ruff automatic fixes

nwb_linkml/conftest.py

@@ -1,9 +1,7 @@
 import os
-import pytest
 from doctest import ELLIPSIS, NORMALIZE_WHITESPACE
 
-from tests.fixtures import tmp_output_dir
+import pytest
-
 from sybil import Sybil
 from sybil.parsers.rest import DocTestParser, PythonCodeBlockParser
 

nwb_linkml/src/nwb_linkml/adapters/__init__.py

@@ -1,6 +1,6 @@
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
-from nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.classes import ClassAdapter
-from nwb_linkml.adapters.group import GroupAdapter
 from nwb_linkml.adapters.dataset import DatasetAdapter
+from nwb_linkml.adapters.group import GroupAdapter
+from nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.schema import SchemaAdapter

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -2,32 +2,29 @@
 Base class for adapters
 """
 
-import pdb
 from abc import abstractmethod
-import warnings
 from dataclasses import dataclass, field
 from typing import (
-    List,
-    Dict,
-    Type,
-    Generator,
     Any,
-    Tuple,
+    Generator,
+    List,
     Optional,
+    Tuple,
+    Type,
     TypeVar,
     TypeVarTuple,
     Unpack,
-    Literal,
 )
-from pydantic import BaseModel, Field, validator
+
 from linkml_runtime.linkml_model import (
-    Element,
-    SchemaDefinition,
     ClassDefinition,
+    SchemaDefinition,
     SlotDefinition,
     TypeDefinition,
 )
-from nwb_schema_language import Dataset, Attribute, Schema, Group
+from pydantic import BaseModel
+
+from nwb_schema_language import Attribute, Dataset, Group, Schema
 
 # SchemaDefClass = dataclass(SchemaDefinition).__pydantic_model__
 

nwb_linkml/src/nwb_linkml/adapters/classes.py

@@ -4,11 +4,13 @@ Adapters to linkML classes
 
 from abc import abstractmethod
 from typing import List, Optional
-from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, DTypeType
+
-from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
+
+from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.maps import QUANTITY_MAP
 from nwb_linkml.maps.naming import camel_to_snake
+from nwb_schema_language import CompoundDtype, Dataset, DTypeType, Group, ReferenceDtype
 
 
 class ClassAdapter(Adapter):

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -2,20 +2,17 @@
 Adapter for NWB datasets to linkml Classes
 """
 
-import pdb
-from typing import Optional, List
-import warnings
 from abc import abstractmethod
+from typing import Optional
 
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
-from pydantic import PrivateAttr
 
-from nwb_schema_language import Dataset, ReferenceDtype, CompoundDtype, DTypeType
-from nwb_linkml.adapters.classes import ClassAdapter
-from nwb_linkml.maps.naming import camel_to_snake
-from nwb_linkml.maps.dtype import flat_to_linkml
 from nwb_linkml.adapters.adapter import BuildResult
+from nwb_linkml.adapters.classes import ClassAdapter
 from nwb_linkml.maps import QUANTITY_MAP, Map
+from nwb_linkml.maps.dtype import flat_to_linkml
+from nwb_linkml.maps.naming import camel_to_snake
+from nwb_schema_language import Dataset
 
 
 class DatasetMap(Map):
@@ -415,10 +412,7 @@ def make_arraylike(cls: Dataset, name: Optional[str] = None) -> ClassDefinition:
     slots = []
     for dims, shape in dims_shape:
         # if there is just a single list of possible dimensions, it's required
-        if not any([isinstance(inner_dim, list) for inner_dim in cls.dims]):
+        if not any([isinstance(inner_dim, list) for inner_dim in cls.dims]) or all([dims in inner_dim for inner_dim in cls.dims]):
-            required = True
-        # if a dim is present in all possible combinations of dims, make it required
-        elif all([dims in inner_dim for inner_dim in cls.dims]):
             required = True
         else:
             required = False
@@ -447,7 +441,7 @@ def make_arraylike(cls: Dataset, name: Optional[str] = None) -> ClassDefinition:
     elif cls.name:
         name = cls.name
     else:
-        raise ValueError(f"Dataset has no name or type definition, what do call it?")
+        raise ValueError("Dataset has no name or type definition, what do call it?")
 
     name = "__".join([name, "Arraylike"])
 

nwb_linkml/src/nwb_linkml/adapters/group.py

@@ -2,16 +2,14 @@
 Adapter for NWB groups to linkml Classes
 """
 
-import pdb
+from linkml_runtime.linkml_model import SlotDefinition
-from typing import List
-from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
 
-from nwb_schema_language import Dataset, Group, ReferenceDtype, CompoundDtype, DTypeType
-from nwb_linkml.adapters.classes import ClassAdapter
-from nwb_linkml.maps.naming import camel_to_snake
-from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.adapters.adapter import BuildResult
+from nwb_linkml.adapters.classes import ClassAdapter
+from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.maps import QUANTITY_MAP
+from nwb_linkml.maps.naming import camel_to_snake
+from nwb_schema_language import Group
 
 
 class GroupAdapter(ClassAdapter):

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -5,26 +5,21 @@ Wraps the :class:`nwb_schema_language.Namespaces` and other objects with conveni
 for extracting information and generating translated schema
 """
 
