Mark schema fields with None default as Optional to pass pydantic v2 validation

pyproject.toml

@@ -162,6 +162,7 @@ ignore = [
     "ANN102",
     "ANN401",
     "BLE001",
+    "C408",   # Unnecessary (dict/list/tuple) call - remove call
     "C901",   # function too complex
     "DTZ",    # datetime-tz-now
     "EM",     # exception message must not use f-string literal

src/atomate2/common/schemas/cclib.py

@@ -34,22 +34,28 @@ class TaskDocument(MoleculeMetadata, extra="allow"):  # type: ignore[call-arg]
     For the list of supported packages, see https://cclib.github.io
     """
 
-    molecule: Molecule = Field(None, description="Final output molecule from the task")
-    energy: float = Field(None, description="Final total energy")
-    dir_name: str = Field(None, description="Directory where the output is parsed")
-    logfile: str = Field(
+    molecule: Optional[Molecule] = Field(
+        None, description="Final output molecule from the task"
+    )
+    energy: Optional[float] = Field(None, description="Final total energy")
+    dir_name: Optional[str] = Field(
+        None, description="Directory where the output is parsed"
+    )
+    logfile: Optional[str] = Field(
         None, description="Path to the log file used in the post-processing analysis"
     )
-    attributes: dict = Field(
+    attributes: Optional[dict] = Field(
         None, description="Computed properties and calculation outputs"
     )
-    metadata: dict = Field(
+    metadata: Optional[dict] = Field(
         None,
         description="Calculation metadata, including input parameters and runtime "
         "statistics",
     )
-    task_label: str = Field(None, description="A description of the task")
-    tags: list[str] = Field(None, description="Optional tags for this task document")
+    task_label: Optional[str] = Field(None, description="A description of the task")
+    tags: Optional[list[str]] = Field(
+        None, description="Optional tags for this task document"
+    )
     last_updated: str = Field(
         default_factory=datetime_str,
         description="Timestamp for this task document was last updated",

src/atomate2/common/schemas/defects.py

@@ -22,52 +22,52 @@ class FormationEnergyDiagramDocument(BaseModel):
     will not necessarily have all the entries in the phase diagram computed.
     """
 
-    bulk_entry: ComputedStructureEntry = Field(
+    bulk_entry: Optional[ComputedStructureEntry] = Field(
         None,
         description="The ComputedEntry representing the bulk structure.",
     )
 
-    defect_entries: list[DefectEntry] = Field(
+    defect_entries: Optional[list[DefectEntry]] = Field(
         None,
         description="The defect entries for the formation energy diagram.",
     )
 
-    pd_entries: list[ComputedEntry] = Field(
+    pd_entries: Optional[list[ComputedEntry]] = Field(
         None,
         description="The entries used to construct the phase diagram.",
     )
 
-    vbm: float = Field(
+    vbm: Optional[float] = Field(
         None,
         description="The VBM of the pristine supercell calculation.",
     )
 
-    band_gap: float = Field(
+    band_gap: Optional[float] = Field(
         None,
         description="The band gap of the pristine supercell calculation.",
     )
 
-    inc_inf_values: bool = Field(
+    inc_inf_values: Optional[bool] = Field(
         None,
         description="Whether or not to include infinite values in the diagram.",
     )
 
-    defect: Defect = Field(
+    defect: Optional[Defect] = Field(
         None,
         description="The defect for which the diagram is being calculated.",
     )
 
-    bulk_sc_dir: str = Field(
+    bulk_sc_dir: Optional[str] = Field(
         None,
         description="The directory name of the pristine supercell calculation.",
     )
 
-    defect_sc_dirs: dict[int, str] = Field(
+    defect_sc_dirs: Optional[dict[int, str]] = Field(
         None,
         description="The directory names of the charged defect calculations.",
     )
 
-    dielectric: Union[float, list[list[float]]] = Field(
+    dielectric: Optional[Union[float, list[list[float]]]] = Field(
         None,
         description="The dielectric constant or tensor, can be used to compute "
         "finite-size corrections.",
@@ -125,42 +125,41 @@ def as_formation_energy_diagram(
 class CCDDocument(BaseModel):
     """Configuration-coordinate definition of configuration-coordinate diagram."""
 
