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Releases: single-cell-data/TileDB-SOMA

TileDB-SOMA 1.14.3

08 Oct 14:04
@johnkerl johnkerl
1.14.3
85339bd
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TileDB-SOMA 1.14.3

What's Changed

Full Changelog: 1.14.2...1.14.3

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.15.0rc2

07 Oct 22:15
@johnkerl johnkerl
1.15.0rc2
29ed055
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TileDB-SOMA 1.15.0rc2 Pre-release
Pre-release

The main content of this release candidate is a technical preview of the new spatial-transcriptomics featureset.

New features added

  • [python] Update TileDB-SOMA to use the somacore release with spatial datatypes by @jp-dark in #3078
  • [python] Add Python implementation of the PointCloudDataFrame class by @jp-dark in #3109
  • [python/c++] Update TileDB-SOMA to somacore 1.0.19 by @jp-dark in #3098
  • [python/r/c++] Update allowed soma types and the metadata encoding version by @jp-dark in #3086
  • [python] Add implementation of the MultiscaleImage to main by @jp-dark in #3112
  • [python] Add the Python implementation of the Scene collection by @jp-dark in #3116
  • [python] Fix MultiscaleImage.read_spatial_region full region read by @jp-dark in #3128
  • [python] Create Group base class for Collection by @jp-dark in #3024
  • [python] Drop extra index array schema name by @jp-dark in #3033
  • [python] Update coordinate space <-> JSON converters by @nguyenv in #3114
  • Add Visium ingestor and sample spatial notebook by @jp-dark in #3123
  • [c++] Add SOMAMultiscaleImage class by @jp-dark in #3094
  • [c++] Add SOMAScene class by @jp-dark in #3093
  • [c++] Add SOMAPointCloudDataFrame class by @jp-dark in #3092

Breaking changes

Bug fixes

  • [Backport release-1.15] [python] Drop anndata version pin; use CSCDataset/CSRDataset by @github-actions in #3144
  • [python] Avoid RCs of dependent packages for our RC by @johnkerl in #3142
  • [Backport release-1.15] Do not fatal on 1.15-related assertions by @github-actions in #3138
  • [python] Fix retrieval of named levels from a MultiscaleImage by @aaronwolen in #3119
  • [python] Fix f-strings in multiscaleimage error messages by @aaronwolen in #3118
  • [c++] Fix bug in nnz of variant-indexed dataframes by @johnkerl in #2990

Minor changes

Full Changelog: 1.14.2...1.15.0rc2

Contributors

ryan-williams, aaronwolen, and 3 other contributors
Assets 2
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TileDB-SOMA 1.15.0rc1

05 Oct 00:20
@johnkerl johnkerl
1.15.0rc1
2221b98
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TileDB-SOMA 1.15.0rc1 Pre-release
Pre-release

The main content of this release candidate is a technical preview of the new spatial-transcriptomics featureset.

New features added

  • [python] Update TileDB-SOMA to use the somacore release with spatial datatypes by @jp-dark in #3078
  • [python] Add Python implementation of the PointCloudDataFrame class by @jp-dark in #3109
  • [python/c++] Update TileDB-SOMA to somacore 1.0.19 by @jp-dark in #3098
  • [python/r/c++] Update allowed soma types and the metadata encoding version by @jp-dark in #3086
  • [python] Add implementation of the MultiscaleImage to main by @jp-dark in #3112
  • [python] Add the Python implementation of the Scene collection by @jp-dark in #3116
  • [python] Fix MultiscaleImage.read_spatial_region full region read by @jp-dark in #3128
  • [python] Create Group base class for Collection by @jp-dark in #3024
  • [python] Drop extra index array schema name by @jp-dark in #3033
  • [python] Update coordinate space <-> JSON converters by @nguyenv in #3114
  • Add Visium ingestor and sample spatial notebook by @jp-dark in #3123
  • [c++] Add SOMAMultiscaleImage class by @jp-dark in #3094
  • [c++] Add SOMAScene class by @jp-dark in #3093
  • [c++] Add SOMAPointCloudDataFrame class by @jp-dark in #3092

