Transformation manager foundation

.gitignore

@@ -61,3 +61,14 @@ node_modules/
 uv.lock
 pixi.lock
 
+# local hatch config
+hatch.toml
+
+# Kilo and plans
+.kilo/
+plans/
+
+# test coverage
+.coverage
+htmlcov/
+

pyproject.toml

@@ -64,6 +64,7 @@ extra  = [
 [dependency-groups]
 dev = [
     "bump2version",
+    "pandas-stubs>=3.0.3.260530",
 ]
 test = [
     "pytest",

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,
@@ -130,6 +131,7 @@ 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]))