v0.7.3

What's Changed

Added

• Add Python 3.14 support by @LucaMarconato in #1114

Changed

• New lazy to_multiscale() for labels by @LucaMarconato in #1068
• Change lower bound anndata by @LucaMarconato in #1083

Fixed

• Fix TableModel validator to accept pandas StringDtype by @jlr13 in #1063
• test: make pre-release tests work by @flying-sheep in #1071
• Fix for FutureWarning: functools.partial ... by @selmanozleyen in #1076
• Fix transform graph by @melonora in #1077
• Fix performance regression for multiscale images (#1079) by @LucaMarconato in #1080
• Faster spatialdata import time by @LucaMarconato in #1075
• Preserve attrs on Dask DataFrame sample() by @LiudengZhang in #1088
• ome zarr chunks by @ArneDefauw in #1092
• fix: don't lower bound anndata so high by @ilan-gold in #1102
• Workaround for KeyError 'ome' when writing multiscale images by @LucaMarconato in #1115
• Reduce warnings by @LucaMarconato in #1113
• Reduce time cost of tests by @LucaMarconato in #1116
• Fix numba JIT configuration failing on airflow runner by @LucaMarconato in #1117

New Contributors

• @jlr13 made their first contribution in #1063
• @flying-sheep made their first contribution in #1071
• @selmanozleyen made their first contribution in #1076
• @LiudengZhang made their first contribution in #1088

Full Changelog: v0.7.2...v0.7.3

v0.7.3a2

What's Changed

Added

• Add Python 3.14 support by @LucaMarconato in #1114

Fixed

• fix: don't lower bound anndata so high by @ilan-gold in #1102
• Workaround for KeyError 'ome' when writing multiscale images by @LucaMarconato in #1115
• Reduce warnings by @LucaMarconato in #1113
• Reduce time cost of tests by @LucaMarconato in #1116
• Fix numba JIT configuration failing on airflow runner by @LucaMarconato in #1117

Full Changelog: v0.7.3a1...v0.7.3a2

v0.7.3a1

What's Changed

Changed

• Change lower bound anndata by @LucaMarconato in #1083

Fixed

• Fix TableModel validator to accept pandas StringDtype by @jlr13 in #1063
• test: make pre-release tests work by @flying-sheep in #1071
• Fix for FutureWarning: functools.partial ... by @selmanozleyen in #1076
• Fix transform graph by @melonora in #1077
• Fix performance regression for multiscale images (#1079) by @LucaMarconato in #1080
• Faster spatialdata import time by @LucaMarconato in #1075
• Preserve attrs on Dask DataFrame sample() by @LiudengZhang in #1088
• ome zarr chunks by @ArneDefauw in #1092

New Contributors

• @jlr13 made their first contribution in #1063
• @flying-sheep made their first contribution in #1071
• @selmanozleyen made their first contribution in #1076
• @LiudengZhang made their first contribution in #1088

Full Changelog: v0.7.3a0...v0.7.3a1

v0.7.3a0

What's Changed

Changed

• New lazy to_multiscale() for labels by @LucaMarconato in #1068

Details: to_multiscale() was calling compute() for labels, leading to poor performance. This release changes the to_multiscale() default implementation to a lazy one (using resize() from scikit-image). Pixels for smaller scales are expected to have some numeric differences with respect to the old implementation (dask_image_nearest via multiscale-spatial-image==2.0.3). The old behavior can be replicated by passing method='dask_image_nearest' to the parsers for raster types.

Full Changelog: v0.7.2...v0.7.3a0

v0.7.2

This releases fixes some installation errors around (dask) distributed and xarray-schema. It also introduces some minor improvements.

What's Changed

Fixed

• Pins distributed; better categorical handing for points parser by @LucaMarconato in #1061
• Remove xarray-schema; validate() are now class methods by @LucaMarconato in #1066

Full Changelog: v0.7.1...v0.7.2

v0.7.1.post1

Post-release to update a problem in the docs (download links for datasets incorrectly generated).

Full Changelog: v0.7.1...v0.7.1.post1

v0.7.1

What's Changed

Fixed

• Upper bound dask <2026.1.2 by @LucaMarconato in #1060

Changed

• Docs datasets are now versioned

Full Changelog: v0.7.0...v0.7.1

v0.7.0

🎉 This release unpins dask! Thanks to @melonora
It also brings many improvements—see notes below.

What's Changed

Added

• pandas 3.0 support by @LucaMarconato in #1034
• Added parameter to sd.concatenate to control whether to merge coordinate systems with the same name by @timtreis in #919
• [experimental] z support get_dims for shapes by @LucaMarconato in #997
• Add User Guide by @Bisho2122 in #909
• Geometry encoding parameter for shapes by @keller-mark in #951
• Added filter_table_by_query by @srivarra in #894

Changed

• unpinning dask by @melonora in #1006

Fixed

• Change: fixed the read_zarr function for zarr.Group objects by @DiDeoxy in #962
• Lazy load torch by @quentinblampey in #1027
• use chunks parameter for dataarray models by @MSHelm in #1031
• Fix attrs-expr bug bounding_box_query points by @LucaMarconato in #1038
• fix categories import by @jonas2612 in #1010
• Design doc: Add note about on-disk locations of point metadata attributes by @keller-mark in #957
• Design doc: Add intrinsic coordinate system name example by @keller-mark in #963
• Remove reference cycle within SpatialData to fix memory leak in bounding_box_query by @nickodell in #914
• When transforming DataTree elements, discard scales resulting in zero shape by @m-albert in #948
• Tests and warnings for issue 399 (nan in table columns) by @LucaMarconato in #1050
• Exclude 1.17.0 for issue anndata 339 by @LucaMarconato in #1057

New Contributors

• @DiDeoxy made their first contribution in #962
• @MSHelm made their first contribution in #1031
• @jonas2612 made their first contribution in #1010
• @keller-mark made their first contribution in #957
• @Bisho2122 made their first contribution in #909
• @nickodell made their first contribution in #914
• @m-albert made their first contribution in #948
• @srivarra made their first contribution in #894

Full Changelog: v0.6.1...v0.7.0

v0.7.0a0

What's Changed

Fixed

• Tests and warnings for issue 399 (nan in table columns) by @LucaMarconato in #1050

Full Changelog: v0.7.0dev1...v0.7.0a0

v0.7.0dev1

What's Changed

Added

• pandas 3.0 support by @LucaMarconato in #1034
• Added parameter to sd.concatenate to control whether to merge coordinate systems with the same name by @timtreis in #919
• [experimental] z support get_dims for shapes by @LucaMarconato in #997
• Add User Guide by @Bisho2122 in #909
• Geometry encoding parameter for shapes by @keller-mark in #951
• Added filter_table_by_query by @srivarra in #894

Fixed

• Fix attrs-expr bug bounding_box_query points by @LucaMarconato in #1038
• fix categories import by @jonas2612 in #1010
• Design doc: Add note about on-disk locations of point metadata attributes by @keller-mark in #957
• Design doc: Add intrinsic coordinate system name example by @keller-mark in #963
• Remove reference cycle within SpatialData to fix memory leak in bounding_box_query by @nickodell in #914
• When transforming DataTree elements, discard scales resulting in zero shape by @m-albert in #948

New Contributors

• @jonas2612 made their first contribution in #1010
• @keller-mark made their first contribution in #957
• @Bisho2122 made their first contribution in #909
• @nickodell made their first contribution in #914
• @m-albert made their first contribution in #948
• @srivarra made their first contribution in #894

Full Changelog: v0.7.0dev0...v0.7.0dev1