Breaking changes

Bug fixes

  • [Backport release-1.15] Do not fatal on 1.15-related assertions by @github-actions in #3138
  • [python] Fix retrieval of named levels from a MultiscaleImage by @aaronwolen in #3119
  • [python] Fix f-strings in multiscaleimage error messages by @aaronwolen in #3118
  • [c++] Fix bug in nnz of variant-indexed dataframes by @johnkerl in #2990

Minor changes

Full Changelog: 1.14.2...1.15.0rc0

Contributors

ryan-williams, aaronwolen, and 3 other contributors
Assets 2
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TileDB-SOMA 1.14.2

26 Sep 18:53
@johnkerl johnkerl
1.14.2
0e63ade
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TileDB-SOMA 1.14.2

What's Changed

  • Bulk-backport Python 3.8 and somacore 1.0.17 mods to release-1.14 branch by @johnkerl in #3074

Full Changelog: 1.14.1...1.14.2

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.14.2rc0

26 Sep 16:58
@johnkerl johnkerl
1.14.2rc0
0e63ade
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TileDB-SOMA 1.14.2rc0 Pre-release
Pre-release

What's Changed

  • Bulk-backport Python 3.8 and somacore 1.0.17 mods to release-1.14 branch by @johnkerl in #3074

Full Changelog: 1.14.1...1.14.2

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.14.1

18 Sep 14:20
@johnkerl johnkerl
1.14.1
570446b
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TileDB-SOMA 1.14.1

What's Changed

Full Changelog: 1.14.0...1.14.1

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.14.0

17 Sep 23:13
@johnkerl johnkerl
1.14.0
7323987
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TileDB-SOMA 1.14.0

New features added

Bug fixes

  • [python] Utilize Arrow schema pa.field nullabilities in DataFrame.create by @johnkerl in #2868
  • [python] Offer better guidance on attribute names with . by @johnkerl in #2864
  • [python] X-write performance improvement for the non-append case by @johnkerl in #2846
  • [c++] Fix ManagedQuery usage in SOMAArray write path by @nguyenv in #2989
  • [c++] Only evolve schema when enumerations are extended by @nguyenv in #2851
  • [c++] Corner-case bug in extend-enumeration logic by @johnkerl in #2897
  • [c++] Remap indexes even if no new enums were added by @nguyenv in #2993

Breaking changes

  • [python] Post-deprecation removal of consolidate_and_vacuum from TileDBCreateOptions by @johnkerl in #3000
  • [python] Implement scheduled removal of TileDBCreateOptions being passed to write methods by @johnkerl in #2842

Upcoming deprecation notices

Minor changes

New Contributors

Full Changelog: 1.13.1...1.14.0

Contributors

ryan-williams, eddelbuettel, and 5 other contributors
Assets 2
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TileDB-SOMA 1.13.1

16 Aug 17:50
@johnkerl johnkerl
1.13.1
1e2b131
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TileDB-SOMA 1.13.1

Bug fixes

  • [Backport release-1.13] [c++] Corner-case bug in extend-enumeration logic by @github-actions in #2903
  • [Backport release-1.13] [python] Offer better guidance on attribute names with . by @github-actions in #2865
  • [Backport release-1.13] python Utilize Arrow schema pa.field nullabilities in DataFrame.create by @github-actions in #2870
  • [Backport release-1.13] [c++] Add dataset_type into SOMAExperiment metadata by @github-actions in #2886
  • [Backport release-1.13] [c++] Apply ArraySchemaEvolution to specified timestamp by @github-actions in #2901

Minor changes

  • [Backport release-1.13] [c++] Only evolve schema when enumerations are extended by @github-actions in #2852
  • [Backport release-1.13] [python] pin pandas-stubs>=2 during pre-commit mypy hook by @github-actions in #2855
  • [Backport release-1.13] [python] Fix a comment by @github-actions in #2877
  • [Backport release-1.13] [c++] Fix typos in unit-test case by @github-actions in #2889
  • [Backport release-1.13] [c++] Remove a temporary gdb hook from #2888 by @github-actions in #2894
  • [Backport release-1.13] [c++] Final update for Python/R metadata typing by @github-actions in #2902

