Enable isort in pre-commit

.pre-commit-config.yaml

@@ -50,3 +50,9 @@ repos:
       - id: mypy
         name: "MyPy"
         additional_dependencies: ["types-all", "pydantic~=1.10"]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        name: "isort"

optimade/adapters/__init__.py

@@ -3,5 +3,4 @@
 from .references import *  # noqa: F403
 from .structures import *  # noqa: F403
 
-
 __all__ = exceptions.__all__ + references.__all__ + structures.__all__  # noqa: F405

optimade/adapters/base.py

@@ -19,13 +19,12 @@
 and [`StructureResource`][optimade.models.structures.StructureResource]s, respectively.
 """
 import re
-from typing import Union, Dict, Callable, Any, Tuple, List, Type
+from typing import Any, Callable, Dict, List, Tuple, Type, Union
 
 from pydantic import BaseModel  # pylint: disable=no-name-in-module
 
-from optimade.models import EntryResource
-
 from optimade.adapters.logger import LOGGER
+from optimade.models import EntryResource
 
 
 class EntryAdapter:

optimade/adapters/references/__init__.py

@@ -1,4 +1,3 @@
 from .adapter import Reference
 
-
 __all__ = ("Reference",)

optimade/adapters/references/adapter.py

@@ -1,5 +1,5 @@
-from optimade.models import ReferenceResource
 from optimade.adapters.base import EntryAdapter
+from optimade.models import ReferenceResource
 
 
 class Reference(EntryAdapter):

optimade/adapters/structures/__init__.py

@@ -1,4 +1,3 @@
 from .adapter import Structure
 
-
 __all__ = ("Structure",)

optimade/adapters/structures/adapter.py

@@ -1,13 +1,14 @@
 from typing import Callable, Dict, Type
-from optimade.models import StructureResource
+
 from optimade.adapters.base import EntryAdapter
+from optimade.models import StructureResource
 
 from .aiida import get_aiida_structure_data
 from .ase import get_ase_atoms
 from .cif import get_cif
-from .proteindatabank import get_pdb, get_pdbx_mmcif
-from .pymatgen import get_pymatgen, from_pymatgen
 from .jarvis import get_jarvis_atoms
+from .proteindatabank import get_pdb, get_pdbx_mmcif
+from .pymatgen import from_pymatgen, get_pymatgen
 
 
 class Structure(EntryAdapter):

optimade/adapters/structures/aiida.py

@@ -7,17 +7,16 @@
 
 This conversion function relies on the [`aiida-core`](https://github.com/aiidateam/aiida-core) package.
 """
-from warnings import warn
 from typing import List, Optional
+from warnings import warn
 
-from optimade.models import StructureResource as OptimadeStructure
-from optimade.models import Species as OptimadeStructureSpecies
-
-from optimade.adapters.warnings import AdapterPackageNotFound, ConversionWarning
 from optimade.adapters.structures.utils import pad_cell, species_from_species_at_sites
+from optimade.adapters.warnings import AdapterPackageNotFound, ConversionWarning
+from optimade.models import Species as OptimadeStructureSpecies
+from optimade.models import StructureResource as OptimadeStructure
 
 try:
-    from aiida.orm.nodes.data.structure import StructureData, Kind, Site
+    from aiida.orm.nodes.data.structure import Kind, Site, StructureData
 except (ImportError, ModuleNotFoundError):
     StructureData = type("StructureData", (), {})
     AIIDA_NOT_FOUND = (

optimade/adapters/structures/ase.py

@@ -9,17 +9,17 @@
 """
 from typing import Dict
 
-from optimade.models import Species as OptimadeStructureSpecies
-from optimade.models import StructureResource as OptimadeStructure
-from optimade.models import StructureFeatures
-
 from optimade.adapters.exceptions import ConversionError
 from optimade.adapters.structures.utils import species_from_species_at_sites
+from optimade.models import Species as OptimadeStructureSpecies
+from optimade.models import StructureFeatures
+from optimade.models import StructureResource as OptimadeStructure
 
 try:
-    from ase import Atoms, Atom
+    from ase import Atom, Atoms
 except (ImportError, ModuleNotFoundError):
     from warnings import warn
+
     from optimade.adapters.warnings import AdapterPackageNotFound
 
