emmet-builders 0.84.2rc0__tar.gz → 0.84.2rc3__tar.gz

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emmet-builders
-Version: 0.84.2rc0
+Version: 0.84.2rc3
 Summary: Builders for the Emmet Library
 Home-page: https://github.com/materialsproject/emmet
 Author: The Materials Project
@@ -12,6 +12,7 @@ Description-Content-Type: text/markdown
 Provides-Extra: test
 Provides-Extra: docs
 Provides-Extra: ml
+Provides-Extra: openmm
 
 # ![Emmet](docs/images/logo_w_text.svg)
 

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet/builders/abinit/phonon.py

@@ -1,41 +1,39 @@
-import tempfile
 import os
+import tempfile
 from math import ceil
-from emmet.builders.settings import EmmetBuildSettings
+from typing import Dict, Iterator, List, Optional, Tuple
+
 import numpy as np
-from typing import Optional, Dict, List, Iterator, Tuple
+from abipy.abio.inputs import AnaddbInput
+from abipy.core.abinit_units import eV_to_THz
+from abipy.dfpt.anaddbnc import AnaddbNcFile
+from abipy.dfpt.ddb import AnaddbError, DdbFile, DielectricTensorGenerator
+from abipy.dfpt.phonons import PhononBands
+from abipy.flowtk.tasks import AnaddbTask, TaskManager
+from maggma.builders import Builder
+from maggma.core import Store
 from maggma.utils import grouper
-
+from pymatgen.core.structure import Structure
+from pymatgen.io.abinit.abiobjects import KSampling
 from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
 from pymatgen.phonon.dos import CompletePhononDos
 from pymatgen.phonon.ir_spectra import IRDielectricTensor
-from pymatgen.core.structure import Structure
-from pymatgen.io.abinit.abiobjects import KSampling
-from pymatgen.symmetry.bandstructure import HighSymmKpath
 from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-from abipy.dfpt.anaddbnc import AnaddbNcFile
-from abipy.abio.inputs import AnaddbInput
-from abipy.flowtk.tasks import AnaddbTask, TaskManager
-from abipy.dfpt.ddb import AnaddbError, DielectricTensorGenerator, DdbFile
-from abipy.dfpt.phonons import PhononBands
-from abipy.core.abinit_units import eV_to_THz
-from maggma.builders import Builder
-from maggma.core import Store
+from pymatgen.symmetry.bandstructure import HighSymmKpath
 
+from emmet.builders.settings import EmmetBuildSettings
 from emmet.core.phonon import (
-    PhononWarnings,
-    ThermodynamicProperties,
     AbinitPhonon,
-    VibrationalEnergy,
-)
-from emmet.core.phonon import (
-    PhononDos,
+    Ddb,
     PhononBandStructure,
+    PhononDos,
+    PhononWarnings,
     PhononWebsiteBS,
-    Ddb,
     ThermalDisplacement,
+    ThermodynamicProperties,
+    VibrationalEnergy,
 )
-from emmet.core.polar import DielectricDoc, BornEffectiveCharges, IRDielectric
+from emmet.core.polar import BornEffectiveCharges, DielectricDoc, IRDielectric
 from emmet.core.utils import jsanitize
 
 SETTINGS = EmmetBuildSettings()
@@ -679,7 +677,7 @@ class PhononBuilder(Builder):
         )
 
         ph_bs_sl = PhononBandStructureSymmLine(
-            qpoints=qpts,
+            qpoints=qpts,  # type: ignore[arg-type]
             frequencies=ph_freqs,
             lattice=structure.reciprocal_lattice,
             has_nac=phbands.non_anal_ph is not None,

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet/builders/materials/alloys.py

@@ -1,19 +1,19 @@
-from itertools import combinations, chain
-from typing import Tuple, List, Dict, Union
+from itertools import chain, combinations
+from typing import Dict, List, Tuple, Union
 
