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TileDB-SOMA 1.15.5

24 Jan 21:50
@johnkerl johnkerl
1.15.5
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TileDB-SOMA 1.15.5 Latest
Latest

Bug fixes

  • [Backport release-1.15] [python] Fix update_obs semantics for some remote configurations by @github-actions in #3627
  • [c++] Fix some build errors for Docker by @johnkerl in #3620
  • [r] TileDB-SOMA 1.15.5 by @johnkerl in #3628

Full Changelog: 1.15.4...1.15.5

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johnkerl
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TileDB-SOMA 1.15.4

22 Jan 22:16
@johnkerl johnkerl
1.15.4
4e92187
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TileDB-SOMA 1.15.4

New features added

  • [Backport release-1.15] [python] Change from_visium to create obs presence matrix by default in #3596
  • [Backport release-1.15][python] Set soma_joinid to always be an index column in the PointCloudDataFrame class in #3575
  • [Backport release-1.15] [python] On is-not-context error, show type in #3584
  • [Backport release-1.15] [python] Make region_key a categorical when exporting to SpatialData in #3589
  • [Backport release-1.15] [python] Update warning on unsupported version in #3600
  • [Backport release-1.15] [python] Add spatial I/O functions to readthedocs in #3604
  • [Backport release-1.15][python] Add the spatial-encoding version to Scene and PointCloudDataFrame objects in #3603
  • [Backport release 1.15][python/c++] Add C++ SOMACoordinateSpace and use it to push Scene metadata down to C++ in #3602
  • [Backport release-1.15] [python] Add Unicode metadata support in #3607

Breaking changes

Upcoming deprecation notices

Bug fixes

  • [Backport release-1.15] [c++] Handle add/drop/re-add of enumerated types in #3572
  • [Backport release-1.15] [python] Throw error in SOMAVFSFilebuf.open on file-not-found in #3569
  • [Backport release-1.15] [python] Fix search in readthedocs in #3576
  • [Backport release-1.15] [python] More readthedocs search fix in #3579
  • [Backport release-1.15] [python] Pass more context in io/shaping.py in #3587
  • [Backport release-1.15] [python] Fix rendering of spatial docs in #3606
  • [Backport release-1.15] [python] Iterate on spatial + readthedocs in #3610
  • [Backport release-1.15] [python] More readthedocs fixes for spatial in #3613
  • [Backport release-1.15] [c++] Correct Arrow offsets for enumeration and boolean columns in #3615

Minor changes

  • [Backport release-1.15] [python] Release GIL in VFS bindings in #3564
  • Fix #3569 backport to release-1.15 in #3571
  • [Backport release-1.15] [python] Merge _axisp_get_array and _axism_get_array into a single function in #3574
  • [Backport release-1.15] [python] Remove AxisName.getattr_from from ExperimentAxisQuery in #3577
  • [Backport release-1.15] [python] Update copyright header in *.py source files in #3593
  • [Backport release-1.15] [r] [CI] Use binaries for packages on macOS in #3601
  • [c++] Downgrade C++20isms to C++17isms for release-1.15 branch in #3609
  • [Backport release-1.15] [c++] Remove some compiler warnings in #3616
  • [r] TileDB-SOMA 1.15.4 in #3617

Full Changelog: 1.15.3...1.15.4

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TileDB-SOMA 1.15.3

10 Jan 22:29
@johnkerl johnkerl
1.15.3
7f0ac88
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TileDB-SOMA 1.15.3

New features added

  • [Backport release-1.15] [python] Add region columns and metadata to SpatialData by @github-actions in #3556
  • [Backport release-1.15] [python] Handle non-list/non-tuple input in tiledbsoma.io registration by @github-actions in #3520
  • [Backport release-1.15] [c++] When a group has no type info, say its name by @github-actions in #3532
  • [Backport release-1.15] [c++] Show which coordinate is out of range in fastercsx error messages by @github-actions in #3541
  • [Backport release-1.15] [python] Add support for Visium v1 by @github-actions in #3550