-import pdb
 
-from typing import List, Optional, Dict
-from pathlib import Path
-from pydantic import BaseModel, Field, validator, PrivateAttr
-from pprint import pformat
-from linkml_runtime.linkml_model import SchemaDefinition, Annotation
-from linkml_runtime.dumpers import yaml_dumper
-from time import sleep
 from copy import copy
+from pathlib import Path
+from pprint import pformat
+from typing import Dict, List, Optional
 
-
+from linkml_runtime.dumpers import yaml_dumper
-from nwb_schema_language import Namespaces
+from linkml_runtime.linkml_model import Annotation, SchemaDefinition
+from pydantic import Field, PrivateAttr
 
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.schema import SchemaAdapter
 from nwb_linkml.lang_elements import NwbLangSchema
-
-
 from nwb_linkml.ui import AdapterProgress
+from nwb_schema_language import Namespaces
 
 
 class NamespacesAdapter(Adapter):

nwb_linkml/src/nwb_linkml/adapters/schema.py

@@ -3,18 +3,16 @@ I don't know if NWB necessarily has a term for a single nwb schema file, so we'r
 to call them "schema" objects
 """
 
-from typing import Optional, List, TYPE_CHECKING, Type
 from pathlib import Path
+from typing import List, NamedTuple, Optional, Type
+
+from linkml_runtime.linkml_model import SchemaDefinition
 from pydantic import Field, PrivateAttr
 
 from nwb_linkml.adapters.adapter import Adapter, BuildResult
 from nwb_linkml.adapters.dataset import DatasetAdapter
 from nwb_linkml.adapters.group import GroupAdapter
-
+from nwb_schema_language import Dataset, Group
-from nwb_schema_language import Group, Dataset
-from typing import NamedTuple
-
-from linkml_runtime.linkml_model import SchemaDefinition
 
 
 class SplitSchema(NamedTuple):

nwb_linkml/src/nwb_linkml/config.py

@@ -3,15 +3,15 @@ Manage the operation of nwb_linkml from environmental variables
 """
 
 import tempfile
-from typing import Any
 from pathlib import Path
+
 from pydantic import (
-    Field,
     DirectoryPath,
+    Field,
+    FieldValidationInfo,
     computed_field,
     field_validator,
     model_validator,
-    FieldValidationInfo,
 )
 from pydantic_settings import BaseSettings, SettingsConfigDict
 

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -25,43 +25,38 @@ The `serialize` method:
 
 """
 
-import pdb
-import re
-from dataclasses import dataclass, field
-from pathlib import Path
-from typing import List, Dict, Set, Tuple, Optional, TypedDict, Type
-import os, sys
-from types import ModuleType
-from copy import deepcopy, copy
-import warnings
 import inspect
+import sys
+import warnings
+from copy import copy
+from dataclasses import dataclass
+from pathlib import Path
+from types import ModuleType
+from typing import Dict, List, Optional, Tuple, Type
 
-from nwb_linkml.maps import flat_to_nptyping
+from jinja2 import Template
 from linkml.generators import PydanticGenerator
+from linkml.generators.common.type_designators import (
+    get_type_designator_value,
+)
+from linkml.utils.ifabsent_functions import ifabsent_value_declaration
 from linkml_runtime.linkml_model.meta import (
     Annotation,
     ClassDefinition,
     ClassDefinitionName,
+    ElementName,
     SchemaDefinition,
     SlotDefinition,
     SlotDefinitionName,
-    TypeDefinition,
-    ElementName,
-)
-from linkml.generators.common.type_designators import (
-    get_accepted_type_designator_values,
-    get_type_designator_value,
 )
+from linkml_runtime.utils.compile_python import file_text
 from linkml_runtime.utils.formatutils import camelcase, underscore
 from linkml_runtime.utils.schemaview import SchemaView
-from linkml_runtime.utils.compile_python import file_text
-from linkml.utils.ifabsent_functions import ifabsent_value_declaration
-
-from nwb_linkml.maps.naming import module_case, version_module_case
-
-from jinja2 import Template
 from pydantic import BaseModel
 
+from nwb_linkml.maps import flat_to_nptyping
+from nwb_linkml.maps.naming import module_case, version_module_case
+
 
 class LinkML_Meta(BaseModel):
     """Extra LinkML Metadata stored as a class attribute"""

nwb_linkml/src/nwb_linkml/io/hdf5.py

@@ -19,29 +19,26 @@ Other TODO:
 
 """
 
-import pdb
+import json
+import os
+import shutil
+import subprocess
 import warnings
-from typing import Optional, Dict, overload, Type, Union, List
 from pathlib import Path
 from types import ModuleType
-from typing import TYPE_CHECKING, NamedTuple
+from typing import TYPE_CHECKING, Dict, List, Optional, Union, overload
-import json
-import subprocess
-import shutil
-import os
 
 import h5py
+import numpy as np
 from pydantic import BaseModel
 from tqdm import tqdm
-import numpy as np
 
-from nwb_linkml.maps.hdf5 import H5SourceItem, flatten_hdf, ReadPhases, ReadQueue
+from nwb_linkml.maps.hdf5 import ReadPhases, ReadQueue, flatten_hdf
 
