Small pydantic related bug fixes and linting (#836)

* No underscore prefix on field

* Mypy fixes

* Fix model validator for task doc

* Add int as possible icsd_id

* Linting

* More mypy fixes

* Fix type union

emmet-builders/emmet/builders/abinit/sound_velocity.py

@@ -63,7 +63,9 @@ def prechunk(self, number_splits: int):  # pragma: no cover
         # All relevant materials that have been updated since phonon props were last calculated
         q = dict(self.query)
 
-        mats = self.phonon.newer_in(self.phonon_materials, exhaustive=True, criteria=q)
+        mats = self.sound_vel.newer_in(
+            self.phonon_materials, exhaustive=True, criteria=q
+        )
 
         N = ceil(len(mats) / number_splits)
 

emmet-core/emmet/core/elasticity.py

@@ -675,7 +675,7 @@ def sanity_check(
         warnings.append(CM.STRAIN_RANK.format(rank))
 
     # elastic tensor eigenvalues
-    eig_vals, _ = np.linalg.eig(elastic_doc.raw)
+    eig_vals, _ = np.linalg.eig(elastic_doc.raw)  # type: ignore
     if np.any(eig_vals < 0.0):
         warnings.append(WM.NEGATIVE_EIGVAL)
 

emmet-core/emmet/core/electronic_structure.py

@@ -444,22 +444,22 @@ def from_bsdos(  # type: ignore[override]
         new_origin_task_id = None
 
         if bs_gap is not None and bs_gap <= dos_gap + 0.2:
-            summary_task = bs_entry.setyawan_curtarolo.task_id
+            summary_task = bs_entry.setyawan_curtarolo.task_id  # type: ignore
             summary_band_gap = bs_gap
             summary_cbm = (
                 bs_entry.setyawan_curtarolo.cbm.get("energy", None)  # type: ignore
-                if bs_entry.setyawan_curtarolo.cbm is not None
+                if bs_entry.setyawan_curtarolo.cbm is not None  # type: ignore
                 else None
             )
             summary_vbm = (
                 bs_entry.setyawan_curtarolo.vbm.get("energy", None)  # type: ignore
-                if bs_entry.setyawan_curtarolo.cbm is not None
+                if bs_entry.setyawan_curtarolo.cbm is not None  # type: ignore
                 else None
             )  # type: ignore
-            summary_efermi = bs_entry.setyawan_curtarolo.efermi
-            is_gap_direct = bs_entry.setyawan_curtarolo.is_gap_direct
-            is_metal = bs_entry.setyawan_curtarolo.is_metal
-            summary_magnetic_ordering = bs_entry.setyawan_curtarolo.magnetic_ordering
+            summary_efermi = bs_entry.setyawan_curtarolo.efermi  # type: ignore
+            is_gap_direct = bs_entry.setyawan_curtarolo.is_gap_direct  # type: ignore
+            is_metal = bs_entry.setyawan_curtarolo.is_metal  # type: ignore
+            summary_magnetic_ordering = bs_entry.setyawan_curtarolo.magnetic_ordering  # type: ignore
 
             for origin in origins:
                 if origin["name"] == "setyawan_curtarolo":

emmet-core/emmet/core/qchem/molecule.py

@@ -532,7 +532,7 @@ def best_lot(
     """
 
     sorted_lots = sorted(
-        mol_doc.best_entries.keys(),
+        mol_doc.best_entries.keys(),  # type: ignore
         key=lambda x: evaluate_lot(x, funct_scores, basis_scores, solvent_scores),
     )
 

emmet-core/emmet/core/structure_group.py

@@ -193,7 +193,7 @@ def from_ungrouped_structure_entries(
                 struct_group = cls.from_grouped_entries(
                     f_group_l, ignored_specie=ignored_specie
                 )
-                cnt_ += len(struct_group.material_ids)
+                cnt_ += len(struct_group.material_ids)  # type: ignore
                 continue
 
             logger.debug(
@@ -203,7 +203,7 @@ def from_ungrouped_structure_entries(
                 struct_group = cls.from_grouped_entries(
                     g, ignored_specie=ignored_specie
                 )
-                cnt_ += len(struct_group.material_ids)
+                cnt_ += len(struct_group.material_ids)  # type: ignore
                 results.append(struct_group)
         if cnt_ != len(entries):
             raise RuntimeError(

emmet-core/emmet/core/substrates.py

@@ -37,9 +37,10 @@ class SubstratesDoc(BaseModel):
         description="The Materials Project ID of the film material. This comes in the form: mp-******.",
     )
 
-    _norients: Optional[int] = Field(
+    norients: Optional[int] = Field(
         None,
         description="Number of possible surface orientations for the substrate.",
+        alias="_norients",
     )
 
     orient: Optional[str] = Field(

emmet-core/emmet/core/tasks.py

@@ -368,7 +368,7 @@ class TaskDoc(StructureMetadata, extra="allow"):
     author: Optional[str] = Field(
         None, description="Author extracted from transformations"
     )
-    icsd_id: Optional[str] = Field(
+    icsd_id: Optional[Union[str, int]] = Field(
         None, description="Inorganic Crystal Structure Database id of the structure"
     )
     transformations: Optional[Dict[str, Any]] = Field(
@@ -404,14 +404,11 @@ class TaskDoc(StructureMetadata, extra="allow"):
     def last_updated_dict_ok(cls, v) -> datetime:
         return v if isinstance(v, datetime) else monty_decoder.process_decoded(v)
 
-    @model_validator(mode="before")
-    @classmethod
-    def set_entry(cls, values) -> datetime:
-        if not values.get("entry", None) and (
-            values.get("calcs_reversed", None) and values.get("task_id")
-        ):
-            values["entry"] = cls.get_entry(values["calcs_reversed"], values["task_id"])
-        return values
+    @model_validator(mode="after")
+    def set_entry(self) -> datetime:
+        if not self.entry and (self.calcs_reversed and self.task_id):
+            self.entry = self.get_entry(self.calcs_reversed, self.task_id)
+        return self
 
     @classmethod
     def from_directory(

emmet-core/emmet/core/vasp/validation.py

@@ -1,8 +1,8 @@
 from datetime import datetime
-from typing import Dict, List, Union, Optional
+from typing import Dict, List, Union, Optional, Any
 
 import numpy as np
-from pydantic import ConfigDict, Field, PyObject
+from pydantic import ConfigDict, Field
 from pymatgen.core.structure import Structure
 from pymatgen.io.vasp.sets import VaspInputSet
 
@@ -63,7 +63,7 @@ def from_task_doc(
         task_doc: TaskDocument,
         kpts_tolerance: float = SETTINGS.VASP_KPTS_TOLERANCE,
         kspacing_tolerance: float = SETTINGS.VASP_KSPACING_TOLERANCE,
-        input_sets: Dict[str, PyObject] = SETTINGS.VASP_DEFAULT_INPUT_SETS,
+        input_sets: Dict[str, Any] = SETTINGS.VASP_DEFAULT_INPUT_SETS,
         LDAU_fields: List[str] = SETTINGS.VASP_CHECKED_LDAU_FIELDS,
         max_allowed_scf_gradient: float = SETTINGS.VASP_MAX_SCF_GRADIENT,
         potcar_hashes: Optional[Dict[CalcType, Dict[str, str]]] = None,