-    q1: int = Field(None, description="Charge state 1.")
-    q2: int = Field(None, description="Charge state 2.")
-    structure1: Structure = Field(
+    q1: Optional[int] = Field(None, description="Charge state 1.")
+    q2: Optional[int] = Field(None, description="Charge state 2.")
+    structure1: Optional[Structure] = Field(
         None,
         description="The structure of defect (supercell) in charge state (q2).",
     )
-    structure2: Structure = Field(
+    structure2: Optional[Structure] = Field(
         None,
         description="The structure of defect (supercell) in charge state (q2).",
     )
 
-    distortions1: list[float] = Field(
+    distortions1: Optional[list[float]] = Field(
         None,
         description="The distortions of the defect (supercell) in charge state (q1).",
     )
-    distortions2: list[float] = Field(
+    distortions2: Optional[list[float]] = Field(
         None,
         description="The distortions of the defect (supercell) in charge state (q2).",
     )
-
-    energies1: list[float] = Field(
+    energies1: Optional[list[float]] = Field(
         None,
         description="The energies of the defect (supercell) in charge state (q1).",
     )
-    energies2: list[float] = Field(
+    energies2: Optional[list[float]] = Field(
         None,
         description="The energies of the defect (supercell) in charge state (q2).",
     )
 
-    static_dirs1: list[str] = Field(
+    static_dirs1: Optional[list[str]] = Field(
         None,
         description="Directories of distorted calculations for the defect (supercell) "
         "in charge state (q1).",
     )
 
-    static_dirs2: list[str] = Field(
+    static_dirs2: Optional[list[str]] = Field(
         None,
         description="Directories of distorted calculations for the defect (supercell) "
         "in charge state (q2).",
@@ -178,13 +177,13 @@ class CCDDocument(BaseModel):
         "charge state (q2).",
     )
 
-    relaxed_index1: int = Field(
+    relaxed_index1: Optional[int] = Field(
         None,
         description="The index of the static calculation in that corresponds to the "
         "relaxed charge state (q1).",
     )
 
-    relaxed_index2: int = Field(
+    relaxed_index2: Optional[int] = Field(
         None,
         description="The index of the static calculation in that corresponds to the "
         "relaxed charge state (q2).",

src/atomate2/common/schemas/elastic.py

@@ -1,5 +1,4 @@
 """Schemas for elastic tensor fitting and related properties."""
-
 from copy import deepcopy
 from typing import Optional
 
@@ -24,51 +23,61 @@
 class DerivedProperties(BaseModel):
     """Properties derived from an elastic tensor."""
 
-    k_voigt: float = Field(None, description="Voigt average of the bulk modulus.")
-    k_reuss: float = Field(None, description="Reuss average of the bulk modulus.")
-    k_vrh: float = Field(
+    k_voigt: Optional[float] = Field(
+        None, description="Voigt average of the bulk modulus."
+    )
+    k_reuss: Optional[float] = Field(
+        None, description="Reuss average of the bulk modulus."
+    )
+    k_vrh: Optional[float] = Field(
         None, description="Voigt-Reuss-Hill average of the bulk modulus."
     )
-    g_voigt: float = Field(None, description="Voigt average of the shear modulus.")
-    g_reuss: float = Field(None, description="Reuss average of the shear modulus.")
-    g_vrh: float = Field(
+    g_voigt: Optional[float] = Field(
+        None, description="Voigt average of the shear modulus."
+    )
+    g_reuss: Optional[float] = Field(
+        None, description="Reuss average of the shear modulus."
+    )
+    g_vrh: Optional[float] = Field(
         None, description="Voigt-Reuss-Hill average of the shear modulus."
     )
-    universal_anisotropy: float = Field(
+    universal_anisotropy: Optional[float] = Field(
         None, description="Universal elastic anisotropy."
     )
-    homogeneous_poisson: float = Field(None, description="Homogeneous poisson ratio.")
-    y_mod: float = Field(
+    homogeneous_poisson: Optional[float] = Field(
+        None, description="Homogeneous poisson ratio."
+    )
+    y_mod: Optional[float] = Field(
         None,
         description="Young's modulus (SI units) from the Voight-Reuss-Hill averages of "
         "the bulk and shear moduli.",
     )
-    trans_v: float = Field(
+    trans_v: Optional[float] = Field(
         None,
         description="Transverse sound velocity (SI units) obtained from the "
         "Voigt-Reuss-Hill average bulk modulus.",
     )
-    long_v: float = Field(
+    long_v: Optional[float] = Field(
         None,
         description="Longitudinal sound velocity (SI units) obtained from the "
         "Voigt-Reuss-Hill average bulk modulus.",
     )
-    snyder_ac: float = Field(
+    snyder_ac: Optional[float] = Field(
         None, description="Synder's acoustic sound velocity (SI units)."
     )
-    snyder_opt: float = Field(
+    snyder_opt: Optional[float] = Field(
         None, description="Synder's optical sound velocity (SI units)."
     )
-    snyder_total: float = Field(
+    snyder_total: Optional[float] = Field(
         None, description="Synder's total sound velocity (SI units)."
     )
     clark_thermalcond: Optional[float] = Field(
         None, description="Clarke's thermal conductivity (SI units)."
     )
-    cahill_thermalcond: float = Field(
+    cahill_thermalcond: Optional[float] = Field(
         None, description="Cahill's thermal conductivity (SI units)."
     )
-    debye_temperature: float = Field(
+    debye_temperature: Optional[float] = Field(
         None,
         description="Debye temperature from longitudinal and transverse sound "
         "velocities (SI units).",
@@ -78,53 +87,57 @@ class DerivedProperties(BaseModel):
 class FittingData(BaseModel):
     """Data used to fit elastic tensors."""
 