 # from nwb_linkml.models.core_nwb_file import NWBFile
 if TYPE_CHECKING:
     from nwb_linkml.models import NWBFile
 from nwb_linkml.providers.schema import SchemaProvider
-from nwb_linkml.types.hdf5 import HDF5_Path
 
 
 class HDF5IO:
@@ -191,7 +188,7 @@ def read_specs_as_dicts(group: h5py.Group) -> dict:
         if isinstance(node, h5py.Dataset):
             # make containing dict if they dont exist
             pieces = node.name.split("/")
-            if pieces[-3] not in spec_dict.keys():
+            if pieces[-3] not in spec_dict:
                 spec_dict[pieces[-3]] = {}
 
             spec = json.loads(node[()])

nwb_linkml/src/nwb_linkml/io/schema.py

@@ -3,24 +3,24 @@ Loading/saving NWB Schema yaml files
 """
 
 from pathlib import Path
-from typing import Optional
 from pprint import pprint
+from typing import Optional
 
-from linkml_runtime.loaders import yaml_loader
 import yaml
+from linkml_runtime.loaders import yaml_loader
 
-from nwb_schema_language import Namespaces, Group, Dataset
-from nwb_linkml.providers.git import NamespaceRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
-from nwb_linkml.maps.postload import PHASES, KeyMap, apply_postload
 from nwb_linkml.adapters.namespaces import NamespacesAdapter
 from nwb_linkml.adapters.schema import SchemaAdapter
+from nwb_linkml.maps.postload import apply_postload
+from nwb_linkml.providers.git import HDMF_COMMON_REPO, NWB_CORE_REPO, NamespaceRepo
+from nwb_schema_language import Dataset, Group, Namespaces
 
 
 def load_yaml(path: Path | str) -> dict:
     if isinstance(path, str) and not Path(path).exists():
         ns_dict = yaml.safe_load(path)
     else:
-        with open(path, "r") as file:
+        with open(path) as file:
             ns_dict = yaml.safe_load(file)
     ns_dict = apply_postload(ns_dict)
     return ns_dict
@@ -108,7 +108,7 @@ def load_namespace_adapter(
     elif isinstance(namespace, Namespaces):
         namespaces = namespace
     else:
-        raise ValueError(f"Namespace must be a path, namespace repo, or already loaded namespaces")
+        raise ValueError("Namespace must be a path, namespace repo, or already loaded namespaces")
 
     if path.is_file():
         # given the namespace file itself, so find paths relative to its directory

nwb_linkml/src/nwb_linkml/lang_elements.py

@@ -3,18 +3,17 @@ Language elements in nwb schema language that have a fixed, alternative represen
 in LinkML. These are exported as an nwb.language.yml file along with every generated namespace
 """
 
-from nwb_schema_language.datamodel.nwb_schema_pydantic import FlatDtype as FlatDtype_source
 from linkml_runtime.linkml_model import (
     ClassDefinition,
     EnumDefinition,
-    SchemaDefinition,
-    SlotDefinition,
-    TypeDefinition,
-    Prefix,
     PermissibleValue,
+    Prefix,
+    SchemaDefinition,
+    TypeDefinition,
 )
-from nwb_linkml.maps import flat_to_linkml
 
+from nwb_linkml.maps import flat_to_linkml
+from nwb_schema_language.datamodel.nwb_schema_pydantic import FlatDtype as FlatDtype_source
 
 FlatDType = EnumDefinition(
     name="FlatDType",

nwb_linkml/src/nwb_linkml/maps/__init__.py

@@ -1,5 +1,5 @@
 # Import everything so it's defined, but shoudlnt' necessarily be used from here
+from nwb_linkml.maps.dtype import flat_to_linkml, flat_to_nptyping
 from nwb_linkml.maps.map import Map
 from nwb_linkml.maps.postload import MAP_HDMF_DATATYPE_DEF, MAP_HDMF_DATATYPE_INC
 from nwb_linkml.maps.quantity import QUANTITY_MAP
-from nwb_linkml.maps.dtype import flat_to_linkml, flat_to_nptyping

nwb_linkml/src/nwb_linkml/maps/dtype.py

@@ -1,7 +1,8 @@
-import numpy as np
-from typing import Any, Type
 from datetime import datetime
+from typing import Any, Type
+
 import nptyping
+import numpy as np
 
 flat_to_linkml = {
     "float": "float",

nwb_linkml/src/nwb_linkml/maps/hdf5.py

@@ -6,23 +6,21 @@ so we will make our own mapping class here and re-evaluate whether they should b
 """
 
 import datetime
-import pdb
-from abc import abstractmethod
-from pathlib import Path
-from typing import Literal, List, Dict, Optional, Type, Union, Tuple
 import inspect
+from abc import abstractmethod
+from enum import StrEnum
+from pathlib import Path
+from typing import Dict, List, Literal, Optional, Tuple, Type, Union
 
 import h5py
-from enum import StrEnum
+from pydantic import BaseModel, ConfigDict, Field
 
-from pydantic import BaseModel, Field, ConfigDict
+from nwb_linkml.annotations import unwrap_optional
-
-from nwb_linkml.providers.schema import SchemaProvider
 from nwb_linkml.maps import Map
 from nwb_linkml.maps.hdmf import dynamictable_to_model
+from nwb_linkml.providers.schema import SchemaProvider
 from nwb_linkml.types.hdf5 import HDF5_Path
 from nwb_linkml.types.ndarray import NDArrayProxy
-from nwb_linkml.annotations import unwrap_optional
 
