emmet-builders 0.84.7rc4__py3-none-any.whl → 0.84.8__py3-none-any.whl

emmet/builders/molecules/vibration.py

@@ -2,18 +2,17 @@ from collections import defaultdict
 from datetime import datetime
 from itertools import chain
 from math import ceil
-from typing import Optional, Iterable, Iterator, List, Dict
+from typing import Iterable, Iterator
 
 from maggma.builders import Builder
 from maggma.core import Store
 from maggma.utils import grouper
 
-from emmet.core.qchem.task import TaskDocument
-from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
+from emmet.builders.settings import EmmetBuildSettings
 from emmet.core.molecules.vibration import VibrationDoc
+from emmet.core.qchem.molecule import MoleculeDoc, evaluate_lot
+from emmet.core.qchem.task import TaskDocument
 from emmet.core.utils import jsanitize
-from emmet.builders.settings import EmmetBuildSettings
-
 
 __author__ = "Evan Spotte-Smith"
 
@@ -44,8 +43,8 @@ class VibrationBuilder(Builder):
         tasks: Store,
         molecules: Store,
         vibes: Store,
-        query: Optional[Dict] = None,
-        settings: Optional[EmmetBuildSettings] = None,
+        query: dict | None = None,
+        settings: EmmetBuildSettings | None = None,
         **kwargs,
     ):
         self.tasks = tasks
@@ -91,7 +90,7 @@ class VibrationBuilder(Builder):
         self.vibes.ensure_index("last_updated")
         self.vibes.ensure_index("formula_alphabetical")
 
-    def prechunk(self, number_splits: int) -> Iterable[Dict]:  # pragma: no cover
+    def prechunk(self, number_splits: int) -> Iterable[dict]:  # pragma: no cover
         """Prechunk the builder for distributed computation"""
 
         temp_query = dict(self.query)
@@ -117,7 +116,7 @@ class VibrationBuilder(Builder):
             query["species_hash"] = {"$in": list(hash_chunk)}
             yield {"query": query}
 
-    def get_items(self) -> Iterator[List[Dict]]:
+    def get_items(self) -> Iterator[list[dict]]:
         """
         Gets all items to process into vibration documents.
         This does no datetime checking; relying on on whether
@@ -164,12 +163,12 @@ class VibrationBuilder(Builder):
 
             yield molecules
 
-    def process_item(self, items: List[Dict]) -> List[Dict]:
+    def process_item(self, items: list[dict]) -> list[dict]:
         """
         Process the tasks into VibrationDocs
 
         Args:
-            items List[Dict] : a list of MoleculeDocs in dict form
+            items list[dict] : a list of MoleculeDocs in dict form
 
         Returns:
             [dict] : a list of new vibration docs
@@ -247,7 +246,7 @@ class VibrationBuilder(Builder):
 
         return jsanitize([doc.model_dump() for doc in vibe_docs], allow_bson=True)
 
-    def update_targets(self, items: List[List[Dict]]):
+    def update_targets(self, items: list[list[dict]]):
         """
         Inserts the new vibration docs into the vibes collection
 

emmet/builders/qchem/molecules.py

@@ -1,25 +1,23 @@
 from datetime import datetime
 from itertools import chain, groupby
 from math import ceil
-from typing import Any, Dict, Iterable, Iterator, List, Optional, Set, Union
+from typing import Any, Iterable, Iterator, Set
 
 import networkx as nx
-
 from maggma.builders import Builder
 from maggma.stores import Store
 from maggma.utils import grouper
 
 from emmet.builders.settings import EmmetBuildSettings
-from emmet.core.utils import get_molecule_id, group_molecules, jsanitize, make_mol_graph
+from emmet.core.qchem.calc_types import CalcType, LevelOfTheory, TaskType
 from emmet.core.qchem.molecule import (
+    MoleculeDoc,
     best_lot,
     evaluate_lot,
     evaluate_task_entry,
-    MoleculeDoc,
 )
 from emmet.core.qchem.task import TaskDocument
-from emmet.core.qchem.calc_types import LevelOfTheory, CalcType, TaskType
-
+from emmet.core.utils import get_molecule_id, group_molecules, jsanitize, make_mol_graph
 
