remove legacy import for pymatgen.core.periodic_table.Specie, now called Species

Author: janosh

crystal_toolkit/components/structure.py

@@ -604,7 +604,7 @@ def get_font_color(hex_code):
         try:
             formula = Composition.from_dict(legend["composition"]).reduced_formula
         except Exception:
-            # TODO: fix legend for Dummy Specie compositions
+            # TODO: fix legend for DummySpecies compositions
             formula = "Unknown"
 
         legend_colors = OrderedDict(

crystal_toolkit/components/transformations/substitution.py

@@ -38,7 +38,7 @@ def options_layouts(self, state=None, structure=None):
             state=state,
             help_str="A mapping from an original species (element or element with oxidation state, e.g. O or O2-) "
             "to a new species (element, element with oxidation state, or a composition, e.g. O or O2- or "
-            '{"Au": 0.5, "Cu": 0.5}). In pymatgen, these are Element, Specie and Composition classes '
+            '{"Au": 0.5, "Cu": 0.5}). In pymatgen, these are Element, Species and Composition classes '
             "respectively.",
             key_name="Original Species",
             value_name="New Species",

crystal_toolkit/core/legend.py

@@ -12,7 +12,7 @@
 from monty.serialization import loadfn
 from palettable.colorbrewer.qualitative import Set1_9
 from pymatgen.analysis.molecule_structure_comparator import CovalentRadius
-from pymatgen.core.periodic_table import Element, Specie
+from pymatgen.core.periodic_table import Element, Species
 from pymatgen.core.structure import Molecule, Site, SiteCollection
 from pymatgen.util.string import unicodeify_species
 from sklearn.preprocessing import LabelEncoder
@@ -255,13 +255,13 @@ def generate_categorical_color_scheme_on_the_fly(
 
         return color_scheme
 
-    def get_color(self, sp: Specie | Element, site: Site | None = None) -> str:
+    def get_color(self, sp: Species | Element, site: Site | None = None) -> str:
         """
         Get a color to render a specific species. Optionally, you can provide
         a site for context, since ...
 
         Args:
-            sp: Specie or Element
+            sp: Species or Element
             site: Site
 
         Returns: Color
@@ -332,7 +332,7 @@ def get_color(self, sp: Specie | Element, site: Site | None = None) -> str:
 
         return html5_serialize_simple_color(color)
 
-    def get_radius(self, sp: Specie | Element, site: Site | None = None) -> float:
+    def get_radius(self, sp: Species | Element, site: Site | None = None) -> float:
 
         # allow manual override by user
         if site and "display_radius" in site.properties:
@@ -351,7 +351,7 @@ def get_radius(self, sp: Specie | Element, site: Site | None = None) -> float:
             radius = float(sp.atomic_radius)
         elif (
             self.radius_scheme == "specified_or_average_ionic"
-            and isinstance(sp, Specie)
+            and isinstance(sp, Species)
             and sp.oxi_state
         ):
             radius = float(sp.ionic_radius)
@@ -395,10 +395,10 @@ def analyze_site_props(site_collection: SiteCollection) -> dict[str, list[str]]:
         return dict(site_prop_names)
 
     @staticmethod
-    def get_species_str(sp: Specie | Element) -> str:
+    def get_species_str(sp: Species | Element) -> str:
         """
         Args:
-            sp: Specie or Element
+            sp: Species or Element
 
         Returns: string representation
         """