enable black preview and automatic linebreaks in long strings

nwb_linkml/src/nwb_linkml/__init__.py

@@ -1,12 +1,11 @@
 """
 NWB in LinkML
 """
+
 from nwb_linkml.monkeypatch import apply_patches
 
 apply_patches()
 
 from nwb_linkml.config import Config  # noqa: E402
 
-__all__ = [
+__all__ = ["Config"]
-    "Config"
-]

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -30,14 +30,15 @@ from nwb_schema_language import Attribute, Dataset, Group, Schema
 
 T = TypeVar("T", Dataset, Attribute, Schema, Group, BaseModel)
 Ts = TypeVarTuple("Ts")
-Td = TypeVar('Td', bound=Union[Definition,SchemaDefinition,TypeDefinition])
+Td = TypeVar("Td", bound=Union[Definition, SchemaDefinition, TypeDefinition])
+
 
 @dataclass
 class BuildResult:
     """
     Container class for propagating nested build results back up to caller
     """
-    # pass
+
     schemas: List[SchemaDefinition] = field(default_factory=list)
     classes: List[ClassDefinition] = field(default_factory=list)
     slots: List[SlotDefinition] = field(default_factory=list)

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -365,7 +365,8 @@ class DatasetAdapter(ClassAdapter):
 
         if len(matches) > 1:  # pragma: no cover
             raise RuntimeError(
-                f"Only one map should apply to a dataset, you need to refactor the maps! Got maps: {matches}"
+                "Only one map should apply to a dataset, you need to refactor the maps! Got maps:"
+                f" {matches}"
             )
 
         # apply matching maps
@@ -412,7 +413,9 @@ 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]) or all([dims in inner_dim 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
         else:
             required = False

nwb_linkml/src/nwb_linkml/adapters/namespaces.py

@@ -5,7 +5,6 @@ Wraps the :class:`nwb_schema_language.Namespaces` and other objects with conveni
 for extracting information and generating translated schema
 """
 
-
 from copy import copy
 from pathlib import Path
 from pprint import pformat
@@ -154,7 +153,8 @@ class NamespacesAdapter(Adapter):
 
         if len(internal_matches) > 1:
             raise KeyError(
-                f"Found multiple schemas in namespace that define {name}:\ninternal: {pformat(internal_matches)}\nimported:{pformat(import_matches)}"
+                f"Found multiple schemas in namespace that define {name}:\ninternal:"
+                f" {pformat(internal_matches)}\nimported:{pformat(import_matches)}"
             )
         elif len(internal_matches) == 1:
             return internal_matches[0]
@@ -168,7 +168,8 @@ class NamespacesAdapter(Adapter):
 
         if len(import_matches) > 1:
             raise KeyError(
-                f"Found multiple schemas in namespace that define {name}:\ninternal: {pformat(internal_matches)}\nimported:{pformat(import_matches)}"
+                f"Found multiple schemas in namespace that define {name}:\ninternal:"
+                f" {pformat(internal_matches)}\nimported:{pformat(import_matches)}"
             )
         elif len(import_matches) == 1:
             return import_matches[0]

nwb_linkml/src/nwb_linkml/adapters/schema.py

@@ -34,7 +34,10 @@ class SchemaAdapter(Adapter):
     )
     version: Optional[str] = Field(
         None,
-        description="Version of schema, populated by NamespacesAdapter since individual schema files dont know their version in NWB Schema Lang",
+        description=(
+            "Version of schema, populated by NamespacesAdapter since individual schema files dont"
+            " know their version in NWB Schema Lang"
+        ),
     )
     _created_classes: List[Type[Group | Dataset]] = PrivateAttr(default_factory=list)
 
@@ -81,7 +84,8 @@ class SchemaAdapter(Adapter):
             len(res.slots) > 0
         ):  # pragma: no cover - hard to induce this error because the child classes don't fuck up like this
             raise RuntimeError(
-                "Generated schema in this translation can only have classes, all slots should be attributes within a class"
+                "Generated schema in this translation can only have classes, all slots should be"
+                " attributes within a class"
             )
 
         sch = SchemaDefinition(

nwb_linkml/src/nwb_linkml/generators/pydantic.py

@@ -253,7 +253,10 @@ class NWBPydanticGenerator(PydanticGenerator):
     SKIP_SLOTS: Tuple[str] = ("",)
     SKIP_CLASSES: Tuple[str] = ("",)
     INJECTED_FIELDS: Tuple[str] = (
-        'hdf5_path: Optional[str] = Field(None, description="The absolute path that this object is stored in an NWB file")',
+        (
+            'hdf5_path: Optional[str] = Field(None, description="The absolute path that this object'
+            ' is stored in an NWB file")'
+        ),
         'object_id: Optional[str] = Field(None, description="Unique UUID for each object")',
     )
     # SKIP_CLASSES=('VectorData','VectorIndex')

nwb_linkml/src/nwb_linkml/maps/hdf5.py

@@ -639,9 +639,7 @@ class CompleteNWBFile(HDF5Map):
     def check(
         cls, src: H5ReadResult, provider: SchemaProvider, completed: Dict[str, H5ReadResult]
     ) -> bool:
-        if src.neurodata_type == "NWBFile" and all(
+        if src.neurodata_type == "NWBFile" and all([depend in completed for depend in src.depends]):
-            [depend in completed for depend in src.depends]
-        ):
             return True
         else:
             return False