 __author__ = "Evan Spotte-Smith <ewcspottesmith@lbl.gov>"
 
@@ -29,9 +27,9 @@ SETTINGS = EmmetBuildSettings()
 
 def evaluate_molecule(
     mol_doc: MoleculeDoc,
-    funct_scores: Dict[str, int] = SETTINGS.QCHEM_FUNCTIONAL_QUALITY_SCORES,
-    basis_scores: Dict[str, int] = SETTINGS.QCHEM_BASIS_QUALITY_SCORES,
-    solvent_scores: Dict[str, int] = SETTINGS.QCHEM_SOLVENT_MODEL_QUALITY_SCORES,
+    funct_scores: dict[str, int] = SETTINGS.QCHEM_FUNCTIONAL_QUALITY_SCORES,
+    basis_scores: dict[str, int] = SETTINGS.QCHEM_BASIS_QUALITY_SCORES,
+    solvent_scores: dict[str, int] = SETTINGS.QCHEM_SOLVENT_MODEL_QUALITY_SCORES,
 ):
     """
     Helper function to order optimization calcs by
@@ -106,8 +104,8 @@ class MoleculesAssociationBuilder(Builder):
         self,
         tasks: Store,
         assoc: Store,
-        query: Optional[Dict] = None,
-        settings: Optional[EmmetBuildSettings] = None,
+        query: dict | None = None,
+        settings: EmmetBuildSettings | None = None,
         **kwargs,
     ):
         """
@@ -146,7 +144,7 @@ class MoleculesAssociationBuilder(Builder):
         self.assoc.ensure_index("task_ids")
         self.assoc.ensure_index("formula_alphabetical")
 
-    def prechunk(self, number_splits: int) -> Iterable[Dict]:  # pragma: no cover
+    def prechunk(self, number_splits: int) -> Iterable[dict]:  # pragma: no cover
         """Prechunk the molecule builder for distributed computation"""
 
         temp_query = dict(self.query)
@@ -170,7 +168,7 @@ class MoleculesAssociationBuilder(Builder):
             query["species_hash"] = {"$in": list(hash_chunk)}
             yield {"query": query}
 
-    def get_items(self) -> Iterator[List[TaskDocument]]:
+    def get_items(self) -> Iterator[list[TaskDocument]]:
         """
         Gets all items to process into molecules (and other) documents.
         This does no datetime checking; relying on on whether
@@ -252,7 +250,7 @@ class MoleculesAssociationBuilder(Builder):
 
             yield to_yield
 
-    def process_item(self, tasks: List[TaskDocument]) -> List[Dict]:
+    def process_item(self, tasks: list[TaskDocument]) -> list[dict]:
         """
         Process the tasks into a MoleculeDoc
 
@@ -288,7 +286,7 @@ class MoleculesAssociationBuilder(Builder):
 
         return jsanitize([mol.model_dump() for mol in molecules], allow_bson=True)
 
-    def update_targets(self, items: List[List[Dict]]):
+    def update_targets(self, items: list[list[dict]]):
         """
         Inserts the new molecules into the molecules collection
 
@@ -314,8 +312,8 @@ class MoleculesAssociationBuilder(Builder):
             self.logger.info("No items to update")
 
     def filter_and_group_tasks(
-        self, tasks: List[TaskDocument]
-    ) -> Iterator[List[TaskDocument]]:
+        self, tasks: list[TaskDocument]
+    ) -> Iterator[list[TaskDocument]]:
         """
         Groups tasks by identical structure
         """
@@ -363,8 +361,8 @@ class MoleculesBuilder(Builder):
         self,
         assoc: Store,
         molecules: Store,
-        query: Optional[Dict] = None,
-        settings: Optional[EmmetBuildSettings] = None,
+        query: dict | None = None,
+        settings: EmmetBuildSettings | None = None,
         **kwargs,
     ):
         """
@@ -401,7 +399,7 @@ class MoleculesBuilder(Builder):
         self.molecules.ensure_index("task_ids")
         self.molecules.ensure_index("formula_alphabetical")
 
-    def prechunk(self, number_splits: int) -> Iterable[Dict]:  # pragma: no cover
+    def prechunk(self, number_splits: int) -> Iterable[dict]:  # pragma: no cover
         """Prechunk the molecule builder for distributed computation"""
 
         temp_query = dict(self.query)
@@ -450,7 +448,7 @@ class MoleculesBuilder(Builder):
             query["species_hash"] = {"$in": list(hash_chunk)}
             yield {"query": query}
 
-    def get_items(self) -> Iterator[List[Dict]]:
+    def get_items(self) -> Iterator[list[dict]]:
         """
         Gets all items to process into molecules (and other) documents.
         This does no datetime checking; relying on on whether
@@ -520,12 +518,12 @@ class MoleculesBuilder(Builder):
 
             yield assoc
 
-    def process_item(self, items: List[Dict]) -> List[Dict]:
+    def process_item(self, items: list[dict]) -> list[dict]:
         """
         Process the tasks into a MoleculeDoc
 
