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fix hdmf forwardrefs, remove numpy types temporarily

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sneakers-the-rat 2024-07-31 01:54:14 -07:00
parent 776078ae67
commit 1d527d8f71
Signed by untrusted user who does not match committer: jonny
GPG key ID: 6DCB96EF1E4D232D
2 changed files with 10 additions and 9 deletions
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10
nwb_linkml/src/nwb_linkml/includes/hdmf.py
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@ -22,7 +22,7 @@ class DynamicTableMixin(BaseModel):
""" """
model_config = ConfigDict(extra="allow") model_config = ConfigDict(extra="allow")
__pydantic_extra__: Dict[str, Union[list, "NDArray", "VectorData"]] __pydantic_extra__: Dict[str, Union[list, "NDArray", "VectorDataMixin"]]
NON_COLUMN_FIELDS: ClassVar[tuple[str]] = ( NON_COLUMN_FIELDS: ClassVar[tuple[str]] = (
"name", "name",
"colnames", "colnames",
@ -33,15 +33,15 @@ class DynamicTableMixin(BaseModel):
colnames: List[str] = Field(default_factory=list) colnames: List[str] = Field(default_factory=list)
@property @property
def _columns(self) -> Dict[str, Union[list, "NDArray", "VectorData"]]: def _columns(self) -> Dict[str, Union[list, "NDArray", "VectorDataMixin"]]:
return {k: getattr(self, k) for i, k in enumerate(self.colnames)} return {k: getattr(self, k) for i, k in enumerate(self.colnames)}
@property @property
def _columns_list(self) -> List[Union[list, "NDArray", "VectorData"]]: def _columns_list(self) -> List[Union[list, "NDArray", "VectorDataMixin"]]:
return [getattr(self, k) for i, k in enumerate(self.colnames)] return [getattr(self, k) for i, k in enumerate(self.colnames)]
@overload @overload
def __getitem__(self, item: str) -> Union[list, "NDArray", "VectorData"]: ... def __getitem__(self, item: str) -> Union[list, "NDArray", "VectorDataMixin"]: ...
@overload @overload
def __getitem__(self, item: int) -> DataFrame: ... def __getitem__(self, item: int) -> DataFrame: ...
@ -54,7 +54,7 @@ class DynamicTableMixin(BaseModel):
DataFrame, DataFrame,
list, list,
"NDArray", "NDArray",
"VectorData", "VectorDataMixin",
]: ... ]: ...
@overload @overload

9
nwb_linkml/src/nwb_linkml/lang_elements.py
View file

@ -12,7 +12,7 @@ from linkml_runtime.linkml_model import (
TypeDefinition, TypeDefinition,
) )
from nwb_linkml.maps import flat_to_linkml, flat_to_np from nwb_linkml.maps import flat_to_linkml
def _make_dtypes() -> List[TypeDefinition]: def _make_dtypes() -> List[TypeDefinition]:
@ -27,12 +27,13 @@ def _make_dtypes() -> List[TypeDefinition]:
if nwbtype.startswith("uint"): if nwbtype.startswith("uint"):
amin = 0 amin = 0
np_type = flat_to_np[nwbtype] # FIXME: Restore numpy types when we wrap them :)
# np_type = flat_to_np[nwbtype]
repr_string = f"np.{np_type.__name__}" if np_type.__module__ == "numpy" else None # repr_string = f"np.{np_type.__name__}" if np_type.__module__ == "numpy" else None
atype = TypeDefinition( atype = TypeDefinition(
name=nwbtype, minimum_value=amin, typeof=linkmltype, repr=repr_string name=nwbtype, minimum_value=amin, typeof=linkmltype, # repr=repr_string
) )
DTypeTypes.append(atype) DTypeTypes.append(atype)
return DTypeTypes return DTypeTypes