emmet-core 0.87.0.dev14__tar.gz → 0.87.0.dev16__tar.gz

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: emmet-core
-Version: 0.87.0.dev14
+Version: 0.87.0.dev16
 Summary: Core Emmet Library
 Author-email: The Materials Project <feedback@materialsproject.org>
 License-Expression: BSD-3-Clause-LBNL

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet/core/connectors/icsd/client.py

@@ -89,12 +89,12 @@ class IcsdClient(BaseModel):
         if response.status_code == 200:
             self._auth_token = response.headers["ICSD-Auth-Token"]
             if self._auth_token is None:
-                logger.warning(
+                raise ValueError(
                     f"{self.__module__}.{self.__class__.__name__} "
                     f"failed to fetch auth token: {response.content}"
                 )
         else:
-            logger.warning(
+            raise ValueError(
                 f"{self.__module__}.{self.__class__.__name__} "
                 "failed to fetch auth token with status code "
                 f"{response.status_code}: {response.content}"
@@ -248,6 +248,10 @@ class IcsdClient(BaseModel):
                     for row in csv_data[1:]
                 ]
             else:
+                if "Authentication not successful" in response.content:
+                    raise ValueError(
+                        "Failed to authenticate ICSD client. Please check your credentials"
+                    )
                 logger.warning(
                     f"{self.__module__}.{self.__class__.__name__} "
                     "csv search failed with status code "

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet/core/connectors/icsd/schemas.py

@@ -148,7 +148,4 @@ class IcsdPropertyDoc(BaseModel):
                 config["cif"]
             )
 
-        if not config.get("cif_parsing_errors"):
-            config.pop("cif_parsing_errors")
-
         return config

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet/core/provenance.py

@@ -30,7 +30,7 @@ class Database(ValueEnum):
     """
 
     ICSD = "icsd"
-    Pauling_Files = "pf"
+    Pauling_Files = "pauling"
     COD = "cod"
 
 
@@ -51,8 +51,8 @@ def _remove_dupe_authors(authors: list[dict[str, Any] | Author]):
 
 
 def _migrate_legacy_history_data(
-    config: list[dict[str, Any]] | list[History],
-) -> list[History]:
+    config: list[dict[str, Any]] | list[History] | None,
+) -> list[History | None]:
     """Migrate legacy provenance and SNL `history` data as a classmethod.
 
     Parameters
@@ -63,6 +63,8 @@ def _migrate_legacy_history_data(
     -----------
     list of History objects.
     """
+    if not config:
+        return []
 
     top_level_history = [
         h.model_dump() if isinstance(h, History) else h for h in config
@@ -250,7 +252,7 @@ class History(BaseModel):
 
 
 HistoryType = Annotated[
-    list[History] | None,
+    list[History | None],
     BeforeValidator(_migrate_legacy_history_data),
 ]
 

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet/core/thermo.py

@@ -5,7 +5,7 @@ from __future__ import annotations
 from collections import defaultdict
 from typing import Annotated
 
-from pydantic import BaseModel, BeforeValidator, Field, PlainSerializer
+from pydantic import BaseModel, BeforeValidator, Field
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
@@ -42,7 +42,6 @@ class DecompositionProduct(BaseModel):
     )
 
 
-@type_override({"thermo_type": ThermoType, "thermo_id": str})
 class ThermoDoc(PropertyDoc):
     """
     A thermo entry document
@@ -60,7 +59,6 @@ class ThermoDoc(PropertyDoc):
         Field(
             description="Unique document ID which is composed of the Material ID and thermo data type.",
         ),
-        PlainSerializer(str),
         BeforeValidator(ThermoID._deserialize),
     ]
 
@@ -187,7 +185,7 @@ class ThermoDoc(PropertyDoc):
             builder_meta = EmmetMeta(license=blessed_entry.data.get("license"))
 
             d = {
-                "thermo_id": "{}_{}".format(material_id, str(thermo_type)),
+                "thermo_id": ThermoID(identifier=material_id, suffix=thermo_type),
                 "material_id": material_id,
                 "thermo_type": thermo_type,
                 "uncorrected_energy_per_atom": blessed_entry.uncorrected_energy

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet/core/types/pymatgen_types/phase_diagram_adapter.py

