Chunk shape (#706)

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* WIP

* format

* re-add upath stub

* format

* pr feedback

Author: normanrz

webknossos/Changelog.md

@@ -13,6 +13,7 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.10.12...HEAD)
 
 ### Breaking Changes
+- Renamed `chunk_size` arguments to `chunk_shape`. `chunk_size` is still available as keyword-only argument, but deprecated. [#706](https://github.com/scalableminds/webknossos-libs/pull/706)
 
 ### Added
 

webknossos/examples/dataset_usage.py

@@ -61,7 +61,7 @@ def main() -> None:
 
     copy_of_dataset = dataset.copy_dataset(
         "testoutput/copy_of_dataset",
-        chunk_size=8,
+        chunk_shape=8,
         chunks_per_shard=8,
         compress=True,
     )

webknossos/script_collection/globalize_floodfill.py

@@ -111,7 +111,7 @@ def execute_floodfill(
     source_id: int,
     target_id: int,
 ) -> None:
-    cube_size = data_mag.info.shard_size
+    cube_size = data_mag.info.shard_shape
     cube_bbox = BoundingBox(Vec3Int(0, 0, 0), cube_size)
     chunk_with_relative_seed: List[Tuple[Vec3Int, Vec3Int]] = [
         get_chunk_pos_and_offset(seed_position, cube_size)
@@ -266,7 +266,7 @@ def merge_with_fallback_layer(
         ]
         output_mag = output_layer.get_mag(input_segmentation_mag.mag)
 
-        cube_size = output_mag.info.chunk_size[0] * output_mag.info.chunks_per_shard[0]
+        cube_size = output_mag.info.chunk_shape[0] * output_mag.info.chunks_per_shard[0]
         chunks_with_bboxes = BoundingBox.group_boxes_with_aligned_mag(
             bboxes, Mag(cube_size)
         )