Full Changelog: 1.13.0...1.13.1

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TileDB-SOMA 1.13.1rc0

16 Aug 16:09
@johnkerl johnkerl
1.13.1rc0
05013fb
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TileDB-SOMA 1.13.1rc0 Pre-release
Pre-release

Bug fixes

  • [Backport release-1.13] [c++] Corner-case bug in extend-enumeration logic by @github-actions in #2903
  • [Backport release-1.13] [python] Offer better guidance on attribute names with . by @github-actions in #2865
  • [Backport release-1.13] python Utilize Arrow schema pa.field nullabilities in DataFrame.create by @github-actions in #2870
  • [Backport release-1.13] [c++] Add dataset_type into SOMAExperiment metadata by @github-actions in #2886
  • [Backport release-1.13] [c++] Apply ArraySchemaEvolution to specified timestamp by @github-actions in #2901

Minor changes

  • [Backport release-1.13] [c++] Only evolve schema when enumerations are extended by @github-actions in #2852
  • [Backport release-1.13] [python] pin pandas-stubs>=2 during pre-commit mypy hook by @github-actions in #2855
  • [Backport release-1.13] [python] Fix a comment by @github-actions in #2877
  • [Backport release-1.13] [c++] Fix typos in unit-test case by @github-actions in #2889
  • [Backport release-1.13] [c++] Remove a temporary gdb hook from #2888 by @github-actions in #2894
  • [Backport release-1.13] [c++] Final update for Python/R metadata typing by @github-actions in #2902

Full Changelog: 1.13.0...1.13.1rc0

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TileDB-SOMA 1.13.0

06 Aug 22:43
@johnkerl johnkerl
1.13.0
faf06e2
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TileDB-SOMA 1.13.0

Deprecation notices

As noted in #2407, there will be new shape support in the upcoming TileDB-SOMA 1.14, with some impact to user API in the append-to-experiment use-case.

As noted in #2843, TileDBCreateOptions may no longer be passed to write methods.

  • [Backport release-1.13] [python] Implement scheduled removal of TileDBCreateOptions being passed to write methods by @github-actions in #2843
  • [python] Deprecate tiledb_ctx usage in TileDBSOMAContext by @nguyenv in #2693
  • [python] Deprecate tiledb.Filter getters in PlatformConfig by @nguyenv in #2720
  • [r/python] Deprecation notices for used_shape by @johnkerl in #2834
  • [r] Use .Deprecated for used_shape in R by @johnkerl in #2835

New features added

  • [python] Optionally drop unused categories in ExperimentAxisQuery.to_anndata by @nguyenv in #2811
  • [Backport release-1.13] [python] X-write performance improvement for the non-append case by @github-actions in #2848
  • [Backport release-1.13] [python] Add CollectionBase.members by @github-actions in #2849
  • [c++/python] Add reopen for SOMAArray and SOMAGroup by @nguyenv in #2802
  • [r] Connect re-indexer to blockwise iterator by @mojaveazure in #2742
  • [r] Add drop_levels to SOMAExperimentAxisQuery -> ecosystem outgestors by @mojaveazure in #2825

Bug fixes

  • [Backport release-1.13] [python] Use original error message when re-raising with DoesNotExistError by @github-actions in #2844
  • [python] Support tiledbsoma.io.update_obs with post-nullable non-string attributes by @johnkerl in #2719
  • [python] Allow platform config to set both extent and filter by @johnkerl in #2808
  • [python] Improve error message on non-constant query-condition RHS by @johnkerl in #2831
  • [python] More gracefully handle invalid operators in query-condition parser by @johnkerl in #2830
  • [python] Allow platform config to set extent and filter by @johnkerl in #2808
  • [c++] Fix enum-of-bool leveling by @johnkerl in #2723