 
 class ReadPhases(StrEnum):
@@ -548,7 +546,7 @@ class CompleteContainerGroups(HDF5Map):
             src.model is None
             and src.neurodata_type is None
             and src.source.h5_type == "group"
-            and all([depend in completed.keys() for depend in src.depends])
+            and all([depend in completed for depend in src.depends])
         ):
             return True
         else:
@@ -580,7 +578,7 @@ class CompleteModelGroups(HDF5Map):
             src.model is not None
             and src.source.h5_type == "group"
             and src.neurodata_type != "NWBFile"
-            and all([depend in completed.keys() for depend in src.depends])
+            and all([depend in completed for depend in src.depends])
         ):
             return True
         else:
@@ -642,7 +640,7 @@ class CompleteNWBFile(HDF5Map):
         cls, src: H5ReadResult, provider: SchemaProvider, completed: Dict[str, H5ReadResult]
     ) -> bool:
         if src.neurodata_type == "NWBFile" and all(
-            [depend in completed.keys() for depend in src.depends]
+            [depend in completed for depend in src.depends]
         ):
             return True
         else:
@@ -661,7 +659,7 @@ class CompleteNWBFile(HDF5Map):
             datetime.datetime.fromisoformat(ts.decode("utf-8"))
             for ts in res["file_create_date"]["array"][:]
         ]
-        if "stimulus" not in res.keys():
+        if "stimulus" not in res:
             res["stimulus"] = provider.get_class("core", "NWBFileStimulus")()
         electrode_groups = []
         egroup_keys = list(res["general"].get("extracellular_ephys", {}).keys())
@@ -830,8 +828,8 @@ def flatten_hdf(h5f: h5py.File | h5py.Group, skip="specifications") -> Dict[str,
             # depends = depends,
             h5_type=h5_type,
             attrs=attrs,
-            namespace=attrs.get("namespace", None),
+            namespace=attrs.get("namespace"),
-            neurodata_type=attrs.get("neurodata_type", None),
+            neurodata_type=attrs.get("neurodata_type"),
         )
 
     h5f.visititems(_itemize)
@@ -895,7 +893,7 @@ def resolve_references(
     res = {}
     for path, item in src.items():
         if isinstance(item, HDF5_Path):
-            other_item = completed.get(item, None)
+            other_item = completed.get(item)
             if other_item is None:
                 errors.append(f"Couldn't find: {item}")
             res[path] = other_item.result

nwb_linkml/src/nwb_linkml/maps/hdmf.py

@@ -2,19 +2,16 @@
 Mapping functions for handling HDMF classes like DynamicTables
 """
 
-from typing import List, Type, Optional, Any
+from typing import Any, List, Optional, Type
-import warnings
 
-
-import h5py
-import nptyping
-from pydantic import create_model, BaseModel
-import numpy as np
 import dask.array as da
+import h5py
+import numpy as np
+from pydantic import BaseModel, create_model
 
+from nwb_linkml.maps.dtype import struct_from_dtype
 from nwb_linkml.types.hdf5 import HDF5_Path
 from nwb_linkml.types.ndarray import NDArray, NDArrayProxy
-from nwb_linkml.maps.dtype import flat_to_nptyping, struct_from_dtype
 
 
 def model_from_dynamictable(group: h5py.Group, base: Optional[BaseModel] = None) -> Type[BaseModel]:

nwb_linkml/src/nwb_linkml/maps/map.py

@@ -1,5 +1,5 @@
-from typing import Any
 from abc import ABC, abstractmethod
+from typing import Any
 
 
 class Map(ABC):

nwb_linkml/src/nwb_linkml/maps/naming.py

@@ -1,4 +1,3 @@
-import pdb
 import re
 from pathlib import Path
 
@@ -53,14 +52,14 @@ def relative_path(target: Path, origin: Path):
     def _relative_path(target: Path, origin: Path):
         try:
             return Path(target).resolve().relative_to(Path(origin).resolve())
-        except ValueError as e:  # target does not start with origin
+        except ValueError:  # target does not start with origin
             # recursion with origin (eventually origin is root so try will succeed)
             return Path("..").joinpath(_relative_path(target, Path(origin).parent))
 
     try:
         successful = Path(target).resolve().relative_to(Path(origin).resolve())
         return successful
-    except ValueError as e:  # target does not start with origin
+    except ValueError:  # target does not start with origin
         # recursion with origin (eventually origin is root so try will succeed)
         relative = Path("..").joinpath(_relative_path(target, Path(origin).parent))
         # remove the first '..' because this thing freaking double counts

nwb_linkml/src/nwb_linkml/maps/postload.py

@@ -2,13 +2,11 @@
 Maps to change the loaded .yaml from nwb schema before it's given to the nwb_schema_language models
 """
 
+import ast
+import re
 from dataclasses import dataclass
 from enum import StrEnum
-from typing import Optional, ClassVar, List
+from typing import ClassVar, List, Optional
-import re
-import ast
-
-from nwb_linkml.maps import Map
 
 
 class SCOPE_TYPES(StrEnum):

nwb_linkml/src/nwb_linkml/monkeypatch.py

@@ -12,13 +12,12 @@ def patch_npytyping_perf():
     References:
         - https://github.com/ramonhagenaars/nptyping/issues/110
     """
-    from nptyping import ndarray
-    from nptyping.pandas_ import dataframe
-    from nptyping import recarray
-    from nptyping import base_meta_classes
     import inspect
     from types import FrameType
 
+    from nptyping import base_meta_classes, ndarray, recarray
+    from nptyping.pandas_ import dataframe
+
     # make a new __module__ methods for the affected classes
     def new_module_ndarray(cls) -> str:
         return cls._get_module(inspect.currentframe(), "nptyping.ndarray")
@@ -63,13 +62,13 @@ def patch_schemaview():
     Returns:
 
