Merge pull request #106 from KingsburyLab/bugfix

Solute.from_formula: fix oxi_states bug (#103)

CHANGELOG.md

@@ -5,10 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## [0.12.1] - 2024-02-25
 
 ### Fixed
 
+- `Solute.from_formula`: Fix bug in which an uncaught exception could occur when
+  if `pymatgen` failed to guess the oxidation state of a solute. (Issue #103 - thanks to @xiaoxiaozhu123 for reporting).
 - `Solution.get_total_amount`: Bugfix that would cause the method to fail if
   mass-based units such as mg/L or ppm were requested.
 

src/pyEQL/solute.py

@@ -115,13 +115,10 @@ def from_formula(cls, formula: str):
         mw = f"{float(pmg_ion.weight / factor)} g/mol"  # weight is a FloatWithUnit
         chemsys = pmg_ion.chemical_system
         # store only the most likely oxi_state guesses
-        oxi_states = pmg_ion.oxi_state_guesses(all_oxi_states=True)
-        # TODO - hack to work around a pymatgen bug in Composition
-        # https://github.com/materialsproject/pymatgen/issues/3324
-        if oxi_states == []:
-            oxi_states = {els[0]: 0.0} if rform in ["O2(aq)", "O3(aq)", "Cl2(aq)", "F2(aq)"] else {}
-        else:
-            oxi_states = oxi_states[0]
+        try:
+            oxi_states = pmg_ion.oxi_state_guesses(all_oxi_states=True)[0]
+        except (IndexError, ValueError):
+            oxi_states = {}
 
         return cls(
             rform,

tests/test_solute.py

@@ -16,6 +16,8 @@ def test_from_formula():
     assert s.n_atoms == 1
     assert s.n_elements == 1
     assert s.oxi_state_guesses == {"Mg": 2.0}
+    # test behavior when oxi_state_guesses fails
+    assert Solute.from_formula("Br[-0.33333333]").oxi_state_guesses == {}
     assert s.molecular_weight == "24.305 g/mol"
     s2 = Solute.from_formula("O6")
     assert s2.formula == "O3(aq)"