From b6af8c97187e8025111eb5c074eff858c4f4e1cd Mon Sep 17 00:00:00 2001 From: sneakers-the-rat Date: Tue, 9 Jul 2024 03:32:37 -0700 Subject: [PATCH] lint --- nwb_linkml/conftest.py | 27 ++++++++++++------- nwb_linkml/src/nwb_linkml/adapters/adapter.py | 2 +- nwb_linkml/src/nwb_linkml/adapters/classes.py | 5 ++-- nwb_linkml/src/nwb_linkml/adapters/dataset.py | 14 +++++----- nwb_linkml/tests/fixtures.py | 2 +- .../test_adapters/test_adapter_dataset.py | 2 +- .../datamodel/nwb_schema_pydantic.py | 1 - pyproject.toml | 1 + 8 files changed, 31 insertions(+), 23 deletions(-) diff --git a/nwb_linkml/conftest.py b/nwb_linkml/conftest.py index 1bd1ae3..450875f 100644 --- a/nwb_linkml/conftest.py +++ b/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 sybil import Document -from sybil import Sybil, Region +from doctest import ELLIPSIS, NORMALIZE_WHITESPACE +from typing import Generator + +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=[ - parse_adapter_blocks - ], + parsers=[parse_adapter_blocks], patterns=["adapters/*.py"], ) diff --git a/nwb_linkml/src/nwb_linkml/adapters/adapter.py b/nwb_linkml/src/nwb_linkml/adapters/adapter.py index 9d0ea51..9984ecb 100644 --- a/nwb_linkml/src/nwb_linkml/adapters/adapter.py +++ b/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 diff --git a/nwb_linkml/src/nwb_linkml/adapters/classes.py b/nwb_linkml/src/nwb_linkml/adapters/classes.py index db65ead..93a7cd7 100644 --- a/nwb_linkml/src/nwb_linkml/adapters/classes.py +++ b/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) diff --git a/nwb_linkml/src/nwb_linkml/adapters/dataset.py b/nwb_linkml/src/nwb_linkml/adapters/dataset.py index 3918235..c1e72d0 100644 --- a/nwb_linkml/src/nwb_linkml/adapters/dataset.py +++ b/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 - spaced, the timestamp of the first sample can be specified and all subsequent - ones calculated from the sampling rate attribute. + description: Timestamp of the first sample in seconds. When timestamps are + uniformly spaced, the timestamp of the first sample can be specified and all + 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 - file, this should be an empty 3D array. + doc: Binary data representing images across frames. If data are stored in an + 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 diff --git a/nwb_linkml/tests/fixtures.py b/nwb_linkml/tests/fixtures.py index e13d91f..e4b8fae 100644 --- a/nwb_linkml/tests/fixtures.py +++ b/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: diff --git a/nwb_linkml/tests/test_adapters/test_adapter_dataset.py b/nwb_linkml/tests/test_adapters/test_adapter_dataset.py index cb74000..21357a8 100644 --- a/nwb_linkml/tests/test_adapters/test_adapter_dataset.py +++ b/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 diff --git a/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py b/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py index e994608..ef04312 100644 --- a/nwb_schema_language/src/nwb_schema_language/datamodel/nwb_schema_pydantic.py +++ b/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 ) - diff --git a/pyproject.toml b/pyproject.toml index d40f248..2ea2cdc 100644 --- a/pyproject.toml +++ b/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__/**/*"