updated to use validated_property and BinaryFile

nipype · Sep 17, 2024 · af43bb6 · af43bb6
1 parent 447e7a1
commit af43bb6
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Showing 4 changed files with 17 additions and 16 deletions.
diff --git a/.github/workflows/ci-cd.yml b/.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

diff --git a/related-packages/fileformats/fileformats/medimage_mrtrix3/dwi.py b/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))
 

diff --git a/related-packages/fileformats/fileformats/medimage_mrtrix3/image.py b/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)
 
@@ -84,7 +84,7 @@ def __attrs_post_init__(self):
         super().__attrs_post_init__()
 
 
-class ImageDataFile(File):
+class ImageDataFile(BinaryFile):
 
     ext = ".dat"
 

diff --git a/related-packages/fileformats/fileformats/medimage_mrtrix3/track.py b/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"