@@ -1,13 +1,15 @@
 from collections.abc import Callable
 from enum import Enum, auto
+from itertools import chain
 from typing import Annotated, Any, TypeVar, ValuesView
 
 import orjson
-from pydantic import BeforeValidator, WrapSerializer
+from pydantic import BeforeValidator, TypeAdapter, WrapSerializer
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from typing_extensions import TypedDict
 
 from emmet.core.types.pymatgen_types.computed_entries_adapter import (
+    TypedCEDataDict,
     TypedComputedStructureEntryDict,
 )
 
@@ -29,14 +31,12 @@ TypedSimplexDict = TypedDict(
 TypedComputedDataDict = TypedDict(
     "TypedComputedDataDict",
     {
-        "dim": int,
-        # "el_refs": list[[str, ComputedStructureEntry]],
+        # "el_refs": list[[str, int]],
         "el_refs_elements": list[str],
-        "el_refs_entries": list[TypedComputedStructureEntryDict],
+        "el_refs_entries": list[int],
         "facets": list[list[int]],
         "qhull_data": list[list[float]],
-        "qhull_entries": list[TypedComputedStructureEntryDict],
-        "simplexes": list[TypedSimplexDict],
+        "qhull_entries": list[int],
         "all_entries": list[TypedComputedStructureEntryDict],
     },
 )
@@ -46,8 +46,7 @@ TypedPhaseDiagramDict = TypedDict(
     {
         "@module": str,
         "@class": str,
-        "all_entries": list[TypedComputedStructureEntryDict],
-        "elements": list[TypedMSONableElementDict],
+        "elements": list[str],
         "computed_data": TypedComputedDataDict,
     },
 )
@@ -63,9 +62,7 @@ def entries_list_serde(entries_list: ValuesView | list[dict], serde_fn: Callable
 
 
 def phase_diagram_serde(d: dict, mode: Mode, serde_fn: Callable):
-    entries_list_serde(d["all_entries"], serde_fn)
-    for key in ["all_entries", "qhull_entries"]:
-        entries_list_serde(d["computed_data"][key], serde_fn)
+    entries_list_serde(d["computed_data"]["all_entries"], serde_fn)
 
     match mode:
         case Mode.SHRED:
@@ -73,11 +70,9 @@ def phase_diagram_serde(d: dict, mode: Mode, serde_fn: Callable):
 
             elements = []
             el_refs_entries = []
-            for element, entry in el_ref_pairs:
+            for element, entry_idx in el_ref_pairs:
                 elements.append(str(element))
-                el_refs_entries.append(entry.as_dict())
-
-            entries_list_serde(el_refs_entries, serde_fn)
+                el_refs_entries.append(entry_idx)
 
             d["computed_data"]["el_refs_elements"] = elements
             d["computed_data"]["el_refs_entries"] = el_refs_entries
@@ -86,29 +81,19 @@ def phase_diagram_serde(d: dict, mode: Mode, serde_fn: Callable):
             elements = d["computed_data"].pop("el_refs_elements")
             el_refs_entries = d["computed_data"].pop("el_refs_entries")
 
-            entries_list_serde(el_refs_entries, serde_fn)
-
             d["computed_data"]["el_refs"] = [
                 (i, j) for i, j in zip(elements, el_refs_entries)
             ]
 
 
 def phase_diagram_serializer(phase_diagram, nxt, info) -> dict[str, Any]:
-    default_serialized_object = nxt(phase_diagram.as_dict(), info)
+    for entry in chain(
+        phase_diagram.computed_data["qhull_entries"],
+        phase_diagram.computed_data["all_entries"],
+    ):
+        entry.data = TypeAdapter(TypedCEDataDict).dump_python(entry.data)
 
-    for key in ["all_entries", "qhull_entries", "simplexes"]:
-        default_serialized_object["computed_data"][key] = [
-            entry.as_dict() for entry in default_serialized_object["computed_data"][key]
-        ]
-
-    # ndarray -> list[list[int]]
-    for simplex in default_serialized_object["computed_data"]["simplexes"]:
-        simplex["coords"] = simplex["coords"].tolist()
-
-    # ndarray -> list[list[float]]
-    default_serialized_object["computed_data"]["qhull_data"] = (
-        default_serialized_object["computed_data"]["qhull_data"].tolist()
-    )
+    default_serialized_object = nxt(phase_diagram.as_dict(), info)
 
     format = info.context.get("format") if info.context else None
     if format == "arrow":