     """
-    from typing import List
     from functools import lru_cache
-    from linkml_runtime.utils.schemaview import SchemaView
+    from typing import List
 
     from linkml_runtime.linkml_model import SchemaDefinitionName
+    from linkml_runtime.utils.schemaview import SchemaView
 
-    @lru_cache()
+    @lru_cache
     def imports_closure(
         self, imports: bool = True, traverse=True, inject_metadata=True
     ) -> List[SchemaDefinitionName]:

nwb_linkml/src/nwb_linkml/plot.py

@@ -2,17 +2,17 @@
 Various visualization routines, mostly to help development for now
 """
 
-from typing import TYPE_CHECKING, Optional, List, TypedDict
-from rich import print
 import random
+from typing import TYPE_CHECKING, List, Optional, TypedDict
 
-from dash import Dash, html
 import dash_cytoscape as cyto
+from dash import Dash, html
+from rich import print
 
 cyto.load_extra_layouts()
 
-from nwb_schema_language import Namespace, Group, Dataset
 from nwb_linkml.io import load_nwb_core
+from nwb_schema_language import Dataset, Group, Namespace
 
 if TYPE_CHECKING:
     from nwb_linkml.adapters import NamespacesAdapter

nwb_linkml/src/nwb_linkml/providers/__init__.py

@@ -1 +1 @@
-from nwb_linkml.providers.schema import LinkMLProvider, SchemaProvider, PydanticProvider
+from nwb_linkml.providers.schema import LinkMLProvider, PydanticProvider, SchemaProvider

nwb_linkml/src/nwb_linkml/providers/git.py

@@ -2,15 +2,14 @@
 Define and manage NWB namespaces in external repositories
 """
 
-import pdb
+import shutil
-from typing import Optional, Dict, List
+import subprocess
+import tempfile
 import warnings
 from pathlib import Path
-import tempfile
+from typing import List, Optional
-import subprocess
-import shutil
 
-from pydantic import BaseModel, HttpUrl, FilePath, DirectoryPath, Field
+from pydantic import BaseModel, DirectoryPath, Field, HttpUrl
 
 from nwb_linkml.config import Config
 

nwb_linkml/src/nwb_linkml/providers/schema.py

@@ -41,35 +41,29 @@ so eg. for the linkML and pydantic providers:
 
 """
 
-import pdb
-import shutil
-from pprint import pformat
-from typing import Dict, TypedDict, List, Optional, Literal, TypeVar, Any, Dict, Type, Callable
-from types import ModuleType
-from pathlib import Path
-import os
-from abc import abstractmethod, ABC
-from importlib.abc import MetaPathFinder
-import warnings
 import importlib
+import os
+import shutil
 import sys
+from abc import ABC, abstractmethod
+from importlib.abc import MetaPathFinder
+from pathlib import Path
+from types import ModuleType
+from typing import Any, Dict, List, Optional, Type, TypedDict, TypeVar
 
+from linkml_runtime import SchemaView
+from linkml_runtime.dumpers import yaml_dumper
+from linkml_runtime.linkml_model import SchemaDefinition, SchemaDefinitionName
 from pydantic import BaseModel
 
-from linkml_runtime.linkml_model import SchemaDefinition, SchemaDefinitionName
+from nwb_linkml import adapters, io
-from linkml_runtime.dumpers import yaml_dumper
-from linkml_runtime import SchemaView
-
-from nwb_linkml.config import Config
-from nwb_linkml import io
-from nwb_linkml import adapters
 from nwb_linkml.adapters.adapter import BuildResult
-from nwb_linkml.maps.naming import module_case, version_module_case, relative_path
+from nwb_linkml.config import Config
-from nwb_schema_language import Namespaces
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator
+from nwb_linkml.maps.naming import module_case, relative_path, version_module_case
 from nwb_linkml.providers.git import DEFAULT_REPOS
 from nwb_linkml.ui import AdapterProgress
-
+from nwb_schema_language import Namespaces
 
 P = TypeVar("P")
 
@@ -212,7 +206,7 @@ class Provider(ABC):
         for ns_dir in builtin_namespaces + tmp_paths:
             if not ns_dir.is_dir():
                 continue
-            if ns_dir.name not in versions.keys():
+            if ns_dir.name not in versions:
                 versions[ns_dir.name] = []
 
             versions[ns_dir.name].extend([v for v in ns_dir.iterdir() if v.is_dir()])
@@ -589,7 +583,7 @@ class PydanticProvider(Provider):
 
     def _build_unsplit(self, path, versions, default_kwargs, dump, out_file, force):
         if out_file.exists() and not force:
-            with open(out_file, "r") as ofile:
+            with open(out_file) as ofile:
                 serialized = ofile.read()
             return serialized
 

nwb_linkml/src/nwb_linkml/types/df.py

@@ -13,22 +13,20 @@ Pydantic models that behave like pandas dataframes
 """
 
 import ast
-import pdb
+from typing import Any, Dict, Optional, Type
-from typing import List, Any, get_origin, get_args, Union, Optional, Dict, Type
-from types import NoneType
 
 import h5py
 import numpy as np
 import pandas as pd
 from pydantic import (
     BaseModel,
-    model_serializer,
-    SerializerFunctionWrapHandler,
     ConfigDict,
+    SerializerFunctionWrapHandler,
+    model_serializer,
     model_validator,
 )
 
