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More dependency upgrades: support for latest pymatgen and numpy #928

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merged 5 commits into from
Mar 26, 2024
Merged

More dependency upgrades: support for latest pymatgen and numpy #928

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9c97e0d
update dependencies for ubuntu-latest/py3.10
invalid-email-address Mar 26, 2024
425ce71
update dependencies for ubuntu-latest/py3.11
invalid-email-address Mar 26, 2024
0b6fee0
update dependencies for ubuntu-latest/py3.9
invalid-email-address Mar 26, 2024
ea849c5
Handle deprecation of pymatgen `Specie.from_string`
ml-evs Mar 26, 2024
802a119
Cast columns to list for compatibility with numpy 1.26+
ml-evs Mar 26, 2024
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2 changes: 2 additions & 0 deletions matminer/featurizers/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
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5 changes: 3 additions & 2 deletions matminer/featurizers/structure/bonding.py
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Expand Up @@ -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)
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