Centralizing and simplifying transformation system in SpatialData

.gitignore

@@ -54,3 +54,29 @@ _version.py
 # benchmarking and profiling
 .asv/
 profile.speedscope.json
+
+# other
+node_modules/
+
+.mypy_cache
+.ruff_cache
+
+# Kilo and plans
+.kilo/
+plans/
+
+# test coverage
+.coverage
+htmlcov/
+
+# local hatch config
+hatch.toml
+
+# Kilo and plans
+.kilo/
+plans/
+
+# test coverage
+.coverage
+htmlcov/
+

pyproject.toml

@@ -39,7 +39,8 @@ dependencies = [
   "networkx",
   "numba>=0.55",
   "numpy",
-  "ome-zarr>=0.16",
+  "ome-zarr>=0.19.2",
+  "ome-zarr-models>=1.8",
   "pandas",
   "pooch",
   "pyarrow",
@@ -51,7 +52,7 @@ dependencies = [
   "spatial-image>=1.2.3",
   "typing-extensions>=4.8",
   "universal-pathlib>=0.2.6",
-  "xarray>=2024.10",
+  "xarray>=2025.4",
   "xarray-spatial>=0.3.5",
   "zarr>=3",
 ]

src/spatialdata/__init__.py

@@ -59,7 +59,6 @@
     "polygon_query": "spatialdata._core.query.spatial_query",
     # _core.spatialdata
     "SpatialData": "spatialdata._core.spatialdata",
-    # _io._utils
     "get_dask_backing_files": "spatialdata._io._utils",
     # _io.format
     "SpatialDataFormatType": "spatialdata._io.format",

src/spatialdata/_core/spatialdata.py

@@ -22,6 +22,7 @@
 from zarr.errors import GroupNotFoundError
 
 from spatialdata._core._elements import Images, Labels, Points, Shapes, Tables
+from spatialdata._core.transformation_manager import TransformationManager
 from spatialdata._core.validation import (
     check_all_keys_case_insensitively_unique,
     check_target_region_column_symmetry,
@@ -132,6 +133,7 @@ def __init__(
         self._shapes: Shapes = Shapes(shared_keys=self._shared_keys)
         self._tables: Tables = Tables(shared_keys=self._shared_keys)
         self.attrs = attrs if attrs else {}  # type: ignore[assignment]
+        self.transformation_manager = TransformationManager()  # Initialize the TransformationManager
 
         element_names = list(chain.from_iterable([e.keys() for e in [images, labels, points, shapes] if e is not None]))