Merge remote-tracking branch 'origin/refactor/split-wsireader-into-modules' into refactor/split-wsireader-into-modules

Author: shaneahmed

tiatoolbox/wsicore/wsireader.py

@@ -40,7 +40,6 @@
     re,
     zarr,
 )
-from tiatoolbox.wsicore.wsireader import ArrayView
 
 __all__ = [
     # Standard library imports (re-exported for backward compatibility)

tiatoolbox/wsicore/wsireader/__init__.py

@@ -20,15 +20,16 @@
 
 # Import base classes and utility functions
 from .base import (
-    WSIReader,
+    ArrayView,
     VirtualWSIReader,
+    WSIReader,
     _handle_tiff_wsi,
     _handle_virtual_wsi,
     fix_mangled_url_by_pathlib,
     is_dicom,
     is_ngff,
     is_tiled_tiff,
-    is_zarr, ArrayView,
+    is_zarr,
 )
 from .dicom import DICOMWSIReader
 from .fsspec_json import FsspecJsonWSIReader

tiatoolbox/wsicore/wsireader/base.py

@@ -37,7 +37,15 @@
     )
     from tiatoolbox.wsicore import WSIReaderParams
     from tiatoolbox.wsicore.metadata.ngff import Multiscales
-    from . import TIFFWSIReader, OpenSlideWSIReader, DICOMWSIReader, FsspecJsonWSIReader, AnnotationStoreReader, NGFFWSIReader
+
+    from . import (
+        AnnotationStoreReader,
+        DICOMWSIReader,
+        FsspecJsonWSIReader,
+        NGFFWSIReader,
+        OpenSlideWSIReader,
+        TIFFWSIReader,
+    )
 
 pixman_warning()
 

tiatoolbox/wsicore/wsireader/fsspec_json.py

@@ -19,11 +19,11 @@
 from tiatoolbox import logger
 from tiatoolbox.wsicore.wsimeta import WSIMeta
 
-from .base import WSIReader, ArrayView
+from .base import ArrayView, WSIReader
 from .tiff import TIFFWSIReaderDelegate
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.type_hints import IntPair, Resolution, Units, IntBounds
+    from tiatoolbox.type_hints import IntBounds, IntPair, Resolution, Units
 
 
 class FsspecJsonWSIReader(WSIReader):

tiatoolbox/wsicore/wsireader/ngff.py

@@ -12,10 +12,10 @@
 from tiatoolbox import logger, utils
 from tiatoolbox.wsicore.wsimeta import WSIMeta
 
-from .base import WSIReader, ArrayView
+from .base import ArrayView, WSIReader
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.type_hints import Resolution, Units, IntPair, IntBounds
+    from tiatoolbox.type_hints import IntBounds, IntPair, Resolution, Units
     from tiatoolbox.wsicore import WSIReaderParams
 
 

tiatoolbox/wsicore/wsireader/tiff.py

@@ -3,29 +3,29 @@
 from __future__ import annotations
 
 from collections import defaultdict
-from datetime import datetime, UTC
+from datetime import UTC, datetime
 from numbers import Number
 from pathlib import Path
 from typing import TYPE_CHECKING
 
+import matplotlib.colors as mcolors
 import numpy as np
 import tifffile
 import zarr
 from defusedxml import ElementTree
 from tifffile import TiffPages
-from zarr.storage import MemoryStore
 from zarr.experimental.cache_store import CacheStore
+from zarr.storage import MemoryStore
 
 from tiatoolbox import logger, utils
+from tiatoolbox.utils import postproc_defs
 from tiatoolbox.utils.exceptions import FileNotSupportedError
 from tiatoolbox.wsicore.wsimeta import WSIMeta
-import matplotlib.colors as mcolors
 
-from .base import WSIReader, ArrayView
-from tiatoolbox.utils import postproc_defs
+from .base import ArrayView, WSIReader
 
 if TYPE_CHECKING:  # pragma: no cover
-    from tiatoolbox.type_hints import IntPair, Resolution, Units, IntBounds
+    from tiatoolbox.type_hints import IntBounds, IntPair, Resolution, Units
 
 
 class TIFFWSIReader(WSIReader):

tiatoolbox/wsicore/wsireader/transformed.py

@@ -15,7 +15,7 @@
 from tiatoolbox import utils
 from tiatoolbox.wsicore.wsimeta import WSIMeta
 
-from .base import WSIReader, VirtualWSIReader
+from .base import VirtualWSIReader, WSIReader
 
 if TYPE_CHECKING:  # pragma: no cover
     from tiatoolbox.type_hints import IntPair, Resolution, Units