-from nwb_linkml.maps.hdmf import model_from_dynamictable, dereference_reference_vector
+from nwb_linkml.maps.hdmf import dereference_reference_vector, model_from_dynamictable
 from nwb_linkml.types.hdf5 import HDF5_Path
 
 

nwb_linkml/src/nwb_linkml/types/hdf5.py

@@ -1,6 +1,7 @@
 from typing import Any
-from pydantic_core import CoreSchema, core_schema
+
 from pydantic import GetCoreSchemaHandler
+from pydantic_core import CoreSchema, core_schema
 
 
 class HDF5_Path(str):

nwb_linkml/src/nwb_linkml/types/ndarray.py

@@ -5,31 +5,23 @@ Extension of nptyping NDArray for pydantic that allows for JSON-Schema serializa
 """
 
 import base64
-import pdb
-from pathlib import Path
-from typing import Any, Callable, Tuple
 import sys
 from copy import copy
-from functools import reduce
+from pathlib import Path
-from operator import or_
+from typing import Any, Callable
 
-import nptyping.structure
-from pydantic_core import core_schema
-from pydantic import BaseModel, GetJsonSchemaHandler, ValidationError, GetCoreSchemaHandler
-from pydantic.json_schema import JsonSchemaValue
-
-import numpy as np
-import h5py
-from dask.array.core import Array as DaskArray
 import blosc2
-
+import h5py
+import nptyping.structure
+import numpy as np
+from dask.array.core import Array as DaskArray
 from nptyping import NDArray as _NDArray
 from nptyping.ndarray import NDArrayMeta as _NDArrayMeta
-from nptyping import Shape, Number
 from nptyping.nptyping_type import NPTypingType
 from nptyping.shape_expression import check_shape
+from pydantic_core import core_schema
 
-from nwb_linkml.maps.dtype import np_to_python, allowed_precisions
+from nwb_linkml.maps.dtype import allowed_precisions, np_to_python
 
 
 def _list_of_lists_schema(shape, array_type_handler):
@@ -196,7 +188,7 @@ class NDArrayProxy:
             return obj[slice]
 
     def __setitem__(self, slice, value):
-        raise NotImplementedError(f"Can't write into an arrayproxy yet!")
+        raise NotImplementedError("Can't write into an arrayproxy yet!")
 
     @classmethod
     def __get_pydantic_core_schema__(

nwb_linkml/src/nwb_linkml/ui.py

@@ -6,7 +6,7 @@ from typing import TYPE_CHECKING
 
 from rich.live import Live
 from rich.panel import Panel
-from rich.progress import Progress, SpinnerColumn, BarColumn, TextColumn, Column
+from rich.progress import BarColumn, Column, Progress, SpinnerColumn, TextColumn
 
 if TYPE_CHECKING:
     from nwb_linkml.adapters.namespaces import NamespacesAdapter
@@ -42,7 +42,7 @@ class AdapterProgress:
                 )
 
         self.panel = Panel(
-            self.progress, title=f"Building Namespaces", border_style="green", padding=(2, 2)
+            self.progress, title="Building Namespaces", border_style="green", padding=(2, 2)
         )
 
     def update(self, namespace: str, **kwargs):

nwb_linkml/tests/fixtures.py

@@ -1,22 +1,21 @@
-import pytest
+import shutil
-import os
-from typing import NamedTuple, Optional, List, Dict
 from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Dict, Optional
 
+import pytest
 from linkml_runtime.dumpers import yaml_dumper
-
-from nwb_linkml.io import schema as io
-from nwb_linkml.adapters.namespaces import NamespacesAdapter
-from nwb_schema_language import Schema, Group, Dataset, Attribute
 from linkml_runtime.linkml_model import (
-    SchemaDefinition,
     ClassDefinition,
-    SlotDefinition,
     Prefix,
+    SchemaDefinition,
+    SlotDefinition,
     TypeDefinition,
 )
-import shutil
+
-from pathlib import Path
+from nwb_linkml.adapters.namespaces import NamespacesAdapter
+from nwb_linkml.io import schema as io
+from nwb_schema_language import Attribute, Dataset, Group
 
 
 @pytest.fixture(scope="session")

nwb_linkml/tests/test_adapters/test_adapter.py

@@ -1,20 +1,15 @@
-import pdb
 
 import numpy as np
 import pytest
-from ..fixtures import nwb_core_fixture
-
 from linkml_runtime.linkml_model import (
-    SchemaDefinition,
     ClassDefinition,
+    SchemaDefinition,
     SlotDefinition,
     TypeDefinition,
 )
-from nwb_schema_language import Dataset, Group, Schema, CompoundDtype, Attribute
 
 from nwb_linkml.adapters import BuildResult
-
+from nwb_schema_language import Attribute, Dataset, Group, Schema
-from ..fixtures import linkml_schema_bare
 
 
 def test_walk(nwb_core_fixture):

nwb_linkml/tests/test_adapters/test_adapter_classes.py

@@ -1,12 +1,9 @@
-import pdb
 
 import pytest
-
-from ..fixtures import linkml_schema_bare, linkml_schema, nwb_schema
-
 from linkml_runtime.linkml_model import SlotDefinition
-from nwb_linkml.adapters import DatasetAdapter, ClassAdapter, GroupAdapter
+
-from nwb_schema_language import Group, Dataset, ReferenceDtype, CompoundDtype
+from nwb_linkml.adapters import DatasetAdapter, GroupAdapter
+from nwb_schema_language import CompoundDtype, Dataset, Group, ReferenceDtype
 