-    cauchy_stresses: list[Matrix3D] = Field(
+    cauchy_stresses: Optional[list[Matrix3D]] = Field(
         None, description="The Cauchy stresses used to fit the elastic tensor."
     )
-    strains: list[Matrix3D] = Field(
+    strains: Optional[list[Matrix3D]] = Field(
         None, description="The strains used to fit the elastic tensor."
     )
-    pk_stresses: list[Matrix3D] = Field(
+    pk_stresses: Optional[list[Matrix3D]] = Field(
         None, description="The Piola-Kirchoff stresses used to fit the elastic tensor."
     )
-    deformations: list[Matrix3D] = Field(
+    deformations: Optional[list[Matrix3D]] = Field(
         None, description="The deformations corresponding to each strain state."
     )
-    uuids: list[str] = Field(None, description="The uuids of the deformation jobs.")
-    job_dirs: list[Optional[str]] = Field(
+    uuids: Optional[list[str]] = Field(
+        None, description="The uuids of the deformation jobs."
+    )
+    job_dirs: Optional[list[Optional[str]]] = Field(
         None, description="The directories where the deformation jobs were run."
     )
 
 
 class ElasticTensorDocument(BaseModel):
     """Raw and standardized elastic tensors."""
 
-    raw: MatrixVoigt = Field(None, description="Raw elastic tensor.")
-    ieee_format: MatrixVoigt = Field(None, description="Elastic tensor in IEEE format.")
+    raw: Optional[MatrixVoigt] = Field(None, description="Raw elastic tensor.")
+    ieee_format: Optional[MatrixVoigt] = Field(
+        None, description="Elastic tensor in IEEE format."
+    )
 
 
 class ElasticDocument(StructureMetadata):
     """Document containing elastic tensor information and related properties."""
 
-    structure: Structure = Field(
+    structure: Optional[Structure] = Field(
         None, description="The structure for which the elastic data is calculated."
     )
-    elastic_tensor: ElasticTensorDocument = Field(
+    elastic_tensor: Optional[ElasticTensorDocument] = Field(
         None, description="Fitted elastic tensor."
     )
     eq_stress: Optional[Matrix3D] = Field(
         None, description="The equilibrium stress of the structure."
     )
-    derived_properties: DerivedProperties = Field(
+    derived_properties: Optional[DerivedProperties] = Field(
         None, description="Properties derived from the elastic tensor."
     )
-    fitting_data: FittingData = Field(
+    fitting_data: Optional[FittingData] = Field(
         None, description="Data used to fit the elastic tensor."
     )
-    fitting_method: str = Field(
+    fitting_method: Optional[str] = Field(
         None, description="Method used to fit the elastic tensor."
     )
-    order: int = Field(
+    order: Optional[int] = Field(
         None, description="Order of the expansion of the elastic tensor."
     )