         Args:
-            tasks List[Dict] : a list of task docs
+            tasks list[dict] : a list of task docs
 
         Returns:
             [dict] : a list of new molecule docs
@@ -556,18 +554,18 @@ class MoleculesBuilder(Builder):
             levels_of_theory = dict()
             solvents = dict()
             lot_solvents = dict()
-            unique_calc_types: Set[Union[str, CalcType]] = set()
-            unique_task_types: Set[Union[str, TaskType]] = set()
-            unique_levels_of_theory: Set[Union[str, LevelOfTheory]] = set()
+            unique_calc_types: Set[str | CalcType] = set()
+            unique_task_types: Set[str | TaskType] = set()
+            unique_levels_of_theory: Set[str | LevelOfTheory] = set()
             unique_solvents: Set[str] = set()
             unique_lot_solvents: Set[str] = set()
             origins = list()
             entries = list()
-            best_entries: Dict[str, Any] = dict()
+            best_entries: dict[str, Any] = dict()
             constituent_molecules = list()
             similar_molecules = list()
 
-            base_doc: Optional[MoleculeDoc] = None
+            base_doc: MoleculeDoc | None = None
 
             # Grab best doc for each solvent
             # A doc is given a solvent based on how the molecule was optimized
@@ -658,7 +656,7 @@ class MoleculesBuilder(Builder):
             [mol.model_dump() for mol in complete_mol_docs], allow_bson=True
         )
 
-    def update_targets(self, items: List[List[Dict]]):
+    def update_targets(self, items: list[list[dict]]):
         """
         Inserts the new molecules into the molecules collection
 
@@ -691,7 +689,7 @@ class MoleculesBuilder(Builder):
         else:
             self.logger.info("No items to update")
 
-    def group_mol_docs(self, assoc: List[MoleculeDoc]) -> Iterator[List[MoleculeDoc]]:
+    def group_mol_docs(self, assoc: list[MoleculeDoc]) -> Iterator[list[MoleculeDoc]]:
         """
         Groups molecules by:
             - highest level of theory
@@ -711,7 +709,7 @@ class MoleculesBuilder(Builder):
 
         # Group by charge and spin
         for c_s, group in groupby(sorted(assoc, key=charge_spin), key=charge_spin):
-            subgroups: List[Dict[str, Any]] = list()
+            subgroups: list[dict[str, Any]] = list()
             for mol_doc in group:
                 mol_graph = make_mol_graph(mol_doc.molecule)
                 mol_hash = mol_doc.species_hash

emmet/builders/settings.py

@@ -1,14 +1,13 @@
 """
 Settings for defaults in the build pipelines for the Materials Project
 """
-from typing import List
 
 from pydantic.fields import Field
 
 from emmet.core.provenance import Author, History
+from emmet.core.qchem.calc_types import TaskType as QChemTaskType
 from emmet.core.settings import EmmetSettings
 from emmet.core.vasp.calc_types import TaskType as VaspTaskType
-from emmet.core.qchem.calc_types import TaskType as QChemTaskType
 
 
 class EmmetBuildSettings(EmmetSettings):
@@ -18,28 +17,28 @@ class EmmetBuildSettings(EmmetSettings):
     EMMET_CONFIG_FILE to point to the json with emmet settings
     """
 
-    BUILD_TAGS: List[str] = Field(
+    BUILD_TAGS: list[str] = Field(
         [], description="Tags for calculations to build materials"
     )
-    EXCLUDED_TAGS: List[str] = Field(
+    EXCLUDED_TAGS: list[str] = Field(
         [],
         description="Tags to exclude from materials",
     )
 
-    DEPRECATED_TAGS: List[str] = Field(
+    DEPRECATED_TAGS: list[str] = Field(
         [], description="Tags for calculations to deprecate"
     )
 
-    NON_COMMERCIAL_TAGS: List[str] = Field(
+    NON_COMMERCIAL_TAGS: list[str] = Field(
         [], description="Tages for which to add BY-NC as license data in builder_meta"
     )
 
-    VASP_ALLOWED_VASP_TYPES: List[VaspTaskType] = Field(
+    VASP_ALLOWED_VASP_TYPES: list[VaspTaskType] = Field(
         [t.value for t in VaspTaskType],
         description="Allowed task_types to build materials from",
     )
 