 
 def test_build_base(nwb_schema):

nwb_linkml/tests/test_adapters/test_adapter_dataset.py

@@ -1,22 +1,11 @@
-import pdb
 
-import pytest
 
-from ..fixtures import nwb_core_fixture
 
-from nwb_schema_language import Namespaces, Namespace, Dataset, Group, Schema
+
-from linkml_runtime.dumpers import yaml_dumper
-import yaml
-from nwb_linkml.adapters import DatasetAdapter
 from nwb_linkml.adapters.dataset import (
     MapScalar,
-    MapListlike,
-    MapArraylike,
-    MapNVectors,
-    Map1DVector,
-    MapScalarAttributes,
-    MapArrayLikeAttributes,
 )
+from nwb_schema_language import Dataset
 
 
 def test_nothing(nwb_core_fixture):

nwb_linkml/tests/test_adapters/test_adapter_group.py

@@ -1,3 +1 @@
-import pytest
 
-from ..fixtures import nwb_core_fixture

nwb_linkml/tests/test_adapters/test_adapter_namespaces.py

@@ -1,8 +1,6 @@
-import pdb
 
 import pytest
-from ..fixtures import nwb_core_fixture
+
-from nwb_schema_language import Dataset, Group
 from nwb_linkml.adapters import SchemaAdapter
 
 

nwb_linkml/tests/test_adapters/test_adapter_schema.py

@@ -1,7 +1,4 @@
 import pytest
-from ..fixtures import nwb_core_fixture
-
-from nwb_schema_language import Dataset, Group, Schema
 
 
 @pytest.mark.parametrize(["schema_name"], [["core.nwb.file"]])

nwb_linkml/tests/test_annotations.py

@@ -1,7 +1,8 @@
+from types import NoneType
+from typing import List
+
 import pytest
 
-from typing import List, Optional, Union
-from types import NoneType
 from nwb_linkml.annotations import get_inner_types
 
 

nwb_linkml/tests/test_config.py

@@ -1,8 +1,7 @@
-import pytest
-import tempfile
-from pathlib import Path
 import os
 import shutil
+import tempfile
+from pathlib import Path
 
 from nwb_linkml.config import Config
 

nwb_linkml/tests/test_generate.py

@@ -6,19 +6,15 @@ to ensure that the basics of the whole thing operate -- not doing any actual dat
 here.
 """
 
-import pdb
 from pathlib import Path
 from typing import Dict
 
 import pytest
-import warnings
-
-from .fixtures import nwb_core_fixture, tmp_output_dir
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import SchemaDefinition
-from nwb_linkml.generators.pydantic import NWBPydanticGenerator
 from linkml_runtime.loaders.yaml_loader import YAMLLoader
 
+from nwb_linkml.generators.pydantic import NWBPydanticGenerator
 from nwb_linkml.lang_elements import NwbLangSchema
 
 

nwb_linkml/tests/test_generators/test_generator_pydantic.py

@@ -5,29 +5,23 @@ Note that since this is largely a subclass, we don't test all of the functionali
 because it's tested in the base linkml package.
 """
 
-import pdb
+import re
 import sys
 import typing
-
-import pytest
-from typing import TypedDict, Optional
 from types import ModuleType
-import re
+from typing import Optional, TypedDict
+
 import numpy as np
-
+import pytest
 from pydantic import BaseModel
 
-from ..fixtures import (
-    tmp_output_dir,
-    tmp_output_dir_mod,
-    linkml_schema,
-    TestSchemas,
-    linkml_schema_bare,
-)
-
 from nwb_linkml.generators.pydantic import NWBPydanticGenerator, compile_python
 from nwb_linkml.types.ndarray import NDArrayMeta
 
+from ..fixtures import (
+    TestSchemas,
+)
+
 
 class TestModules(TypedDict):
     core: ModuleType

nwb_linkml/tests/test_io/test_io_hdf5.py

@@ -1,14 +1,10 @@
 import pdb
+
 import h5py
-
-import pytest
-from pathlib import Path
 import numpy as np
+import pytest
 
-from ..fixtures import tmp_output_dir, data_dir
+from nwb_linkml.io.hdf5 import HDF5IO, truncate_file
-
-from nwb_linkml.io.hdf5 import HDF5IO
-from nwb_linkml.io.hdf5 import truncate_file
 
 
 @pytest.mark.xfail()
@@ -92,7 +88,6 @@ def test_truncate_file(tmp_output_dir):
 
 @pytest.mark.skip()
 def test_flatten_hdf():
-    from nwb_linkml.io.hdf5 import HDF5IO
     from nwb_linkml.maps.hdf5 import flatten_hdf
 
     path = "/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb"

nwb_linkml/tests/test_maps/test_dtype.py

@@ -1,5 +1,6 @@
-import numpy as np
 import nptyping
+import numpy as np
+
 from nwb_linkml.maps.dtype import struct_from_dtype
 
 

nwb_linkml/tests/test_maps/test_hdmf.py

@@ -1,11 +1,10 @@
-import pdb
 
-import pytest
-import h5py
 import time
 
-from nwb_linkml.maps.hdmf import model_from_dynamictable, dynamictable_to_model
+import h5py
-from ..fixtures import data_dir
+import pytest
+
+from nwb_linkml.maps.hdmf import dynamictable_to_model, model_from_dynamictable
 