Minor changes

  • Use core 2.25, TileDB-Py 0.31, TileDB-R 0.29 by @johnkerl in #2813
  • [Backport release-1.13] [python] Debug CI mypy failures related to # type: ignore[misc] by @github-actions in #2845
  • [Backport release-1.13] [python] Misc. ingest/outgest code-neaten improvements by @github-actions in #2847
  • [Backport release-1.13] [python] Ingest/outgest round-trip improvements by @github-actions in #2850
  • [r] Prep for TileDB-SOMA 1.13 (release-1.13 branch) by @johnkerl in #2837
  • [python/r] Update lifecycle tags to "Maturing" by @johnkerl in #2807
  • [python] Pin to numpy < 2.0 for 1.12 release by @johnkerl in #2745
  • [python] Add pybind11 bindings for SOMAGroup 2/5 by @nguyenv in #2732
  • [python] Use bindings for SOMAGroup 3/5 by @nguyenv in #2735
  • [python] Replace TileDBObject with SOMAObject; Remove tiledb.TileDBError usage 4/5 by @nguyenv in #2736
  • [python] Remove tiledb-py from top-level src (sans io and options) 5/5 by @nguyenv in #2740
  • [python] Remove a debug statement by @johnkerl in #2766
  • [python] Continue to use tiledb.Ctx's config until it is removed by @nguyenv in #2768
  • [python] devtools/outgestor stats and neaten by @johnkerl in #2770
  • [python] Update a confusing filename by @johnkerl in #2776
  • [python] Bump the stack level of the tiledb_ctx deprecation warning by @ivirshup in #2788
  • [python] Release GIL where necessary in pybind11 code by @nguyenv in #2733
  • [python] Hold onto GIL for open methods by @nguyenv in #2800
  • [python] Retain GIL for exist by @nguyenv in #2801
  • [python] Replace py::none with py::tuple for column_names default arg by @nguyenv in #2806
  • [python] Typo-fix some parameter names in some internal functions by @johnkerl in #2809
  • [c++/python] Add tiledb_timestamp argument for reopen by @nguyenv in #2820
  • [python] Remove reshape stub by @johnkerl in #2826
  • [python] More reshape neatens by @johnkerl in #2828
  • [python] pin codecov/uploader==0.7.3 in codecov-action by @ryan-williams in #2827
  • [r] R versioning past release-1.12 branch by @johnkerl in #2716
  • [r,c++] Support DenseNDArray write case by @eddelbuettel in #2730
  • Compare core to tiledb-py/tiledb-r major+minor, main branch by @johnkerl in #2784
  • [r] Add missing documentation for set_data_type by @eddelbuettel in #2818
  • [r] Support SparseNDArray writes case by @eddelbuettel in #2755
  • [r] Use exists() to check for (local or) remote arrays by @eddelbuettel in #2803
  • [r] Remove default mode-flipping in $reopen() by @mojaveazure in #2817
  • [r] Expose object-type getter by @eddelbuettel in #2833
  • [c++] Fix a nightly-build issue by @johnkerl in #2718
  • [c++] Add missing SOMACollection getters and setters by @nguyenv in #2508
  • [c++] More SOMAGroup refinements 1/5 by @nguyenv in #2731
  • [c++] Remap TileDBError to TileDBSOMAError by @nguyenv in #2753
  • [c++] General CMake clean-up by @jp-dark in #2762
  • [c++] Split nanoarrow into a separate object library by @jp-dark in #2763
  • [c++] Improve exception-handling for query futures by @johnkerl in #2789
  • [c++] Cast ArrowTable values in SOMAArray::write to match ArraySchema on-disk by @nguyenv in #2786
  • Bump setuptools from 69.5.1 to 70.0.0 in /doc by @dependabot in #2796
  • [c++] exists should take in SOMAContext by @nguyenv in #2794
  • [c++] Add NDArray::soma_data_type by @nguyenv in #2810
  • [c++] Do not call schema evolution for each column by @nguyenv in #2805
  • [c++] Check index in enumeration casting before using by @nguyenv in #2816
  • pre-commit update by @bkmartinjr in #2821

New Contributors

Full Changelog: 1.12.0rc0...1.13.0

Contributors

ryan-williams, eddelbuettel, and 7 other contributors
Assets 2
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