Add material_id: str | int to PhononBSDOSDoc schema (#669)

* add material_id: str | int to PhononBSDOSDoc schema

* set extra="allow" on PhononBSDOSDoc, drop material_id

Author: janosh

src/atomate2/common/schemas/phonons.py

@@ -100,12 +100,11 @@ class PhononJobDirs(BaseModel):
     )
 
 
-class PhononBSDOSDoc(StructureMetadata):
+class PhononBSDOSDoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
     """Collection of all data produced by the phonon workflow."""
 
     structure: Optional[Structure] = Field(
-        None,
-        description="Structure of Materials Project.",
+        None, description="Structure of Materials Project."
     )
 
     phonon_bandstructure: Optional[PhononBandStructureSymmLine] = Field(

tests/common/schemas/test_elastic.py

@@ -16,18 +16,14 @@ def test_elastic_document(test_dir):
     schema_ref = json.loads(schema_path.read_text())
 
     doc = ElasticDocument(**schema_ref)
-    ElasticDocument.model_validate_json(json.dumps(doc, cls=MontyEncoder))
+    validated = ElasticDocument.model_validate_json(json.dumps(doc, cls=MontyEncoder))
+    assert isinstance(validated, ElasticDocument)
 
 
 # schemas where all fields have default values
 @pytest.mark.parametrize(
     "model_cls",
-    [
-        ElasticDocument,
-        ElasticTensorDocument,
-        DerivedProperties,
-        FittingData,
-    ],
+    [ElasticDocument, ElasticTensorDocument, DerivedProperties, FittingData],
 )
 def test_model_validate(model_cls):
     model_cls.model_validate_json(json.dumps(model_cls(), cls=MontyEncoder))

tests/common/schemas/test_phonons.py

@@ -40,9 +40,18 @@ def test_phonon_bs_dos_doc():
     validated = PhononBSDOSDoc.model_validate_json(json.dumps(doc, cls=MontyEncoder))
     assert isinstance(validated, PhononBSDOSDoc)
 
+    # test invalid supercell_matrix type fails
     with pytest.raises(ValidationError):
         doc = PhononBSDOSDoc(**kwargs | {"supercell_matrix": (1, 1, 1)})
 
+    # test optional material_id
+    doc = PhononBSDOSDoc(**kwargs | {"material_id": 1234})
+    assert doc.material_id == 1234
+
+    # test extra="allow" option
+    doc = PhononBSDOSDoc(**kwargs | {"extra_field": "test"})
+    assert doc.extra_field == "test"
+
 
 # schemas where all fields have default values
 @pytest.mark.parametrize("model_cls", [PhononJobDirs, PhononUUIDs])

tests/vasp/flows/test_phonons.py

@@ -180,44 +180,20 @@ def test_phonon_wf_only_displacements_no_structural_transformation(
 
     assert_allclose(
         responses[job.jobs[-1].uuid][1].output.free_energies,
-        [
-            5774.56699647,
-            5616.29786373,
-            4724.73684926,
-            3044.19341280,
-            696.34353154,
-        ],
+        [5774.56699647, 5616.29786373, 4724.73684926, 3044.19341280, 696.34353154],
     )
     assert_allclose(
         responses[job.jobs[-1].uuid][1].output.entropies,
-        [
-            0.0,
-            4.78666294,
-            13.02533234,
-            20.36075467,
-            26.39807246,
-        ],
+        [0.0, 4.78666294, 13.02533234, 20.36075467, 26.39807246],
     )
     assert_allclose(
         responses[job.jobs[-1].uuid][1].output.heat_capacities,
-        [
-            0.0,
-            8.04749769,
-            15.97101906,
-            19.97032648,
-            21.87475268,
-        ],
+        [0.0, 8.04749769, 15.97101906, 19.97032648, 21.87475268],
     )
 
     assert_allclose(
         responses[job.jobs[-1].uuid][1].output.internal_energies,
-        [
-            5774.56699647,
-            6094.96415750,
-            7329.80331668,
-            9152.41981241,
-            11255.57251541,
-        ],
+        [5774.56699647, 6094.96415750, 7329.80331668, 9152.41981241, 11255.57251541],
     )
 
     assert isinstance(