 NWBFILE = "/Users/jonny/Dropbox/lab/p2p_ld/data/nwb/sub-738651046_ses-760693773.nwb"
 

nwb_linkml/tests/test_maps/test_maps.py

@@ -1,9 +1,10 @@
-import pytest
 import os
 import tempfile
+from pathlib import Path
+
 import yaml
 from yaml import CDumper as Dumper
-from pathlib import Path
+
 from nwb_linkml.io.schema import load_yaml
 
 

nwb_linkml/tests/test_providers/test_provider_git.py

@@ -1,8 +1,9 @@
-import pytest
 import shutil
 
+import pytest
 import yaml
-from nwb_linkml.providers.git import GitRepo, NWB_CORE_REPO, HDMF_COMMON_REPO
+
+from nwb_linkml.providers.git import HDMF_COMMON_REPO, NWB_CORE_REPO, GitRepo
 from nwb_schema_language import Namespaces
 
 
@@ -34,7 +35,7 @@ def test_gitrepo(source, commit):
     repo.clone()
     # check that the namespace file exists and has some expected fields
     assert repo.namespace_file.exists()
-    with open(repo.namespace_file, "r") as nsfile:
+    with open(repo.namespace_file) as nsfile:
         ns = yaml.safe_load(nsfile)
     # correct model instantiation confirms the repo was cloned successfully
     ns_model = Namespaces(**ns)

nwb_linkml/tests/test_providers/test_provider_schema.py

@@ -1,25 +1,16 @@
-import pdb
 import shutil
-import os
 import sys
-import warnings
 from pathlib import Path
-import yaml
+from typing import Optional
-from pprint import pformat
-
-from typing import Optional, Union, List
-from ..fixtures import tmp_output_dir
 
 import pytest
+from nptyping import Shape, UByte
 
-from nwb_linkml.providers.schema import LinkMLProvider, PydanticProvider
 import nwb_linkml
 from nwb_linkml.maps.naming import version_module_case
 from nwb_linkml.providers.git import DEFAULT_REPOS
-from nwb_linkml.adapters import NamespacesAdapter
+from nwb_linkml.providers.schema import LinkMLProvider, PydanticProvider
 from nwb_linkml.types.ndarray import NDArray
-from nptyping import Shape, UByte
-
 
 CORE_MODULES = (
     "core.nwb.base",

nwb_linkml/tests/test_types/test_df.py

@@ -1,7 +1,7 @@
-import pytest
+from typing import List, Optional
 
+import pytest
 from pydantic import BaseModel, ValidationError
-from typing import List, Union, Optional
 
 
 @pytest.mark.skip()
@@ -10,6 +10,7 @@ def test_df():
     Dataframe class should behave like both a pydantic model and a dataframe
     """
     import pandas as pd
+
     from nwb_linkml.types.df import DataFrame
 
     class MyDf(DataFrame):

nwb_linkml/tests/test_types/test_ndarray.py

@@ -1,17 +1,13 @@
-import pdb
-from typing import Union, Optional, Any
 import json
+from typing import Any, Optional, Union
 
-import pytest
-
-import numpy as np
 import h5py
+import numpy as np
+import pytest
+from nptyping import Number, Shape
+from pydantic import BaseModel, Field, ValidationError
 
-from pydantic import BaseModel, ValidationError, Field
 from nwb_linkml.types.ndarray import NDArray, NDArrayProxy
-from nptyping import Shape, Number
-
-from ..fixtures import data_dir, tmp_output_dir, tmp_output_dir_func
 
 
 def test_ndarray_type():

nwb_schema_language/src/nwb_schema_language/__init__.py

@@ -3,16 +3,16 @@ from typing import List, Union
 
 try:
     from .datamodel.nwb_schema_pydantic import (
+        Attribute,
+        CompoundDtype,
+        Dataset,
+        FlatDtype,
+        Group,
+        Link,
         Namespace,
         Namespaces,
-        Schema,
-        Group,
-        Attribute,
-        Link,
-        Dataset,
         ReferenceDtype,
-        CompoundDtype,
+        Schema,
-        FlatDtype,
     )
 
     DTypeType = Union[List[CompoundDtype], FlatDtype, ReferenceDtype]

nwb_schema_language/src/nwb_schema_language/_version.py

@@ -1,4 +1,4 @@
-from importlib.metadata import version, PackageNotFoundError
+from importlib.metadata import PackageNotFoundError, version
 
 try:
     __version__ = version(__name__)

nwb_schema_language/src/nwb_schema_language/datamodel/schemaview.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+
 from linkml_runtime.utils.schemaview import SchemaView
 
 SCHEMA_FILE = Path(__file__).parent.parent.resolve() / "schema" / "nwb_schema_language.yaml"

nwb_schema_language/src/nwb_schema_language/patches.py

@@ -2,13 +2,13 @@
 Patching the source code at different stages of the code generation process
 """
 
+import argparse
+import pprint
+import re
 from dataclasses import dataclass
 from enum import StrEnum
 from pathlib import Path
 from typing import ClassVar, List
-import re
-import argparse
-import pprint
 
 
 class Phases(StrEnum):
@@ -89,7 +89,7 @@ def run_patches(phase: Phases, verbose: bool = False):
         if verbose:
             print("Patching:")
             pprint.pprint(patch)
-        with open(patch.path, "r") as pfile:
+        with open(patch.path) as pfile:
             string = pfile.read()
         string = re.sub(patch.match, patch.replacement, string)
         with open(patch.path, "w") as pfile: