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Transformation manager foundation #1164

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30511a7
chore: added pandas-stubs as dev dependency; helps with type checking
ajkswamy Jul 7, 2026
986f0bb
chore: added local hatch.toml to gitignore
ajkswamy Jul 7, 2026
5e0d12f
chore: Add .kilo and plans to .gitignore
ajkswamy Jul 9, 2026
81bb674
feat: added literals and types for element types and group names
ajkswamy Jul 13, 2026
787770a
feat: added .coverage and htmlcov to gitignore
ajkswamy Jul 14, 2026
9b2d259
feat: transformation manager at the root of spatialdata object
ajkswamy Jul 14, 2026
ca80f91
fix: io_zarr.py mixup between ELEMENT_TYPE_VECTOR/RASTER
ajkswamy Jul 16, 2026
8f9d07f
fix: avoid exposing TransformationManager in spatialdata __init__.py
ajkswamy Jul 16, 2026
dce3dc6
fix: element associated to cs -> element belonging to cs
ajkswamy Jul 16, 2026
367d99e
refac: transformation_manager now uses nx.MultiDiGraph
ajkswamy Jul 17, 2026
65aadb6
refac: tests to match new transformation manager implementation
ajkswamy Jul 17, 2026
611abee
fix: restored unintentionally removed functions + others fixes
ajkswamy Jul 17, 2026
fd042a6
feat: custom error messages for transformation graph elements
ajkswamy Jul 17, 2026
070db93
feat: custom exceptions for transform manager
ajkswamy Jul 17, 2026
5314e02
refac: transform manager attributes private; added missing method
ajkswamy Jul 17, 2026
5eadef4
feat: more custom error and warnings + fixes
ajkswamy Jul 20, 2026
ab98633
feat: more test coverage + fixes
ajkswamy Jul 21, 2026
ea28e55
feat: support for transformation management in graph with mutliple edges
ajkswamy Jul 22, 2026
932703c
fix: fixes in tests + renaming for readability
ajkswamy Jul 22, 2026
7658a19
fix: typing Affine Transform
ajkswamy Jul 23, 2026
3692729
feat: TransformationManager return Sequence instead of list
ajkswamy Jul 23, 2026
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11 changes: 11 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -61,3 +61,14 @@ node_modules/
uv.lock
pixi.lock

# local hatch config
hatch.toml

# Kilo and plans
.kilo/
plans/

# test coverage
.coverage
htmlcov/

1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up @@ -64,6 +64,7 @@ extra = [
[dependency-groups]
dev = [
"bump2version",
"pandas-stubs>=3.0.3.260530",
]
test = [
"pytest",
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4 changes: 3 additions & 1 deletion src/spatialdata/__init__.py
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Expand Up @@ -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",
Expand Down Expand Up @@ -208,6 +207,9 @@ def __dir__() -> list[str]:
# _core.spatialdata
from spatialdata._core.spatialdata import SpatialData

# _core.transformation_manager
from spatialdata._core.transformation_manager import TransformationManager
Comment on lines +210 to +211

@LucaMarconato LucaMarconato Jul 16, 2026

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Same here.

@ajkswamy ajkswamy Jul 21, 2026

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Done


# _io._utils
from spatialdata._io._utils import get_dask_backing_files

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2 changes: 2 additions & 0 deletions src/spatialdata/_core/spatialdata.py
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Expand Up @@ -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,
Expand Down Expand Up @@ -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]))

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