-from tqdm import tqdm
 from maggma.builders import Builder
-from pymatgen.core.structure import Structure
 from matminer.datasets import load_dataset
-from emmet.core.thermo import ThermoType
-
 from pymatgen.analysis.alloys.core import (
-    AlloyPair,
-    InvalidAlloy,
     KNOWN_ANON_FORMULAS,
     AlloyMember,
+    AlloyPair,
     AlloySystem,
+    InvalidAlloy,
 )
+from pymatgen.core.structure import Structure
+from tqdm import tqdm
+
+from emmet.core.thermo import ThermoType
 
 # rough sort of ANON_FORMULAS by "complexity"
 ANON_FORMULAS = sorted(KNOWN_ANON_FORMULAS, key=lambda af: len(af))
@@ -291,7 +291,7 @@ class AlloyPairMemberBuilder(Builder):
                             is_ordered=structure.is_ordered,
                             x=pair.get_x(structure.composition),
                         )
-                        pair_members["members"].append(member.as_dict())
+                        pair_members["members"].append(member.as_dict())  # type: ignore[attr-defined]
                 except Exception as exc:
                     print(f"Exception for {db_id}: {exc}")
             if pair_members["members"]:

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet/builders/materials/corrected_entries.py

@@ -1,20 +1,20 @@
+import copy
 import warnings
 from collections import defaultdict
+from datetime import datetime
 from itertools import chain
-from typing import Dict, Iterable, Iterator, List, Optional
 from math import ceil
-import copy
-from datetime import datetime
+from typing import Dict, Iterable, Iterator, List, Optional, Union
 
 from maggma.core import Builder, Store
 from maggma.utils import grouper
-from pymatgen.entries.computed_entries import ComputedStructureEntry
 from pymatgen.entries.compatibility import Compatibility
+from pymatgen.entries.computed_entries import ComputedStructureEntry
 
-from emmet.core.utils import jsanitize
-from emmet.builders.utils import chemsys_permutations, HiddenPrints
-from emmet.core.thermo import ThermoType
+from emmet.builders.utils import HiddenPrints, chemsys_permutations
 from emmet.core.corrected_entries import CorrectedEntriesDoc
+from emmet.core.thermo import ThermoType
+from emmet.core.utils import jsanitize
 
 
 class CorrectedEntriesBuilder(Builder):
@@ -24,7 +24,7 @@ class CorrectedEntriesBuilder(Builder):
         corrected_entries: Store,
         oxidation_states: Optional[Store] = None,
         query: Optional[Dict] = None,
-        compatibility: Optional[List[Compatibility]] = None,
+        compatibility: Optional[Union[List[Compatibility], List[None]]] = [None],
         chunk_size: int = 1000,
         **kwargs,
     ):
@@ -45,10 +45,10 @@ class CorrectedEntriesBuilder(Builder):
         self.materials = materials
         self.query = query if query else {}
         self.corrected_entries = corrected_entries
-        self.compatibility = compatibility or [None]
+        self.compatibility = compatibility
         self.oxidation_states = oxidation_states
         self.chunk_size = chunk_size
-        self._entries_cache: Dict[str, List[ComputedStructureEntry]] = defaultdict(list)
+        self._entries_cache: Dict[str, List[Dict]] = defaultdict(list)
 
         if self.corrected_entries.key != "chemsys":
             warnings.warn(

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet/builders/materials/electrodes.py

@@ -1,22 +1,22 @@
 import operator
+from collections import defaultdict
 from datetime import datetime
 from functools import lru_cache
 from itertools import chain
 from math import ceil
-from typing import Any, Iterator, Dict, List, Optional
-from collections import defaultdict
+from typing import Any, Dict, Iterator, List, Optional
 
 from maggma.builders import Builder
 from maggma.stores import MongoStore
 from maggma.utils import grouper
-from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
+from pymatgen.analysis.phase_diagram import Composition, PhaseDiagram
 from pymatgen.entries.compatibility import MaterialsProject2020Compatibility
-from pymatgen.analysis.phase_diagram import PhaseDiagram, Composition
+from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
 