     Atoms = type("Atoms", (), {})

optimade/adapters/structures/cif.py

@@ -18,19 +18,19 @@
 """
 from typing import Dict
 
-from optimade.models import Species as OptimadeStructureSpecies
-from optimade.models import StructureResource as OptimadeStructure
-
 from optimade.adapters.structures.utils import (
     cell_to_cellpar,
     fractional_coordinates,
     valid_lattice_vector,
 )
+from optimade.models import Species as OptimadeStructureSpecies
+from optimade.models import StructureResource as OptimadeStructure
 
 try:
     import numpy as np
 except ImportError:
     from warnings import warn
+
     from optimade.adapters.warnings import AdapterPackageNotFound
 
     np = None

optimade/adapters/structures/jarvis.py

@@ -10,14 +10,15 @@
 !!! success "Contributing author"
     This conversion function was contributed by Kamal Choudhary ([@knc6](https://github.com/knc6)).
 """
-from optimade.models import StructureResource as OptimadeStructure
-from optimade.models import StructureFeatures
 from optimade.adapters.exceptions import ConversionError
+from optimade.models import StructureFeatures
+from optimade.models import StructureResource as OptimadeStructure
 
 try:
     from jarvis.core.atoms import Atoms
 except (ImportError, ModuleNotFoundError):
     from warnings import warn
+
     from optimade.adapters.warnings import AdapterPackageNotFound
 
     Atoms = type("Atoms", (), {})

optimade/adapters/structures/proteindatabank.py

@@ -27,22 +27,21 @@
     import numpy as np
 except ImportError:
     from warnings import warn
+
     from optimade.adapters.warnings import AdapterPackageNotFound
 
     np = None
     NUMPY_NOT_FOUND = "NumPy not found, cannot convert structure to your desired format"
 
-from optimade.models import Species as OptimadeStructureSpecies
-from optimade.models import StructureResource as OptimadeStructure
-
 from optimade.adapters.structures.utils import (
     cell_to_cellpar,
     cellpar_to_cell,
     fractional_coordinates,
     scaled_cell,
     valid_lattice_vector,
 )
-
+from optimade.models import Species as OptimadeStructureSpecies
+from optimade.models import StructureResource as OptimadeStructure
 
 __all__ = ("get_pdb", "get_pdbx_mmcif")
 

optimade/adapters/structures/pymatgen.py

@@ -7,22 +7,22 @@
 
 For more information on the pymatgen code see [their documentation](https://pymatgen.org).
 """
-from typing import Union, Dict, List, Optional
+from typing import Dict, List, Optional, Union
 
-from optimade.models import Species as OptimadeStructureSpecies
-from optimade.models import StructureResource as OptimadeStructure
 from optimade.adapters.structures.utils import (
     species_from_species_at_sites,
     valid_lattice_vector,
 )
+from optimade.models import Species as OptimadeStructureSpecies
+from optimade.models import StructureResource as OptimadeStructure
 from optimade.models import StructureResourceAttributes
 
-
 try:
-    from pymatgen.core import Structure, Molecule, Composition, Lattice
+    from pymatgen.core import Composition, Lattice, Molecule, Structure
 
 except (ImportError, ModuleNotFoundError):
     from warnings import warn
+
     from optimade.adapters.warnings import AdapterPackageNotFound
 
     Structure = type("Structure", (), {})
@@ -193,6 +193,7 @@ def from_pymatgen(pmg_structure: Structure) -> StructureResourceAttributes:
 def _pymatgen_anonymized_formula_to_optimade(composition: Composition) -> str:
     """Construct an OPTIMADE `chemical_formula_anonymous` from a pymatgen `Composition`."""
     import re
+
     from optimade.models.utils import anonymous_element_generator
 
     return "".join(

optimade/adapters/structures/utils.py

@@ -3,14 +3,16 @@
 
 Most of these functions rely on the [NumPy](https://numpy.org/) library.
 """
-from typing import List, Optional, Tuple, Iterable
-from optimade.models.structures import Vector3D
+from typing import Iterable, List, Optional, Tuple
+
 from optimade.models.structures import Species as OptimadeStructureSpecies
+from optimade.models.structures import Vector3D
 
 try:
     import numpy as np
 except ImportError:
     from warnings import warn
+
     from optimade.adapters.warnings import AdapterPackageNotFound
 
     np = None

optimade/client/cli.py

@@ -1,6 +1,6 @@
-import sys
 import json
 import pathlib
+import sys
 
 import click
 import rich

optimade/client/client.py

@@ -5,21 +5,21 @@
 
 """
 