-    QCHEM_ALLOWED_TASK_TYPES: List[QChemTaskType] = Field(
+    QCHEM_ALLOWED_TASK_TYPES: list[QChemTaskType] = Field(
         [
             "Single Point",
             "Force",

emmet/builders/utils.py

@@ -7,7 +7,7 @@ from gzip import GzipFile
 from io import BytesIO
 from itertools import chain, combinations
 from pathlib import Path
-from typing import Any, Literal, Optional, Set, Union
+from typing import Any, Literal, Set
 
 import orjson
 from botocore.exceptions import ClientError
@@ -65,7 +65,7 @@ def get_hop_cutoff(
     algorithm: str = "min_distance",
     min_hop_distance: float = 1,
     max_hop_distance: float = 7,
-) -> Union[float, None]:
+) -> float | None:
     """
     A function to get an appropriate hop distance cutoff for a given migration
     graph structure which can be used for MigrationGraph.with_distance()
@@ -165,7 +165,7 @@ def query_open_data(
     key: str,
     monty_decode: bool = True,
     s3_resource: Any = None,
-) -> Union[dict, None]:
+) -> dict | None:
     """Query a Materials Project AWS S3 Open Data bucket directly with boto3
 
     Args:
@@ -173,7 +173,7 @@ def query_open_data(
         prefix (str): Full set of file prefixes
         key (str): Key for file
         monty_decode (bool): Whether to monty decode or keep as dictionary. Defaults to True.
-        s3_resource (Optional[Any]): S3 resource. One will be instantiated if none are provided
+        s3_resource (Any | None): S3 resource. One will be instantiated if none are provided
 
     Returns:
         dict: MontyDecoded data or None
@@ -222,7 +222,7 @@ class HiddenPrints:
 
 def get_potcar_stats(
     method: Literal["potcar", "pymatgen", "stored"] = "potcar",
-    path_to_stored_stats: Optional[Union[str, os.PathLike, Path]] = None,
+    path_to_stored_stats: str | os.PathLike | Path | None = None,
 ) -> dict[str, Any]:
     """
     Get the POTCAR stats used in MP calculations to validate POTCARs.

emmet/builders/vasp/materials.py

@@ -1,17 +1,17 @@
 from datetime import datetime
 from itertools import chain
 from math import ceil
-from typing import Dict, Iterable, Iterator, List, Optional, Union
+from typing import Iterable, Iterator
 
 from maggma.builders import Builder
 from maggma.stores import Store
 from maggma.utils import grouper
 
 from emmet.builders.settings import EmmetBuildSettings
+from emmet.core.tasks import TaskDoc
 from emmet.core.utils import group_structures, jsanitize, undeform_structure
 from emmet.core.vasp.calc_types import TaskType
 from emmet.core.vasp.material import MaterialsDoc
-from emmet.core.tasks import TaskDoc
 
 __author__ = "Shyam Dwaraknath <shyamd@lbl.gov>"
 
@@ -38,9 +38,9 @@ class MaterialsBuilder(Builder):
         self,
         tasks: Store,
         materials: Store,
-        task_validation: Optional[Store] = None,
-        query: Optional[Dict] = None,
-        settings: Optional[EmmetBuildSettings] = None,
+        task_validation: Store | None = None,
+        query: dict | None = None,
+        settings: EmmetBuildSettings | None = None,
         **kwargs,
     ):
         """
@@ -84,7 +84,7 @@ class MaterialsBuilder(Builder):
             self.task_validation.ensure_index("task_id")
             self.task_validation.ensure_index("valid")
 
-    def prechunk(self, number_splits: int) -> Iterable[Dict]:  # pragma: no cover
+    def prechunk(self, number_splits: int) -> Iterable[dict]:  # pragma: no cover
         """Prechunk the materials builder for distributed computation"""
         temp_query = dict(self.query)
         temp_query["state"] = "successful"
@@ -114,7 +114,7 @@ class MaterialsBuilder(Builder):
         for formula_chunk in grouper(to_process_forms, N):
             yield {"query": {"formula_pretty": {"$in": list(formula_chunk)}}}
 
-    def get_items(self) -> Iterator[List[Dict]]:
+    def get_items(self) -> Iterator[list[dict]]:
         """
         Gets all items to process into materials documents.
         This does no datetime checking; relying on whether
@@ -213,7 +213,7 @@ class MaterialsBuilder(Builder):
 
             yield tasks
 
-    def process_item(self, items: List[Dict]) -> List[Dict]:
+    def process_item(self, items: list[dict]) -> list[dict]:
         """
         Process the tasks into a list of materials
 