-from emmet.core.electrode import InsertionElectrodeDoc, ConversionElectrodeDoc
+from emmet.builders.settings import EmmetBuildSettings
+from emmet.core.electrode import ConversionElectrodeDoc, InsertionElectrodeDoc
 from emmet.core.structure_group import StructureGroupDoc, _get_id_lexi
 from emmet.core.utils import jsanitize
-from emmet.builders.settings import EmmetBuildSettings
 
 
 def s_hash(el):
@@ -564,9 +564,11 @@ class ConversionElectrodeBuilder(Builder):
                 # Get lowest material_id with matching composition
                 material_ids = [
                     (
-                        lambda x: x.data["material_id"]
-                        if x.composition.reduced_formula == v[1].reduced_formula
-                        else None
+                        lambda x: (
+                            x.data["material_id"]  # type: ignore[attr-defined]
+                            if x.composition.reduced_formula == v[1].reduced_formula
+                            else None
+                        )
                     )(e)
                     for e in pd.entries
                 ]
@@ -597,7 +599,7 @@ class ConversionElectrodeBuilder(Builder):
             relevant_entry_data = []
             for e in pd.entries:
                 if e.composition == Composition(c):
-                    relevant_entry_data.append((e.energy_per_atom, e.entry_id))
+                    relevant_entry_data.append((e.energy_per_atom, e.entry_id))  # type: ignore[attr-defined]
             relevant_entry_data.sort(key=lambda x: x[0])
             entry_id_mapping[c] = relevant_entry_data[0][1]
 

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet/builders/materials/provenance.py

@@ -1,7 +1,7 @@
 from collections import defaultdict
-from typing import Dict, Iterable, List, Optional, Tuple
-from math import ceil
 from datetime import datetime
+from math import ceil
+from typing import Dict, Iterable, List, Optional, Tuple
 
 from maggma.core import Builder, Store
 from maggma.utils import grouper
@@ -168,7 +168,7 @@ class ProvenanceBuilder(Builder):
             for snl in snls:
                 struc = Structure.from_dict(snl)
                 snl_sg = get_sg(struc)
-                struc.snl = SNLDict(**snl)
+                struc.snl = SNLDict(**snl)  # type: ignore[attr-defined]
                 snl_groups[snl_sg].append(struc)
 
             mat_sg = get_sg(Structure.from_dict(mat["structure"]))

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet/builders/utils.py

@@ -1,17 +1,19 @@
 from __future__ import annotations
-from typing import Set, Union, Any, Literal, Optional
-import sys
+
+import json
 import os
-from pathlib import Path
+import sys
 from gzip import GzipFile
-import orjson
-import json
 from io import BytesIO
-from monty.serialization import MontyDecoder
-from botocore.exceptions import ClientError
 from itertools import chain, combinations
-from pymatgen.core import Structure
+from pathlib import Path
+from typing import Any, Literal, Optional, Set, Union
+
+import orjson
+from botocore.exceptions import ClientError
+from monty.serialization import MontyDecoder
 from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph
+from pymatgen.core import Structure
 from pymatgen.io.vasp.inputs import PotcarSingle
 
 from emmet.builders.settings import EmmetBuildSettings
@@ -275,16 +277,16 @@ def get_potcar_stats(
                 # fallback method for validation - use header hash and symbol
                 # note that the potcar_spec assigns PotcarSingle.symbol to "titel"
                 # whereas the ***correct*** field is `header`
-                summary_stats["titel"] = potcar.header
-                summary_stats["hash"] = potcar.md5_header_hash
-                summary_stats = [summary_stats]
+                summary_stats["titel"] = potcar.header  # type: ignore[assignment]
+                summary_stats["hash"] = potcar.md5_header_hash  # type: ignore[assignment]
+                summary_stats = [summary_stats]  # type: ignore[assignment]
 
             elif method == "pymatgen":
-                summary_stats = []
+                summary_stats = []  # type: ignore[assignment]
                 for _, entries in PotcarSingle._potcar_summary_stats[
                     functional
                 ].items():
-                    summary_stats += [
+                    summary_stats += [  # type: ignore[operator]
                         {**entry, "titel": None, "hash": None}
                         for entry in entries
                         if entry["symbol"] == potcar_symbol