-from typing import Dict, List, Union, Iterable, Optional, Any, Tuple
-from urllib.parse import urlparse
-from collections import defaultdict
 import asyncio
-import time
-import json
 import functools
+import json
+import time
+from collections import defaultdict
+from typing import Any, Dict, Iterable, List, Optional, Tuple, Union
+from urllib.parse import urlparse
 
 from pydantic import AnyUrl
 
 # External deps that are only used in the client code
 try:
     import httpx
-    from rich.progress import TaskID
     from rich.panel import Panel
+    from rich.progress import TaskID
 except ImportError as exc:
     raise ImportError(
         "Could not find dependencies required for the `OptimadeClient`. "
@@ -28,17 +28,17 @@
     ) from exc
 
 
-from optimade.utils import get_all_databases
-from optimade.filterparser import LarkParser
 from optimade import __api_version__, __version__
 from optimade.client.utils import (
     OptimadeClientProgress,
-    TooManyRequestsException,
     QueryResults,
     RecoverableHTTPError,
+    TooManyRequestsException,
     silent_raise,
 )
+from optimade.filterparser import LarkParser
 from optimade.server.exceptions import BadRequest
+from optimade.utils import get_all_databases
 
 ENDPOINTS = ("structures", "references", "calculations", "info", "extensions")
 

optimade/client/utils.py

@@ -1,17 +1,17 @@
-from dataclasses import dataclass, field, asdict
-from contextlib import contextmanager
-from typing import List, Dict, Set, Union
 import sys
+from contextlib import contextmanager
+from dataclasses import asdict, dataclass, field
+from typing import Dict, List, Set, Union
 
+from rich.console import Console
 from rich.progress import (
+    BarColumn,
     Progress,
     SpinnerColumn,
-    TimeElapsedColumn,
     TaskProgressColumn,
-    BarColumn,
     TextColumn,
+    TimeElapsedColumn,
 )
-from rich.console import Console
 
 __all__ = (
     "RecoverableHTTPError",

optimade/filterparser/lark_parser.py

@@ -4,9 +4,9 @@
 
 """
 
+from collections import defaultdict
 from pathlib import Path
 from typing import Dict, Tuple
-from collections import defaultdict
 
 from lark import Lark, Tree
 

optimade/filtertransformers/base_transformer.py

@@ -6,16 +6,15 @@
 """
 
 import abc
-from typing import Dict, Any, Type, Optional
 import warnings
+from typing import Any, Dict, Optional, Type
 
-from lark import Transformer, v_args, Tree
+from lark import Transformer, Tree, v_args
 
-from optimade.server.mappers import BaseResourceMapper
 from optimade.server.exceptions import BadRequest
+from optimade.server.mappers import BaseResourceMapper
 from optimade.server.warnings import UnknownProviderProperty
 
-
 __all__ = (
     "BaseTransformer",
     "Quantity",

optimade/filtertransformers/elasticsearch.py

@@ -1,6 +1,7 @@
-from typing import Dict, Union, Type, Optional
+from typing import Dict, Optional, Type, Union
+
+from elasticsearch_dsl import Field, Integer, Keyword, Q, Text
 from lark import v_args
-from elasticsearch_dsl import Q, Text, Keyword, Integer, Field
 
 from optimade.filtertransformers import BaseTransformer, Quantity
 from optimade.server.mappers import BaseResourceMapper

optimade/filtertransformers/mongo.py

@@ -5,10 +5,12 @@
 
 
 import copy
-import warnings
 import itertools
-from typing import Dict, List, Any, Union
-from lark import v_args, Token
+import warnings
+from typing import Any, Dict, List, Union
+
+from lark import Token, v_args
+
 from optimade.filtertransformers.base_transformer import BaseTransformer, Quantity
 from optimade.server.exceptions import BadRequest
 from optimade.server.warnings import TimestampNotRFCCompliant

optimade/models/__init__.py

@@ -1,14 +1,14 @@
 # pylint: disable=undefined-variable
-from .jsonapi import *  # noqa: F403
-from .utils import *  # noqa: F403
 from .baseinfo import *  # noqa: F403
 from .entries import *  # noqa: F403
 from .index_metadb import *  # noqa: F403
+from .jsonapi import *  # noqa: F403
 from .links import *  # noqa: F403
 from .optimade_json import *  # noqa: F403
 from .references import *  # noqa: F403
 from .responses import *  # noqa: F403
 from .structures import *  # noqa: F403
+from .utils import *  # noqa: F403
 
 __all__ = (
     jsonapi.__all__  # noqa: F405