fix issue with add_mag() using wrong shard shape for zarr2 (#1315)

* fix issue with add_mag() using wrong shard shape for zarr2

* lint and update changelog.

* update changelog.

Author: markbader

webknossos/Changelog.md

@@ -19,6 +19,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Changed
 
 ### Fixed
+- Fixed an issue that creates an Error when `add_mag()` was called just with a `chunk_shape`. [#1315](https://github.com/scalableminds/webknossos-libs/pull/1315)
 
 
 ## [2.3.8](https://github.com/scalableminds/webknossos-libs/releases/tag/v2.3.8) - 2025-05-28

webknossos/tests/dataset/test_layer.py

@@ -4,6 +4,7 @@
 import tensorstore
 
 import webknossos as wk
+from webknossos.dataset.data_format import DataFormat
 
 
 def test_add_mag_from_zarrarray(tmp_path: Path) -> None:
@@ -62,3 +63,18 @@ def test_add_mag_from_zarrarray(tmp_path: Path) -> None:
     assert layer.get_mag("1").info.num_channels == 1
     assert layer.get_mag("1").info.dimension_names == ("c", "x", "y", "z")
     assert (layer.get_mag("1").read()[0] == zarr_data).all()
+
+
+def test_add_mag_with_chunk_shape_zarr2(tmp_path: Path) -> None:
+    dataset = wk.Dataset(
+        tmp_path / "test_add_mag_with_chunk_shape_zarr2", voxel_size=(10, 10, 10)
+    )
+    layer = dataset.add_layer(
+        "color",
+        wk.COLOR_CATEGORY,
+        data_format=DataFormat.Zarr,
+        bounding_box=wk.BoundingBox((0, 0, 0), (16, 16, 16)),
+    )
+    mag = layer.add_mag("1", chunk_shape=(8, 8, 8))
+
+    assert mag.info.chunk_shape == (8, 8, 8)

webknossos/webknossos/dataset/__init__.py

@@ -22,6 +22,7 @@
 from .layer_categories import COLOR_CATEGORY, SEGMENTATION_CATEGORY, LayerCategoryType
 from .length_unit import LengthUnit
 from .mag_view import MagView
+from .properties import VoxelSize
 from .remote_folder import RemoteFolder
 from .sampling_modes import SamplingModes
 from .view import View

webknossos/webknossos/dataset/layer.py

@@ -619,7 +619,7 @@ def add_mag(
         )
         if shard_shape is None:
             if self.data_format == DataFormat.Zarr:
-                shard_shape = DEFAULT_CHUNK_SHAPE
+                shard_shape = chunk_shape
             else:
                 shard_shape = DEFAULT_SHARD_SHAPE