeHs=False),
-        ".pdb": partial(
-            rdkit.MolFromPDBFile,
-            sanitize=False,
-            removeHs=False,
-            proximityBonding=False,
-        ),
     }
 
     _placer_ids: frozenset[int]
@@ -452,15 +445,6 @@ def init_from_file(
 
         _, extension = os.path.splitext(path)
 
-        if extension == ".pdb":
-            warnings.warn(
-                "Loading from .pdb files is deprecated and will be "
-                "removed from stk versions released after 1st Nov "
-                "2022. Please use .mol files for loading molecules "
-                "instead.",
-                category=FutureWarning,
-            )
-
         if extension not in cls._init_funcs:
             raise ValueError(f'Unable to initialize from "{extension}" files.')
         # This remake needs to be here because molecules loaded

src/stk/_internal/ea/plotters/selection.py

@@ -232,7 +232,7 @@ def _plot(self, population, counter):
         ax.get_legend().remove()
         # https://tinyurl.com/2p9drmkh
         plt.rcParams["axes.grid"] = False
-        ax.figure.colorbar(sm).set_label(self._heat_map_label)
+        ax.figure.colorbar(sm, ax=ax).set_label(self._heat_map_label)
         plt.tight_layout()
         fig.savefig(f"{self._filename}_{self._plots}.png", dpi=fig.dpi)
         plt.close("all")

src/stk/_internal/topology_graphs/cof/cof.py

@@ -446,7 +446,7 @@ def __init__(
 
         self._check_building_block_vertices(
             num_vertices=(
-                np.product(lattice_size) * len(self._vertex_prototypes)
+                np.prod(lattice_size) * len(self._vertex_prototypes)
             ),
             building_block_vertices=building_block_vertices,
         )

tests/molecular/molecules/building_block/fixtures/init_from_file.py

@@ -7,7 +7,6 @@
 @pytest.fixture(
     params=[
         "building_block.mol",
-        "building_block.pdb",
     ],
 )
 def path(tmpdir, request):