fixes typing of read_metadata

Author: tclose

conftest.py

@@ -1,4 +1,5 @@
 import os
+import typing as ty
 import pytest
 from pathlib import Path
 
@@ -22,9 +23,10 @@ def cli_parse_only():
 if os.getenv("_PYTEST_RAISE", "0") != "0":
 
     @pytest.hookimpl(tryfirst=True)
-    def pytest_exception_interact(call):
-        raise call.excinfo.value
+    def pytest_exception_interact(call: pytest.CallInfo[ty.Any]) -> None:
+        if call.excinfo is not None:
+            raise call.excinfo.value
 
     @pytest.hookimpl(tryfirst=True)
-    def pytest_internalerror(excinfo):
+    def pytest_internalerror(excinfo: pytest.ExceptionInfo[BaseException]) -> None:
         raise excinfo.value

related-packages/fileformats-extras/conftest.py

@@ -2,6 +2,7 @@
 import logging
 from pathlib import Path
 import tempfile
+import typing as ty
 import pytest
 from fileformats.medimage import DicomDir, Nifti
 
@@ -24,11 +25,12 @@
 if os.getenv("_PYTEST_RAISE", "0") != "0":
 
     @pytest.hookimpl(tryfirst=True)
-    def pytest_exception_interact(call):
-        raise call.excinfo.value
+    def pytest_exception_interact(call: pytest.CallInfo[ty.Any]) -> None:
+        if call.excinfo is not None:
+            raise call.excinfo.value
 
     @pytest.hookimpl(tryfirst=True)
-    def pytest_internalerror(excinfo):
+    def pytest_internalerror(excinfo: pytest.ExceptionInfo[BaseException]) -> None:
         raise excinfo.value
 
 

related-packages/fileformats-extras/fileformats/extras/medimage_mrtrix3/gradients.py

@@ -1,11 +1,15 @@
-import numpy as np
+import typing  # noqa: F401
+import numpy.typing
 from fileformats.core import extra_implementation
 from fileformats.medimage import DwiEncoding
+from fileformats.medimage.diffusion import EncodingArrayType
 from fileformats.medimage_mrtrix3 import BFile
 
 
 @extra_implementation(DwiEncoding.read_array)
-def bfile_read_array(bfile: BFile) -> np.ndarray:
-    return np.asarray(
+def bfile_read_array(
+    bfile: BFile,
+) -> EncodingArrayType:
+    return numpy.asarray(
         [[float(x) for x in ln.split()] for ln in bfile.read_contents().splitlines()]
     )

related-packages/fileformats/conftest.py

@@ -1,5 +1,6 @@
 import os
 import logging
+import typing as ty
 from pathlib import Path
 import tempfile
 import pytest
@@ -23,11 +24,12 @@
 if os.getenv("_PYTEST_RAISE", "0") != "0":
 
     @pytest.hookimpl(tryfirst=True)
-    def pytest_exception_interact(call):
-        raise call.excinfo.value
+    def pytest_exception_interact(call: pytest.CallInfo[ty.Any]) -> None:
+        if call.excinfo is not None:
+            raise call.excinfo.value
 
     @pytest.hookimpl(tryfirst=True)
-    def pytest_internalerror(excinfo):
+    def pytest_internalerror(excinfo: pytest.ExceptionInfo[BaseException]) -> None:
         raise excinfo.value
 
 

related-packages/fileformats/fileformats/medimage_mrtrix3/image.py

@@ -91,7 +91,7 @@ class ImageDataFile(File):
 
 @extra_implementation(FileSet.read_metadata)
 def mrtrix_read_metadata(
-    mif: BaseMrtrixImage, selected_keys: ty.Optional[ty.Collection[str]] = None
+    mif: BaseMrtrixImage, **kwargs: ty.Any
 ) -> ty.Mapping[str, ty.Any]:
     metadata = {}
     with open(mif.fspath, "rb") as f:
@@ -127,6 +127,4 @@ def mrtrix_read_metadata(
             else:
                 metadata[key] = value
             line = f.readline().decode("utf-8")
-    if selected_keys:
-        metadata = {k: v for k, v in metadata.items() if k in selected_keys}
     return metadata