Breaking: rename get_ax3d_fig_plt->get_ax3d_fig and `get_ax_fig_plt…

…->get_ax_fig` plus no longer return `plt` (#3329)

* breaking: rename get_ax3d_fig_plt->get_ax3d_fig and stop returning matplotlib.pyplot

* breaking: same for get_ax_fig_plt->get_ax_fig

* remove :class:`SomeObject` from doc strings

probably doesn't work with new markdown docs, can't check without network atm

* simplify doc strings: pymatgen.core.(lattice.->'')Lattice

* blank line before all Args: and Returns: doc string section headers

* use dict.setdefault() instead of checking key presence first

* doc string indentation and line break fixes

* fix doc string Returns: sections

* define reusable LatticeType and CrystalSystem types

* simplify with_local_env_strategy() sg.add_edge() call

pymatgen/alchemy/filters.py

@@ -59,7 +59,8 @@ def __init__(self, species, strict_compare=False, AND=True, exclude=False):
     def test(self, structure: Structure):
         """Method to execute the test.
 
-        Returns: True if structure do not contain specified species.
+        Returns:
+            bool: True if structure does not contain specified species.
         """
         # set up lists to compare
         if not self._strict:
@@ -139,8 +140,8 @@ def test(self, structure: Structure):
         Args:
             structure (Structure): Input structure to test
 
-        Returns: True if structure does not contain species within specified
-            distances.
+        Returns:
+            bool: True if structure does not contain species within specified distances.
         """
         all_species = set(self.specie_and_min_dist)
         for site in structure:
@@ -203,7 +204,8 @@ def test(self, structure: Structure):
         Args:
             structure (Structure): Input structure to test.
 
-        Returns: True if structure is not in list.
+        Returns:
+            bool: True if structure is not in list.
         """
         hash = self.structure_matcher._comparator.get_hash(structure.composition)
         if not self.structure_list[hash]:
@@ -253,7 +255,8 @@ def test(self, structure: Structure):
         Args:
             structure (Structure): Input structure to test
 
-        Returns: True if structure is not in existing list.
+        Returns:
+            bool: True if structure is not in existing list.
         """
 
         def get_sg(s):
@@ -297,7 +300,8 @@ def test(self, structure: Structure):
         Args:
             structure (Structure): Input structure to test
 
-        Returns: True if structure is neutral.
+        Returns:
+            bool: True if structure is neutral.
         """
         return structure.charge == 0.0
 
@@ -329,8 +333,9 @@ def test(self, structure: Structure):
         Args:
             structure (Structure): Input structure to test
 
-        Returns: True if structure does not contain the two species are distances
-            greater than max_dist.
+        Returns:
+            bool: True if structure does not contain the two species are distances
+                greater than max_dist.
         """
         sp1_indices = [idx for idx, site in enumerate(structure) if site.specie == self.sp1]
         sp2_indices = [idx for idx, site in enumerate(structure) if site.specie == self.sp2]

pymatgen/alchemy/transmuters.py

@@ -40,11 +40,11 @@ def __init__(
         self,
         transformed_structures,
         transformations=None,
-        extend_collection=0,
-        ncores=None,
+        extend_collection: int = 0,
+        ncores: int | None = None,
     ):
         """Initializes a transmuter from an initial list of
-        :class:`pymatgen.alchemy.materials.TransformedStructure`.
+        pymatgen.alchemy.materials.TransformedStructure.
 
         Args:
             transformed_structures ([TransformedStructure]): Input transformed

pymatgen/analysis/bond_dissociation.py

@@ -70,7 +70,7 @@ def __init__(
                 raise RuntimeError(key + " must be present in molecule entry! Exiting...")
             for entry in self.filtered_entries:
                 if key not in entry:
-                    raise RuntimeError(key + " must be present in all fragment entries! Exiting...")
+                    raise RuntimeError(f"{key=} must be present in all fragment entries! Exiting...")
 
         # Define expected charges
         final_charge = int(molecule_entry["final_molecule"]["charge"])  # type: ignore[index]

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -27,9 +27,6 @@ def draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None):
         ax: Axes object in which the network should be drawn.
         sg: Not used currently (drawing of supergraphs).
         periodicity_vectors: List of periodicity vectors that should be drawn.
-
-    Returns: None
-
     """
     for n in env_graph:
         c = Circle(pos[n], radius=0.02, alpha=0.5)
@@ -124,18 +121,18 @@ def draw_network(env_graph, pos, ax, sg=None, periodicity_vectors=None):
 
 
 def make_supergraph(graph, multiplicity, periodicity_vectors):
-    """Make supergraph from a graph of environments.
+    """Make super graph from a graph of environments.
 
     Args:
         graph: Graph of environments.
-        multiplicity: Multiplicity of the supergraph.
-        periodicity_vectors: Periodicity vectors needed to make the supergraph.
-
-    Returns: Super graph of the environments.
+        multiplicity: Multiplicity of the super graph.
+        periodicity_vectors: Periodicity vectors needed to make the super graph.
 
+    Returns:
+        nx.MultiGraph: Super graph of the environments.
     """
-    supergraph = nx.MultiGraph()
-    print("peridoicity vectors :")
+    super_graph = nx.MultiGraph()
+    print("periodicity vectors :")
     print(periodicity_vectors)
     if isinstance(multiplicity, int) or len(multiplicity) == 1:
         mult = multiplicity if isinstance(multiplicity, int) else multiplicity[0]
@@ -173,25 +170,25 @@ def make_supergraph(graph, multiplicity, periodicity_vectors):
                 new_data = dict(data)
                 new_data["start"] = (imult * len(nodes)) + indices_nodes[n1]
                 new_data["end"] = (imult * len(nodes)) + indices_nodes[n2]
-                supergraph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
+                super_graph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
             for n1, n2, key, data in connecting_edges:
                 new_data = dict(data)
                 new_data["start"] = (imult * len(nodes)) + indices_nodes[n1]
                 new_data["end"] = np.mod(((imult + 1) * len(nodes)) + indices_nodes[n2], len(nodes) * mult)
                 new_data["delta"] = (0, 0, 0)
-                supergraph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
+                super_graph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
         imult = mult - 1
         for n1, n2, key, data in other_edges:
             new_data = dict(data)
             new_data["start"] = (imult * len(nodes)) + indices_nodes[n1]
             new_data["end"] = (imult * len(nodes)) + indices_nodes[n2]
-            supergraph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
+            super_graph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
         for n1, n2, key, data in connecting_edges:
             new_data = dict(data)
             new_data["start"] = (imult * len(nodes)) + indices_nodes[n1]
             new_data["end"] = indices_nodes[n2]
-            supergraph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
-        return supergraph
+            super_graph.add_edge(new_data["start"], new_data["end"], key=key, attr_dict=new_data)
+        return super_graph
 
     raise NotImplementedError("make_supergraph not yet implemented for 2- and 3-periodic graphs")