nwb_linkml/src/nwb_linkml/providers/git.py

@@ -20,14 +20,20 @@ class NamespaceRepo(BaseModel):
     """
 
     name: str = Field(
-        description="Short name used to refer to this namespace (usually equivalent to the name field within a namespaces NWB list)"
+        description=(
+            "Short name used to refer to this namespace (usually equivalent to the name field"
+            " within a namespaces NWB list)"
+        )
     )
     repository: HttpUrl | DirectoryPath = Field(
         description="URL or local absolute path to the root repository"
     )
     path: Path = Field(description="Relative path from the repository root to the namespace file")
     versions: List[str] = Field(
-        description="Known versions for this namespace repository, correspond to commit hashes or git tags that can be checked out by :class:`.GitRepo`",
+        description=(
+            "Known versions for this namespace repository, correspond to commit hashes or git tags"
+            " that can be checked out by :class:`.GitRepo`"
+        ),
         default_factory=list,
     )
 
@@ -248,7 +254,8 @@ class GitRepo:
         # Check that the remote matches
         if self.remote != str(self.namespace.repository):
             warnings.warn(
-                f'Repository exists, but has the wrong remote URL.\nExpected: {self.namespace.repository}\nGot:{self.remote.strip(".git")}'
+                "Repository exists, but has the wrong remote URL.\nExpected:"
+                f" {self.namespace.repository}\nGot:{self.remote.strip('.git')}"
             )
             return False
 
@@ -269,7 +276,8 @@ class GitRepo:
             or str(self.temp_directory).startswith(str(Config().git_dir))
         ):
             warnings.warn(
-                "Temp directory is outside of the system temp dir or git directory set by environmental variables, not deleting in case this has been changed by mistake"
+                "Temp directory is outside of the system temp dir or git directory set by"
+                " environmental variables, not deleting in case this has been changed by mistake"
             )
             self._temp_directory = None
             return
@@ -293,7 +301,8 @@ class GitRepo:
             else:
                 if not self.check():
                     warnings.warn(
-                        "Destination directory is not empty and does not pass checks for correctness! cleaning up"
+                        "Destination directory is not empty and does not pass checks for"
+                        " correctness! cleaning up"
                     )
                     self.cleanup()
                 else:

nwb_linkml/src/nwb_linkml/providers/schema.py

@@ -467,7 +467,8 @@ class LinkMLProvider(Provider):
         ns_repo = DEFAULT_REPOS.get(namespace, None)
         if ns_repo is None:
             raise KeyError(
-                f"Namespace {namespace} could not be found, and no git repository source has been configured!"
+                f"Namespace {namespace} could not be found, and no git repository source has been"
+                " configured!"
             )
         ns_file = ns_repo.provide_from_git(commit=version)
         res = self.build_from_yaml(ns_file)

nwb_linkml/tests/fixtures.py

@@ -117,7 +117,10 @@ def linkml_schema_bare() -> TestSchemas:
                         ),
                         SlotDefinition(
                             name="inline_dict",
-                            description="This should be inlined as a dictionary despite this class having an identifier",
+                            description=(
+                                "This should be inlined as a dictionary despite this class having"
+                                " an identifier"
+                            ),
                             multivalued=True,
                             inlined=True,
                             inlined_as_list=False,

nwb_linkml/tests/test_adapters/test_adapter.py

@@ -1,4 +1,3 @@
-
 import numpy as np
 import pytest
 from linkml_runtime.linkml_model import (

nwb_linkml/tests/test_adapters/test_adapter_classes.py

@@ -1,4 +1,3 @@
-
 import pytest
 from linkml_runtime.linkml_model import SlotDefinition
 

nwb_linkml/tests/test_adapters/test_adapter_dataset.py

@@ -1,7 +1,3 @@
-
-
-
-
 from nwb_linkml.adapters.dataset import (
     MapScalar,
 )

nwb_linkml/tests/test_adapters/test_adapter_namespaces.py

@@ -1,4 +1,3 @@
-
 import pytest
 
 from nwb_linkml.adapters import SchemaAdapter

nwb_linkml/tests/test_maps/test_hdmf.py

@@ -1,4 +1,3 @@
-
 import time
 
 import h5py

nwb_schema_language/src/nwb_schema_language/__init__.py

@@ -18,5 +18,6 @@ try:
     DTypeType = Union[List[CompoundDtype], FlatDtype, ReferenceDtype]
 except (NameError, RecursionError):
     warnings.warn(
-        "Error importing pydantic classes, passing because we might be in the process of patching them, but it is likely they are broken and you will be unable to use them!"
+        "Error importing pydantic classes, passing because we might be in the process of patching"
+        " them, but it is likely they are broken and you will be unable to use them!"
     )

nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py

@@ -510,7 +510,9 @@ class ReftypeOptions(EnumDefinitionImpl):
     )
     region = PermissibleValue(
         text="region",
-        description="Reference to a region (i.e. subset) of another dataset of the given target_type",
+        description=(
+            "Reference to a region (i.e. subset) of another dataset of the given target_type"
+        ),
     )
 
     _defn = EnumDefinition(

pyproject.toml

@@ -88,5 +88,6 @@ warn_unreachable = true
 [tool.black]
 target-version = ['py38', 'py39', 'py310', 'py311']
 enable-unstable-feature = ["string_processing"]
+preview = true
 include = "nwb_linkml/.*\\.py$|nwb_schema_language/.*\\.py$"
 line-length = 100