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet_builders.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: emmet-builders
-Version: 0.84.2rc0
+Version: 0.84.2rc3
 Summary: Builders for the Emmet Library
 Home-page: https://github.com/materialsproject/emmet
 Author: The Materials Project
@@ -12,6 +12,7 @@ Description-Content-Type: text/markdown
 Provides-Extra: test
 Provides-Extra: docs
 Provides-Extra: ml
+Provides-Extra: openmm
 
 # ![Emmet](docs/images/logo_w_text.svg)
 

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet_builders.egg-info/SOURCES.txt

@@ -59,8 +59,6 @@ requirements/ubuntu-latest_py3.10.txt
 requirements/ubuntu-latest_py3.10_extras.txt
 requirements/ubuntu-latest_py3.11.txt
 requirements/ubuntu-latest_py3.11_extras.txt
-requirements/ubuntu-latest_py3.9.txt
-requirements/ubuntu-latest_py3.9_extras.txt
 tests/__init__.py
 tests/conftest.py
 tests/test_absorption.py

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/emmet_builders.egg-info/requires.txt

@@ -19,6 +19,9 @@ jinja2
 [ml]
 emmet-core[ml]
 
+[openmm]
+transport-analysis>=0.1.0
+
 [test]
 pre-commit
 pytest

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/requirements/deployment.txt

@@ -4,7 +4,7 @@
 #
 #    pip-compile --output-file=emmet/emmet-builders/requirements/deployment.txt emmet/emmet-builders/setup.py python/requirements.txt
 #
-aiohttp==3.9.3
+aiohttp==3.9.4
     # via fsspec
 aioitertools==0.11.0
     # via maggma
@@ -36,7 +36,7 @@ botocore==1.34.34
     # via
     #   boto3
     #   s3transfer
-certifi==2024.2.2
+certifi==2024.7.4
     # via requests
 cffi==1.16.0
     # via
@@ -53,7 +53,7 @@ click==8.1.7
     #   uvicorn
 contourpy==1.2.0
     # via matplotlib
-cryptography==42.0.2
+cryptography==42.0.4
     # via paramiko
 cycler==0.12.1
     # via matplotlib
@@ -61,7 +61,7 @@ cython==3.0.8
     # via chgnet
 dgl==1.1.3
     # via matgl
-dnspython==2.5.0
+dnspython==2.6.1
     # via
     #   maggma
     #   pymongo
@@ -95,7 +95,7 @@ h11==0.14.0
     # via uvicorn
 h5py==3.10.0
     # via phonopy
-idna==3.6
+idna==3.7
     # via
     #   anyio
     #   requests
@@ -104,7 +104,7 @@ inflect==7.0.0
     # via robocrys
 itsdangerous==2.1.2
     # via flask
-jinja2==3.1.3
+jinja2==3.1.4
     # via
     #   flask
     #   torch
@@ -230,7 +230,7 @@ nvidia-nvjitlink-cu12==12.3.101
     #   nvidia-cusparse-cu12
 nvidia-nvtx-cu12==12.1.105
     # via torch
-orjson==3.9.13
+orjson==3.9.15
     # via maggma
 packaging==23.2
     # via
@@ -251,7 +251,7 @@ paramiko==3.4.0
     # via sshtunnel
 phonopy==2.21.0
     # via matcalc
-pillow==10.2.0
+pillow==10.3.0
     # via matplotlib
 plotly==5.18.0
     # via pymatgen
@@ -281,7 +281,7 @@ pydantic-settings==2.1.0
     #   maggma
 pydash==7.0.7
     # via maggma
-pymatgen==2024.1.27
+pymatgen==2024.2.20
     # via
     #   chgnet
     #   emmet-core
@@ -295,7 +295,7 @@ pymatgen-analysis-alloys==0.0.6
     # via emmet-core
 pymatgen-analysis-diffusion==2023.8.15
     # via emmet-core
-pymongo==4.6.1
+pymongo==4.6.3
     # via
     #   maggma
     #   matminer
@@ -327,7 +327,7 @@ referencing==0.33.0
     # via
     #   jsonschema
     #   jsonschema-specifications
-requests==2.31.0
+requests==2.32.2
     # via
     #   dgl
     #   matminer
@@ -348,7 +348,7 @@ ruamel-yaml-clib==0.2.8
     # via ruamel-yaml
 s3transfer==0.10.0
     # via boto3
-scikit-learn==1.4.0
+scikit-learn==1.5.0
     # via matminer
 scipy==1.12.0
     # via
@@ -400,7 +400,7 @@ torch==2.2.0
     #   torchmetrics
 torchmetrics==1.3.0.post0
     # via pytorch-lightning
-tqdm==4.66.1
+tqdm==4.66.3
     # via
     #   dgl
     #   maggma
@@ -424,13 +424,13 @@ typing-extensions==4.9.0
     #   uvicorn
 uncertainties==3.1.7
     # via pymatgen
-urllib3==2.0.7
+urllib3==2.2.2
     # via
     #   botocore
     #   requests
 uvicorn==0.27.0.post1
     # via maggma
-werkzeug==3.0.1
+werkzeug==3.0.3
     # via flask
 yarl==1.9.4
     # via aiohttp

{emmet-builders-0.84.2rc0 → emmet-builders-0.84.2rc3}/requirements/ubuntu-latest_py3.10.txt

@@ -15,15 +15,15 @@ attrs==23.2.0
     #   jsonlines
     #   jsonschema
     #   referencing
-bcrypt==4.1.3
+bcrypt==4.2.0
     # via paramiko
-boto3==1.34.137
+boto3==1.34.151
     # via maggma
-botocore==1.34.137
+botocore==1.34.151
     # via
     #   boto3
     #   s3transfer
-certifi==2024.6.2
+certifi==2024.7.4
     # via requests
 cffi==1.16.0
     # via
@@ -33,7 +33,7 @@ charset-normalizer==3.3.2
     # via requests
 contourpy==1.2.1
     # via matplotlib
-cryptography==42.0.8
+cryptography==43.0.0
     # via paramiko
 cycler==0.12.1
     # via matplotlib
@@ -45,11 +45,11 @@ emmet-core[all]==0.84.1
     # via
     #   emmet-builders (setup.py)
     #   mp-api
-exceptiongroup==1.2.1
+exceptiongroup==1.2.2
     # via pytest
 fasteners==0.19
     # via mdanalysis
-fonttools==4.53.0
+fonttools==4.53.1
     # via matplotlib
 griddataformats==1.0.2
     # via mdanalysis
@@ -57,7 +57,7 @@ h5py==3.11.0
     # via phonopy
 idna==3.7
     # via requests
-inflect==7.3.0
+inflect==7.3.1
     # via robocrys
 iniconfig==2.0.0
     # via pytest
@@ -74,7 +74,7 @@ joblib==1.4.2
     #   scikit-learn
 jsonlines==4.0.0
     # via maggma
-jsonschema==4.22.0
+jsonschema==4.23.0
     # via maggma
 jsonschema-specifications==2023.12.1
     # via jsonschema
@@ -82,7 +82,7 @@ kiwisolver==1.4.5
     # via matplotlib
 latexcodec==3.0.0
     # via pybtex
-maggma==0.69.0
+maggma==0.69.1
     # via
     #   emmet-builders (setup.py)
     #   mp-api
@@ -92,7 +92,7 @@ matminer==0.9.2
     # via
     #   emmet-builders (setup.py)
     #   robocrys
-matplotlib==3.9.0
+matplotlib==3.9.1
     # via
     #   ase
     #   mdanalysis
@@ -110,7 +110,7 @@ mmtf-python==1.1.3
     # via mdanalysis
 mongomock==4.1.2
     # via maggma
-monty==2024.5.24
+monty==2024.7.30
     # via
     #   emmet-core
     #   maggma
@@ -124,7 +124,7 @@ mp-api==0.41.2
     # via robocrys
 mpmath==1.3.0
     # via sympy
-mrcfile==1.5.0
+mrcfile==1.5.3
     # via griddataformats
 msgpack==1.0.8
     # via
@@ -160,7 +160,7 @@ numpy==1.26.4
     #   solvation-analysis
     #   spglib
     #   statsmodels
-orjson==3.10.5
+orjson==3.10.6
     # via maggma
 packaging==24.1
     # via
@@ -183,13 +183,13 @@ paramiko==3.4.0
     # via sshtunnel
 patsy==0.5.6
     # via statsmodels
-phonopy==2.25.0
+phonopy==2.26.6