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet/core/types/pymatgen_types/structure_graph_adapter.py

@@ -1,6 +1,6 @@
-from typing import Annotated, TypeVar, NotRequired
+from typing import Annotated, NotRequired, TypeVar
 
-from pydantic import BeforeValidator, WrapSerializer, PlainSerializer
+from pydantic import BeforeValidator, WrapSerializer
 from pymatgen.analysis.graphs import MoleculeGraph, StructureGraph
 from typing_extensions import TypedDict
 
@@ -17,15 +17,7 @@ class GraphDescriptorDict(TypedDict):
     edge_weight_units: NotRequired[str]
 
 
-GraphDescriptors = Annotated[
-    GraphDescriptorDict,
-    BeforeValidator(
-        lambda x: GraphDescriptorDict(
-            **({row[0]: row[1] for row in x} if isinstance(x, list) else x)
-        )
-    ),
-    PlainSerializer(lambda x: list(x.items()) if isinstance(x, dict) else x),
-]
+GraphDescriptors = tuple[str, str]
 
 
 class TypedNodeDict(TypedDict):
@@ -42,7 +34,7 @@ class TypedAdjacencyDict(TypedDict):
 class TypedGraphDict(TypedDict):
     directed: bool
     multigraph: bool
-    graph: GraphDescriptors
+    graph: list[GraphDescriptors]
     nodes: list[TypedNodeDict]
     adjacency: list[list[TypedAdjacencyDict]]
 

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet/core/vasp/calculation.py

@@ -2,24 +2,18 @@
 
 from __future__ import annotations
 
-from copy import deepcopy
-from functools import cached_property
 import logging
 import os
+from copy import deepcopy
 from datetime import datetime
+from functools import cached_property
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Annotated, Type
+from typing import TYPE_CHECKING, Annotated, Any, Type
 
 import numpy as np
 import orjson
 from monty.io import zopen
-from pydantic import (
-    BaseModel,
-    ConfigDict,
-    Field,
-    model_validator,
-    BeforeValidator,
-)
+from pydantic import BaseModel, BeforeValidator, ConfigDict, Field, model_validator
 from pymatgen.command_line.bader_caller import bader_analysis_from_path
 from pymatgen.command_line.chargemol_caller import ChargemolAnalysis
 from pymatgen.core.structure import Structure
@@ -32,8 +26,8 @@ from typing_extensions import NotRequired, TypedDict
 
 from emmet.core.band_theory import ElectronicBS, ElectronicDos
 from emmet.core.math import ListMatrix3D, Matrix3D, Vector3D
+from emmet.core.settings import EmmetSettings
 from emmet.core.trajectory import RelaxTrajectory, Trajectory
-from emmet.core.vasp.models import ElectronicStep, ChgcarLike
 from emmet.core.types.enums import StoreTrajectoryOption, TaskState, VaspObject
 from emmet.core.types.pymatgen_types.bader import BaderAnalysis
 from emmet.core.types.pymatgen_types.kpoints_adapter import KpointsType
@@ -50,15 +44,14 @@ from emmet.core.vasp.calc_types import (
     run_type,
     task_type,
 )
-
-from emmet.core.settings import EmmetSettings
+from emmet.core.vasp.models import ChgcarLike, ElectronicStep
 
 SETTINGS = EmmetSettings()
 
 if TYPE_CHECKING:
-    from typing_extensions import Self
     from pymatgen.electronic_structure.bandstructure import BandStructure
     from pymatgen.electronic_structure.dos import CompleteDos
+    from typing_extensions import Self
 
 
 logger = logging.getLogger(__name__)
@@ -485,6 +478,13 @@ class FrequencyDependentDielectric(BaseModel):
         "constant are given",
     )
 
+    @model_validator(mode="before")
+    def migrate_legacy_fields(cls, data: Any) -> Any:
+        if "imag" in data:
+            data["imaginary"] = data["imag"]
+
+        return data
+
     @classmethod
     def from_vasprun(cls, vasprun: Vasprun) -> Self:
         """

{emmet_core-0.87.0.dev14 → emmet_core-0.87.0.dev16}/emmet_core.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: emmet-core
-Version: 0.87.0.dev14
+Version: 0.87.0.dev16
 Summary: Core Emmet Library
 Author-email: The Materials Project <feedback@materialsproject.org>
 License-Expression: BSD-3-Clause-LBNL