Merge pull request #928 from hackingmaterials/ml-evs/deps

More dependency upgrades: support for latest pymatgen and numpy

Author: ml-evs

matminer/featurizers/base.py

@@ -334,6 +334,8 @@ def featurize_dataframe(
         # Check names to avoid overwriting the current columns
         # ConversionFeaturizer have attribute called _overwrite_data which
         # determines whether an Error is thrown
+        if not isinstance(labels, list):
+            labels = labels.tolist()
         overwrite = getattr(self, "_overwrite_data", False)
         if not overwrite:
             for col in df.columns.values:

matminer/featurizers/structure/bonding.py

@@ -356,8 +356,9 @@ def _species_from_bondstr(self, bondstr):
         species = []
         for ss in bondstr.split(self.token):
             try:
-                species.append(Specie.from_string(ss))
-            except ValueError:
+                species.append(Specie.from_str(ss))
+            # pymatgen deprecated from_string in favour of from_str, if it is missing then fallback to from_dict
+            except (ValueError, AttributeError):
                 d = {"element": ss, "oxidation_state": 0}
                 species.append(Specie.from_dict(d))
         return tuple(species)