     # via matcalc
 pillow==10.4.0
     # via
     #   matplotlib
     #   rdkit
-plotly==5.22.0
+plotly==5.23.0
     # via
     #   pymatgen
     #   solvation-analysis
@@ -204,18 +204,18 @@ pybtex==0.24.0
     #   robocrys
 pycparser==2.22
     # via cffi
-pydantic==2.8.0
+pydantic==2.8.2
     # via
     #   emmet-core
     #   maggma
     #   pydantic-settings
-pydantic-core==2.20.0
+pydantic-core==2.20.1
     # via pydantic
-pydantic-settings==2.3.4
+pydantic-settings==2.4.0
     # via
     #   emmet-core
     #   maggma
-pydash==8.0.1
+pydash==8.0.3
     # via maggma
 pymatgen==2024.4.13
     # via
@@ -238,7 +238,7 @@ pynacl==1.5.0
     # via paramiko
 pyparsing==3.1.2
     # via matplotlib
-pytest==8.2.2
+pytest==8.3.2
     # via solvation-analysis
 python-dateutil==2.9.0.post0
     # via
@@ -256,7 +256,7 @@ pyyaml==6.0.1
     #   pybtex
 pyzmq==26.0.3
     # via maggma
-rdkit==2024.3.1
+rdkit==2024.3.3
     # via solvation-analysis
 referencing==0.35.1
     # via
@@ -269,7 +269,7 @@ requests==2.32.3
     #   pymatgen
 robocrys==0.2.9
     # via emmet-core
-rpds-py==0.18.1
+rpds-py==0.19.1
     # via
     #   jsonschema
     #   referencing
@@ -282,9 +282,9 @@ ruamel-yaml-clib==0.2.8
     # via ruamel-yaml
 s3transfer==0.10.2
     # via boto3
-scikit-learn==1.5.0
+scikit-learn==1.5.1
     # via matminer
-scipy==1.12.0
+scipy==1.14.0
     # via
     #   ase
     #   griddataformats
@@ -298,7 +298,7 @@ seekpath==2.1.0
     # via emmet-core
 sentinels==1.0.0
     # via mongomock
-shapely==2.0.4
+shapely==2.0.5
     # via pymatgen-analysis-alloys
 six==1.16.0
     # via
@@ -307,11 +307,11 @@ six==1.16.0
     #   python-dateutil
 smart-open==7.0.4
     # via mp-api
-solvation-analysis==0.4.0
+solvation-analysis==0.4.1
     # via
     #   emmet-builders (setup.py)
     #   emmet-core
-spglib==2.4.0
+spglib==2.5.0
     # via
     #   phonopy
     #   pymatgen
@@ -321,13 +321,13 @@ sshtunnel==0.4.0
     # via maggma
 statsmodels==0.14.2
     # via solvation-analysis
-sympy==1.12.1
+sympy==1.13.1
     # via
     #   matminer
     #   pymatgen
 tabulate==0.9.0
     # via pymatgen
-tenacity==8.4.2
+tenacity==9.0.0
     # via plotly
 threadpoolctl==3.5.0
     # via
@@ -353,7 +353,7 @@ typing-extensions==4.12.2
     #   typeguard
 tzdata==2024.1
     # via pandas
-uncertainties==3.2.1
+uncertainties==3.2.2
     # via pymatgen
 urllib3==2.2.2
     # via