Merge branch 'main' into sph_harm

Author: jan-janssen

.ci_support/release.py

@@ -15,7 +15,7 @@ def get_setup_version_and_pattern(setup_content):
                     version_lst.append(dep.split("==")[1])
                     depend_lst.append(dep.split("==")[0])
 
-    version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
+    version_high_dict = {d: v for d, v in zip(depend_lst, version_lst, strict=True)}
     return version_high_dict
 
 
@@ -30,7 +30,7 @@ def get_env_version(env_content):
             if len(lst) == 2:
                 depend_lst.append(lst[0])
                 version_lst.append(lst[1])
-    return {d: v for d, v in zip(depend_lst, version_lst)}
+    return {d: v for d, v in zip(depend_lst, version_lst, strict=True)}
 
 
 def update_dependencies(setup_content, version_low_dict, version_high_dict):

structuretoolkit/analyse/neighbors.py

@@ -294,7 +294,7 @@ def _contract(
             return value
         return [
             vv[: np.sum(dist < np.inf)]
-            for vv, dist in zip(value, self.filled.distances)
+            for vv, dist in zip(value, self.filled.distances, strict=True)
         ]
 
     def _allow_ragged_to_mode(self, new_bool: bool) -> str:
@@ -1321,7 +1321,7 @@ def get_cluster(
         el_list = self._ref_structure.get_chemical_symbols()
 
         ind_shell = []
-        for d, i in zip(dist, ind):
+        for d, i in zip(dist, ind, strict=True):
             id_list = get_cluster(d[d < radius], i[d < radius])
             ia_shells_dict = {}
             for i_shell_list in id_list:

structuretoolkit/analyse/pyscal.py

@@ -55,7 +55,7 @@ def get_steinhardt_parameters(
 
         cl = cluster.KMeans(n_clusters=n_clusters)
 
-        ind = cl.fit(list(zip(*sysq))).labels_
+        ind = cl.fit(list(zip(*sysq, strict=True))).labels_
         return sysq, ind
     else:
         return sysq
@@ -197,7 +197,10 @@ def get_adaptive_cna_descriptors(
         if not ovito_compatibility:
             return cna
         else:
-            return {o: cna[p] for o, p in zip(ovito_parameter, pyscal_parameter)}
+            return {
+                o: cna[p]
+                for o, p in zip(ovito_parameter, pyscal_parameter, strict=True)
+            }
     else:
         cnalist = np.array(sys.atoms.structure)
         if mode == "numeric":

structuretoolkit/analyse/snap.py

@@ -524,7 +524,7 @@ def _set_computes_snap(lmp, bispec_options: dict):
     kw_substrings = [f"{k} {v}" for k, v in kw_options.items()]
     kwargs = " ".join(kw_substrings)
 
-    for _op, base in zip(("b", "db", "vb"), (base_b, base_db, base_vb)):
+    for _op, base in zip(("b", "db", "vb"), (base_b, base_db, base_vb), strict=True):
         command = f"{base} {radelem} {wj} {kwargs}"
         lmp.command(command)
 

structuretoolkit/build/sqs.py

@@ -154,7 +154,7 @@ def transpose(it: Iterable[Iterable]) -> Iterable[tuple]:
         Iterable[tuple]: The transposed iterable.
 
     """
-    return zip(*it)
+    return zip(*it, strict=True)
 
 
 def sqs_structures(

structuretoolkit/visualize.py

@@ -195,7 +195,7 @@ def _draw_box_plotly(fig: Any, structure: Atoms, px: Any, go: Any) -> Any:
     cell = get_cell(structure)
     data = fig.data
     for lines in _get_box_skeleton(cell):
-        fig = px.line_3d(**dict(zip(["x", "y", "z"], lines.T)))
+        fig = px.line_3d(**dict(zip(["x", "y", "z"], lines.T, strict=True)))
         fig.update_traces(line_color="#000000")
         data = fig.data + data
     return go.Figure(data=data)
@@ -462,7 +462,7 @@ def _plot3d(
             vector_color = np.ones((len(structure), 3)) * vector_color
 
     if vector_field is not None:
-        for arr, pos, col in zip(vector_field, positions, vector_color):
+        for arr, pos, col in zip(vector_field, positions, vector_color, strict=True):
             view.shape.add_arrow(list(pos), list(pos + arr), list(col), 0.2)
 
     if show_axes:  # Add axes
@@ -689,7 +689,7 @@ def _add_colorscheme_spacefill(
     Returns:
         (nglview.NGLWidget): The modified widget.
     """
-    for elem, num in set(zip(elements, atomic_numbers)):
+    for elem, num in set(zip(elements, atomic_numbers, strict=True)):
         view.add_spacefill(
             selection="#" + elem,
             radius_type="vdw",

tests/test_neighbors.py

@@ -396,7 +396,7 @@ def test_atom_numbers(self):
         neigh = stk.analyse.get_neighbors(
             structure=structure, cutoff_radius=r, num_neighbors=None, mode="ragged"
         )
-        for i, (a, d) in enumerate(zip(neigh.atom_numbers, neigh.distances)):
+        for i, (a, d) in enumerate(zip(neigh.atom_numbers, neigh.distances, strict=True)):
             self.assertEqual(np.sum(a - len(d) * [i]), 0)
         neigh = stk.analyse.get_neighbors(
             structure=structure, cutoff_radius=r, num_neighbors=None, mode="flattened"

tests/test_symmetry.py

@@ -285,7 +285,7 @@ def test_permutations(self):
         vec[neigh.indices[0]] = neigh.vecs[0]
         sym = stk.analyse.get_symmetry(structure=structure)
         all_vectors = np.einsum("ijk,ink->inj", sym.rotations, vec[sym.permutations])
-        for i, v in zip(neigh.indices, neigh.vecs):
+        for i, v in zip(neigh.indices, neigh.vecs, strict=True):
             vec = np.zeros_like(structure.positions)
             vec[i] = v
             self.assertAlmostEqual(