lint

nwb_linkml/conftest.py

@@ -1,11 +1,17 @@
+"""
+Test fixtures primarily for doctests for adapters
+"""
+
 import re
 import textwrap
-from doctest import NORMALIZE_WHITESPACE, ELLIPSIS
+from doctest import ELLIPSIS, NORMALIZE_WHITESPACE
-from sybil import Document
+from typing import Generator
-from sybil import Sybil, Region
+
+import yaml
+from sybil import Document, Example, Region, Sybil
 from sybil.parsers.codeblock import PythonCodeBlockParser
 from sybil.parsers.doctest import DocTestParser
-import yaml
+
 from nwb_linkml import adapters
 
 # Test adapter generation examples
@@ -24,7 +30,7 @@ def _strip_nwb(nwb: str) -> str:
     return nwb
 
 
-def test_adapter_block(example):
+def test_adapter_block(example: Example) -> None:
     """
     The linkml generated from a nwb example input should match
     that provided in the docstring.
@@ -44,10 +50,13 @@ def test_adapter_block(example):
     assert generated == expected
 
 
-def parse_adapter_blocks(document: Document):
+def parse_adapter_blocks(document: Document) -> Generator[Region, None, None]:
+    """
+    Parse blocks with adapter directives, yield to test with :func:`.test_adapter_block`
+    """
     for start_match, end_match, source in document.find_region_sources(ADAPTER_START, ADAPTER_END):
         # parse
-        sections = re.split(r":\w+?:", source, re.MULTILINE)
+        sections = re.split(r":\w+?:", source, flags=re.MULTILINE)
         sections = [textwrap.dedent(section).strip() for section in sections]
 
         sections[1] = _strip_nwb(sections[1])
@@ -56,9 +65,7 @@ def parse_adapter_blocks(document: Document):
 
 
 adapter_parser = Sybil(
-    parsers=[
+    parsers=[parse_adapter_blocks],
-        parse_adapter_blocks
-    ],
     patterns=["adapters/*.py"],
 )
 

nwb_linkml/src/nwb_linkml/adapters/adapter.py

@@ -16,6 +16,7 @@ from typing import (
     Union,
 )
 
+from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.linkml_model import (
     ClassDefinition,
     Definition,
@@ -23,7 +24,6 @@ from linkml_runtime.linkml_model import (
     SlotDefinition,
     TypeDefinition,
 )
-from linkml_runtime.dumpers import yaml_dumper
 from pydantic import BaseModel
 
 from nwb_schema_language import Attribute, Dataset, Group, Schema

nwb_linkml/src/nwb_linkml/adapters/classes.py

@@ -3,16 +3,15 @@ Adapters to linkML classes
 """
 
 from abc import abstractmethod
-from typing import Type, TypeVar, List, Optional
+from typing import List, Optional, Type, TypeVar
 
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
 from pydantic import field_validator
 
-
 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, FlatDtype
+from nwb_schema_language import CompoundDtype, Dataset, DTypeType, FlatDtype, Group, ReferenceDtype
 
 T = TypeVar("T", bound=Type[Dataset] | Type[Group])
 TI = TypeVar("TI", bound=Dataset | Group)

nwb_linkml/src/nwb_linkml/adapters/dataset.py

@@ -1,6 +1,7 @@
 """
 Adapter for NWB datasets to linkml Classes
 """
+
 from abc import abstractmethod
 from typing import ClassVar, Optional, Type
 
@@ -14,7 +15,7 @@ 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, CompoundDtype
+from nwb_schema_language import CompoundDtype, Dataset
 
 
 class DatasetMap(Map):
@@ -141,9 +142,9 @@ class MapScalarAttributes(DatasetMap):
             :linkml:
                 classes:
                 - name: starting_time
-                  description: Timestamp of the first sample in seconds. When timestamps are uniformly
+                  description: Timestamp of the first sample in seconds. When timestamps are
-                    spaced, the timestamp of the first sample can be specified and all subsequent
+                    uniformly spaced, the timestamp of the first sample can be specified and all
-                    ones calculated from the sampling rate attribute.
+                    subsequent ones calculated from the sampling rate attribute.
                   attributes:
                     name:
                       name: name
@@ -328,8 +329,8 @@ class MapArraylike(DatasetMap):
                     - null
                     - null
                     - null
-                  doc: Binary data representing images across frames. If data are stored in an external
+                  doc: Binary data representing images across frames. If data are stored in an
-                    file, this should be an empty 3D array.
+                    external file, this should be an empty 3D array.
             :linkml:
                 slots:
                 - name: data
@@ -754,6 +755,7 @@ def is_1d(cls: Dataset) -> bool:
 
 
 def is_compound(cls: Dataset) -> bool:
+    """Check if dataset has a compound dtype"""
     return (
         isinstance(cls.dtype, list)
         and len(cls.dtype) > 0

nwb_linkml/tests/fixtures.py

@@ -36,7 +36,7 @@ def tmp_output_dir() -> Path:
     path = Path(__file__).parent.resolve() / "__tmp__"
     if path.exists():
         for subdir in path.iterdir():
-            if subdir.name == 'git':
+            if subdir.name == "git":
                 # don't wipe out git repos every time, they don't rly change
                 continue
             elif subdir.is_file() and subdir.parent != path:

nwb_linkml/tests/test_adapters/test_adapter_dataset.py

@@ -1,6 +1,6 @@
 import pytest
-from nwb_linkml.adapters.dataset import MapScalar
 
+from nwb_linkml.adapters.dataset import MapScalar
 from nwb_schema_language import Dataset
 
 

nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py

@@ -265,4 +265,3 @@ class Dataset(DtypeMixin):
     dtype: Optional[Union[List[CompoundDtype], FlatDtype, ReferenceDtype]] = Field(
         default_factory=list
     )
-

pyproject.toml

@@ -24,6 +24,7 @@ target-version = "py311"
 include = ["nwb_linkml/**/*.py", "nwb_schema_language/src/**/*.py", "pyproject.toml"]
 exclude = [
     "docs",
+    "nwb_linkml/src/nwb_linkml/models/**/*.py",
     "nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_language.py",
     "nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py",
     "tests/__tmp__/**/*"