changed signature of read_metadata to have collection instead of sequence

Author: tclose

extras/fileformats/extras/application/medical.py

@@ -9,7 +9,7 @@
 
 @extra_implementation(FileSet.read_metadata)
 def dicom_read_metadata(
-    dicom: Dicom, selected_keys: ty.Optional[ty.Sequence[str]] = None
+    dicom: Dicom, selected_keys: ty.Optional[ty.Collection[str]] = None
 ) -> ty.Mapping[str, ty.Any]:
     dcm = pydicom.dcmread(
         dicom.fspath,

fileformats/core/fileset.py

@@ -92,13 +92,13 @@ class FileSet(DataType):
     # Member attributes
     fspaths: ty.FrozenSet[Path]
     _explicit_metadata: ty.Optional[ty.Mapping[str, ty.Any]]
-    _metadata_keys: ty.Optional[ty.List[str]]
+    _metadata_keys: ty.Optional[ty.Collection[str]]
 
     def __init__(
         self,
         fspaths: FspathsInputType,
         metadata: ty.Optional[ty.Dict[str, ty.Any]] = None,
-        metadata_keys: ty.Optional[ty.List[str]] = None,
+        metadata_keys: ty.Optional[ty.Collection[str]] = None,
     ):
         self._explicit_metadata = metadata
         self._metadata_keys = metadata_keys
@@ -263,7 +263,7 @@ def metadata(self) -> ty.Mapping[str, ty.Any]:
 
     @extra
     def read_metadata(
-        self, selected_keys: ty.Optional[ty.Sequence[str]] = None
+        self, selected_keys: ty.Optional[ty.Collection[str]] = None
     ) -> ty.Mapping[str, ty.Any]:
         """Reads any metadata associated with the fileset and returns it as a dict
 

fileformats/core/mixin.py

@@ -183,7 +183,7 @@ def header(self) -> "fileformats.core.FileSet":
         return self.header_type(self.select_by_ext(self.header_type))  # type: ignore[attr-defined]
 
     def read_metadata(
-        self, selected_keys: ty.Optional[ty.Sequence[str]] = None
+        self, selected_keys: ty.Optional[ty.Collection[str]] = None
     ) -> ty.Mapping[str, ty.Any]:
         header: ty.Dict[str, ty.Any] = self.header.load()  # type: ignore[attr-defined]
         if selected_keys:
@@ -221,7 +221,7 @@ def side_cars(self) -> ty.Tuple["fileformats.core.FileSet", ...]:
         return tuple(tp(self.select_by_ext(tp)) for tp in self.side_car_types)  # type: ignore[attr-defined]
 
     def read_metadata(
-        self, selected_keys: ty.Optional[ty.Sequence[str]] = None
+        self, selected_keys: ty.Optional[ty.Collection[str]] = None
     ) -> ty.Mapping[str, ty.Any]:
         metadata: ty.Dict[str, ty.Any] = dict(self.primary_type.read_metadata(self, selected_keys=selected_keys))  # type: ignore[arg-type]
         for side_car in self.side_cars:

fileformats/core/tests/test_general.py

@@ -135,7 +135,7 @@ class ImageWithInlineHeader(File):
     header_separator = b"---END HEADER---"
 
     def read_metadata(
-        self, selected_keys: ty.Optional[ty.Sequence[str]] = None
+        self, selected_keys: ty.Optional[ty.Collection[str]] = None
     ) -> ty.Mapping[str, ty.Any]:
         hdr = self.contents.split(self.header_separator)[0].decode("utf-8")
         return {k: int(v) for k, v in (ln.split(":") for ln in hdr.splitlines())}

fileformats/core/tests/test_metadata.py

@@ -11,7 +11,7 @@ class FileWithMetadata(File):
 
 @extra_implementation(FileSet.read_metadata)
 def aformat_read_metadata(
-    mf: FileWithMetadata, selected_keys: ty.Optional[ty.Sequence[str]] = None
+    mf: FileWithMetadata, selected_keys: ty.Optional[ty.Collection[str]] = None
 ) -> ty.Mapping[str, ty.Any]:
     with open(mf) as f:
         metadata = f.read()

fileformats/core/tests/test_mixin.py

@@ -108,7 +108,7 @@ class ImageWithInlineHeader(File):
     header_separator = b"---END HEADER---"
 
     def read_metadata(
-        self, selected_keys: ty.Optional[ty.Sequence[str]] = None
+        self, selected_keys: ty.Optional[ty.Collection[str]] = None
     ) -> ty.Mapping[str, ty.Any]:
         hdr = self.contents.split(self.header_separator)[0].decode("utf-8")
         return dict(ln.split(":") for ln in hdr.splitlines())

fileformats/image/raster.py

@@ -13,7 +13,7 @@
 
 DataArrayType: TypeAlias = (
     ty.Any
-)  # "numpy.typing.NDArray[ty.Union[np.float_, np.int_]]"
+)  # "numpy.typing.NDArray[ty.Union[np.floating, np.integer]]"
 
 
 class RasterImage(Image):