v0.4.0

What's Changed

Added

• Docker automatic build by @LucaMarconato in #841
• Partial reading by @aeisenbarth in #765
• Add warning (raster models) when large chunks are detected by @LucaMarconato in #874
• allow filtering by ids by @melonora in #627

Changed

• Replace pip with uv for test workflow by @LucaMarconato in #877
• Specify NGFF 0.6-dev in output data by @LucaMarconato in #849

Fixed

• Restore support for Python >=3.13 by @LucaMarconato in #840
• bug with 3d data test in transform_to_data_extent by @LucaMarconato in #787
• Fix JoinTypes.dict empty python 3.13 by @LucaMarconato in #853
• Fix rechunk bug after spatial query by @LucaMarconato in #861
• Fix bug join operation with non-annotating table by @LucaMarconato in #864
• Fix bug custom region_key concatenate by @LucaMarconato in #871
• fix suffix concatenate when each table annotates > 1 elements by @LucaMarconato in #873
• fix max chunk size calculation by @LucaMarconato in #876
• pin numba to earlierst version supporting python 3.10 by @giovp in #883
• Resolve AnnData FutureWarnings The dtype argument is deprecated by @Zethson in #896

Full Changelog: v0.3.0...v0.4.0

v0.3.0

What's Changed

Major

• Adding attrs at the SpatialData object level by @quentinblampey in #711
• More robust name validation (full naming changes described in the PR) by @aeisenbarth in #703

Minor

• Add asv benchmark code by @berombau in #784
• Add relabel_sequential() for relabeling label data after map_raster() by @ArneDefauw in #664
• validate tables while parsing by @melonora in #808
• rasterize_bins() can now produce a labels element by @ArneDefauw in #811
• Improved docs: adding glossary + refactor API reference display by @quentinblampey in #785
• add support for layer selection in get_values() method by @Sonja-Stockhaus in #818
• Added a spatialdata-io mirror by @quentinblampey in #778
• get_attrs(): helper function to return keys in the sdata.attrs slot in an specific format by @timtreis in #806

Fixed

• relaxed fsspec version by @LucaMarconato in #798
• fix for to_polygons() when using processes instead of threads in dask by @ArneDefauw in #756
• Fix transform_to_data_extent converting labels to images by @aeisenbarth in #791
• add warning when running bounding box query if points is present by @BioinfoTongLI in #777

Join operations

• fix join non matching table by @melonora in #813
• Fix bug with join with duplicate obs indices by @melonora in #822
• fix index cannot be reshaped with inner join by @melonora in #832
• fix index error left join by @melonora in #833

New Contributors

• @BioinfoTongLI made their first contribution in #777
• @Sonja-Stockhaus made their first contribution in #818

Full Changelog: v0.2.6...v0.3.0

v0.2.7-pre0

Making a pre-release to unlock the CI in spatialdata-io, but before the full release #815 needs to be addressed.

v0.2.6

[0.2.6] - 2024-11-26

Added

• Added set_channel_names method to SpatialData to change the channel names of an
  image element in SpatialData #786
• Added write_channel_names method to SpatialData to overwrite channel metadata on disk
  without overwriting the image array itself. #786

Changed

• Argument c_coords is moved out of kwargs for the ImageModels. #779
• get_channels is marked for deprecation in SpatialData v0.3.0. Function is replaced
  by get_channel_names #786
• Updated dependency of multiscale-spatial-image #792
• Adjust to new version of xarray with DataTree # 752

Fixed

• Updated deprecated default stages of pre-commit #771
• Preserve points feature_key during queries #794

v0.2.6-pre0

fix CHANGELOG.md

v0.2.5post0

Fixed broken documentation (a release was made from a machine with an older version of the spatialdata-notebook submodule)

v0.2.5

[0.2.5] - 2024-11-06

Fixed

• Incompatibility issues due to newest release of multiscale-spatial-image #760

v0.2.4

[0.2.4] - 2024-11-06

Major

• Enable vectorization of bounding_box_query for all SpatialData elements. #699

Minor

• Added shortest_path parameter to get_transformation_between_coordinate_systems #714
• Added get_pyramid_levels() utils API #719
• Improved ergonomics of concatenate() when element names are non-unique #720
• Improved performance of writing images with multiscales #577

v0.2.3

[0.2.3] - 2024-09-25

Minor

• Added clip: bool = False parameter to polygon_query() #670
• Add sort parameter to PointsModel.parse() #672

Fixed

• Fix interpolation artifact multiscale computation for labels #697

v0.2.2

[0.2.2] - 2024-08-07

Major

• New disk format for shapes using GeoParquet (the change is backward compatible) #542

Minor

• Add return_background as argument to get_centroids and get_element_instances #621
• Ability to save data using older disk formats #542

Fixed

• Circles validation now checks for inf or nan radii #653
• Bug with table name in torch dataset #654 @LLehner