add test for TransformedStructure.set_parameter()

fix get_decomp_and_e_above_hull doc str ValueError condition

Author: janosh

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.1
+    rev: v0.3.2
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

pymatgen/alchemy/materials.py

@@ -229,15 +229,20 @@ def __str__(self) -> str:
         output.extend(("\nOther parameters", "------------", str(self.other_parameters)))
         return "\n".join(output)
 
-    def set_parameter(self, key: str, value: Any) -> None:
+    def set_parameter(self, key: str, value: Any) -> TransformedStructure:
         """Sets a parameter.
 
         Args:
             key (str): The string key.
             value (Any): The value.
+
+        Returns:
+            TransformedStructure
         """
         self.other_parameters[key] = value
 
+        return self
+
     @property
     def was_modified(self) -> bool:
         """Boolean describing whether the last transformation on the structure

pymatgen/analysis/phase_diagram.py

@@ -753,7 +753,8 @@ def get_decomp_and_e_above_hull(
                 'ignore' just returns (None, None). Defaults to 'raise'.
 
         Raises:
-            ValueError: If no valid decomposition exists in this phase diagram for given entry.
+            ValueError: If on_error is 'raise' and no valid decomposition exists in this
+                phase diagram for given entry.
 
         Returns:
             tuple[decomp, energy_above_hull]: The decomposition is provided
@@ -825,9 +826,9 @@ def get_equilibrium_reaction_energy(self, entry: PDEntry) -> float | None:
             return 0
 
         entries = [e for e in self._get_stable_entries_in_space(frozenset(elem_space)) if e != entry]
-        modpd = PhaseDiagram(entries, elements=elem_space)
+        mod_pd = PhaseDiagram(entries, elements=elem_space)
 
-        return modpd.get_decomp_and_e_above_hull(entry, allow_negative=True)[1]
+        return mod_pd.get_decomp_and_e_above_hull(entry, allow_negative=True)[1]
 
     def get_decomp_and_phase_separation_energy(
         self,
@@ -1752,6 +1753,9 @@ def get_pd_for_entry(self, entry: Entry | Composition) -> PhaseDiagram:
 
         Returns:
             PhaseDiagram: phase diagram that the entry is part of
+
+        Raises:
+            ValueError: If no suitable PhaseDiagram is found for the entry.
         """
         entry_space = frozenset(entry.elements) if isinstance(entry, Composition) else frozenset(entry.elements)
 

pymatgen/analysis/structure_analyzer.py

@@ -330,8 +330,8 @@ def get_connections(self):
     def get_sitej(self, site_index, image_index):
         """
         Assuming there is some value in the connectivity array at indices
-        (1, 3, 12). sitei can be obtained directly from the input structure
-        (structure[1]). sitej can be obtained by passing 3, 12 to this function.
+        (1, 3, 12). site_i can be obtained directly from the input structure
+        (structure[1]). site_j can be obtained by passing 3, 12 to this function.
 
         Args:
             site_index (int): index of the site (3 in the example)

tests/alchemy/test_materials.py

@@ -95,6 +95,11 @@ def test_undo_and_redo_last_change(self):
         ts.undo_last_change()
         ts.redo_next_change()
 
+    def test_set_parameter(self):
+        trans = self.trans.set_parameter("author", "will")
+        assert trans.other_parameters["author"] == "will"
+        assert trans is self.trans
+
     def test_as_dict(self):
         self.trans.set_parameter("author", "will")
         dct = self.trans.as_dict()