Merge pull request #25 from nipype/fileformats-typing

fixes typing of read_metadata

Author: tclose

.github/workflows/ci-cd.yml

@@ -115,19 +115,19 @@ jobs:
           --log-errors
           --latest
       - name: Upload MRtrix3 install
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: MRtrix3
           path: ${{ env.MRTRIX_INSTALL}}
       - name: Upload auto-gen pydra
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: AutoGen
           path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
       - name: Write version file
         run: echo $MRTRIX_VERSION > mrtrix3_version.txt
       - name: Upload version file
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: VersionFile
           path: mrtrix3_version.txt
@@ -352,7 +352,7 @@ jobs:
         git tag -d ${{ steps.latest_tag.outputs.TAG }};
         git tag -a ${{ steps.latest_tag.outputs.TAG }} -m"Tag used to create a pydra-mrtrix3 $MRTRIX_VERSION release";
     - name: Set up Python 3.11
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       with:
         python-version: 3.11
     - name: Install build tools
@@ -362,7 +362,7 @@ jobs:
     - name: Check distributions
       run: twine check dist/*
     - name: Upload sdist
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name: SDist
         path: dist/*.tar.gz

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/dwi.py

@@ -1,3 +1,4 @@
+from fileformats.core import validated_property
 from fileformats.core.mixin import WithAdjacentFiles
 from fileformats.medimage import DwiEncoding, Nifti1, NiftiGz, NiftiX, NiftiGzX
 from .image import ImageFormat, ImageHeader, ImageFormatGz
@@ -11,7 +12,7 @@ class BFile(DwiEncoding):
 
 # NIfTI file format gzipped with BIDS side car
 class WithBFile(WithAdjacentFiles):
-    @property
+    @validated_property
     def encoding(self) -> BFile:
         return BFile(self.select_by_ext(BFile))
 

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

@@ -1,7 +1,7 @@
 from pathlib import Path
 import typing as ty
-from fileformats.core import FileSet, extra_implementation
-from fileformats.generic import File
+from fileformats.core import FileSet, extra_implementation, validated_property
+from fileformats.generic import BinaryFile
 from fileformats.application.archive import BaseGzip
 from fileformats.core.mixin import WithMagicNumber
 from fileformats.core.exceptions import FormatMismatchError
@@ -12,12 +12,12 @@ class MultiLineMetadataValue(list):
     pass
 
 
-class BaseMrtrixImage(WithMagicNumber, fileformats.medimage.MedicalImage, File):
+class BaseMrtrixImage(WithMagicNumber, fileformats.medimage.MedicalImage, BinaryFile):
 
     magic_number = b"mrtrix image\n"
     binary = True
 
-    @property
+    @validated_property
     def data_fspath(self):
         data_fspath = self.metadata["file"].split()[0]
         if data_fspath == ".":
@@ -48,8 +48,8 @@ class ImageFormat(BaseMrtrixImage):
     ext = ".mif"
     iana_mime = "application/x-mrtrix-image-format"
 
-    @property
-    def check_data_file(self):
+    @validated_property
+    def _check_data_file(self):
         if self.data_fspath != self.fspath:
             raise FormatMismatchError(
                 f"Data file ('{self.data_fspath}') is not set to the same file as header "
@@ -73,7 +73,7 @@ class ImageHeader(BaseMrtrixImage):
     ext = ".mih"
     iana_mime = "application/x-mrtrix-image-header"
 
-    @property
+    @validated_property
     def data_file(self):
         return ImageDataFile(self.data_fspath)
 
@@ -84,14 +84,14 @@ def __attrs_post_init__(self):
         super().__attrs_post_init__()
 
 
-class ImageDataFile(File):
+class ImageDataFile(BinaryFile):
 
     ext = ".dat"
 
 
 @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

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

@@ -1,8 +1,8 @@
-from fileformats.generic import File
+from fileformats.generic import BinaryFile
 from fileformats.core.mixin import WithMagicNumber
 
 
-class Tracks(WithMagicNumber, File):
+class Tracks(WithMagicNumber, BinaryFile):
 
     ext = ".tck"
     magic_number = b"mrtrix tracks\n"