@@ -273,7 +273,7 @@ class MaterialsBuilder(Builder):
 
         return jsanitize([mat.model_dump() for mat in materials], allow_bson=True)
 
-    def update_targets(self, items: List[List[Dict]]):
+    def update_targets(self, items: list[list[dict]]):
         """
         Inserts the new task_types into the task_types collection
 
@@ -297,8 +297,8 @@ class MaterialsBuilder(Builder):
             self.logger.info("No items to update")
 
     def filter_and_group_tasks(
-        self, tasks: List[TaskDoc], task_transformations: List[Union[Dict, None]]
-    ) -> Iterator[List[TaskDoc]]:
+        self, tasks: list[TaskDoc], task_transformations: list[dict | None]
+    ) -> Iterator[list[TaskDoc]]:
         """
         Groups tasks by structure matching
         """

emmet/builders/vasp/task_validator.py

@@ -1,5 +1,3 @@
-from typing import Dict, Optional
-
 from maggma.builders import MapBuilder
 from maggma.core import Store
 
@@ -15,9 +13,9 @@ class TaskValidator(MapBuilder):
         self,
         tasks: Store,
         task_validation: Store,
-        potcar_stats: Optional[Dict[CalcType, Dict[str, str]]] = None,
-        settings: Optional[EmmetBuildSettings] = None,
-        query: Optional[Dict] = None,
+        potcar_stats: dict[CalcType, dict[str, str]] | None = None,
+        settings: EmmetBuildSettings | None = None,
+        query: dict | None = None,
         **kwargs,
     ):
         """

{emmet_builders-0.84.7rc4.dist-info → emmet_builders-0.84.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: emmet-builders
-Version: 0.84.7rc4
+Version: 0.84.8
 Summary: Builders for the Emmet Library
 Home-page: https://github.com/materialsproject/emmet
 Author: The Materials Project

emmet_builders-0.84.8.dist-info/RECORD

@@ -0,0 +1,54 @@
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+emmet/builders/settings.py,sha256=BcVjKgBUyJ0ntAbqaq_t7tAL3ocNS4Vyms_lesQ0cb4,2880
+emmet/builders/utils.py,sha256=6oI0-Fdhg0kgecnbS4PDgShs4hZQNh_-owq26I9YibE,10883
+emmet/builders/abinit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+emmet/builders/abinit/phonon.py,sha256=1prLeHyR10pg03K9v5LU9X44ZGhzEp-kRoqRw7bV15E,32013
+emmet/builders/abinit/sound_velocity.py,sha256=w79Htwl6RAXjmvjcq9yCNmvHSuTEprUXUbrUDL4LeE4,6999
+emmet/builders/feff/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+emmet/builders/feff/xas.py,sha256=wQnO0IcxAclYY4fVoyc4sDqs1Cx7vFzMq-_oIHnk3EU,2068
+emmet/builders/materials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+emmet/builders/materials/absorption_spectrum.py,sha256=i_MlMjFMQVIv03KjteddMk_DEteGl3vr-a_EBdZHSj0,6641
+emmet/builders/materials/alloys.py,sha256=ZAGvwWiPImOvmoHHn3tmSEx07r9gEwU3K249h_YeqAw,14194
+emmet/builders/materials/basic_descriptors.py,sha256=IVCkN0vjkoNis2d_OUezVhPzGpaVcP6IkX123UwB6oQ,5845
+emmet/builders/materials/bonds.py,sha256=TFfkfKG1-7zcim9gPJqRz1UcyVN_px0889VWhSICc5g,1847
+emmet/builders/materials/chemenv.py,sha256=ZTR6_VyAif3yvcSy8xagBkmKczZsDD3LC77RMKi4E0U,1191
+emmet/builders/materials/corrected_entries.py,sha256=n-TpinKzlmeyFpHd_Ienp02Soav440tomOphsCvk_70,12373
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+emmet/builders/materials/thermo.py,sha256=1MQkfHpul1aeKccUA8lmcsHO-6YpHhegR2krzWRJ98k,10891
+emmet/builders/matscholar/missing_compositions.py,sha256=rQZELoRXXS-Ew7UPeCwBr1qynI56px1m12VWUYfKKm0,8638
+emmet/builders/mobility/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+emmet/builders/molecules/atomic.py,sha256=9pyClWlyorHohNPTxhm8NJyxw3SL5gpjWYVq_Bj9j3U,20798
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+emmet/builders/molecules/electric.py,sha256=vDnxDj-AzNgxZWx54AyMrscWqa2HnLaQHjXeO_eOpNA,10036
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