Bug fixes

  • [Backport release-1.15] [python] Link lifetimes of SOMAArray and ManagedQuery by @github-actions in #3522
  • [Backport release-1.15] [python] Fix casting bug in IntIndexer by @github-actions in #3527
  • [Backport release-1.15] [python] Account for missing end-rows in shape-upgrader by @github-actions in #3540
  • [Backport release-1.15] [python] Implement read, seek, and tell for SOMAVFSFilebuf by @github-actions in #3547
  • [Backport release-1.15] [C++] Fix ManagedQuery segv: ctor/dtor order fix by @github-actions in #3549
  • [Backport release-1.15] [python] Validate byteorder on fastercsx argument arrays by @github-actions in #3521

Minor changes

  • [Backport release-1.15] [python] Fix and clean up basic Scene test by @github-actions in #3523
  • [Backport release-1.15] [python] Unpin scipy by @github-actions in #3528
  • [Backport release-1.15] [c++] Bump spdlog to 1.15 and remove patch by @github-actions in #3531
  • [c++] Fix backport on #3541 by @johnkerl in #3542
  • [Backport release-1.15] Bump jinja2 from 3.1.4 to 3.1.5 in /doc by @github-actions in #3546
  • [Backport release-1.15] [python] Inline _read and AxisQueryResult to to_anndata by @github-actions in #3555
  • [r] TileDB-SOMA 1.15.3 by @johnkerl in #3551

Full Changelog: 1.15.2...1.15.3

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johnkerl
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TileDB-SOMA 1.15.2

20 Dec 19:21
@johnkerl johnkerl
1.15.2
ac4e912
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TileDB-SOMA 1.15.2

New features added

  • [Backport release-1.15] [python] Update add_new_collection method to support Scene collections by @github-actions in #3499

Bug fixes

  • [Backport release-1.15] [python] Make ExperimentAxisQuery inherit somacore, restore its .close by @github-actions in #3500

Minor changes

  • [Backport release-1.15] [c++] Use const references and std::string_view in create function by @github-actions in #3483
  • [Backport release-1.15] [c++] Make destructors of base classes virtual by @github-actions in #3487
  • [Backport release-1.15] [python] Fix a test deprecation warning by @github-actions in #3488
  • [Backport release-1.15] [python] tiledbsoma.__init__.py: restore lint checks by @github-actions in #3498
  • [r] TileDB-SOMA 1.15.2 by @johnkerl in #3497
  • [Backport release-1.15] [c++, python] fastercsx: improved duplicate coordinate handling by @github-actions in #3485
  • [Backport release-1.15] [c++] Set overriding user-provided prefix to be off by default by @github-actions in #3489
  • [Backport release-1.15] [c++/ci] Disable leak detection and add ASAN CI job to all C++ PRs by @github-actions in #3492
  • [Backport release-1.15] [python] Filter spatial disclaimer from pytest by @github-actions in #3496

Full Changelog: 1.15.1...1.15.2

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johnkerl
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TileDB-SOMA 1.15.1

19 Dec 14:35
@johnkerl johnkerl
1.15.1
80e1825
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TileDB-SOMA 1.15.1

The primary bugfix for this release is #3479, which is a backport of #3476. This releases fixes the error message

TypeError: ExperimentAxisQuery() takes no arguments

Bug fixes

  • [Backport release-1.15] [python] Re-enable tiledbsoma.ExperimentAxisQuery by @github-actions in #3479
  • [docs] Fix broken tutorial-doc symlinks in release-1.15 by @johnkerl in #3466
  • [Backport release-1.15] [python/c++] Fix invalid memory read in fastercsx by @github-actions in #3464
  • [Backport release-1.15] [python] Fix stochastic failure of to_spatialdata method by @github-actions in #3477
  • [Backport release-1.15] [python] Add extra asserts for SpatialData tests by @github-actions in #3474
  • [Backport release-1.15][r] Write group-level string metadata as TILEDB_STRING_UTF8; 1.15.1 by @johnkerl in #3481

Minor changes

  • [Backport release-1.15] [python/c++] Deprecate config_options_from_schema in favor of new function by @github-actions in #3465
  • [Backport release-1.15] [c++, r, python] read_next clean-up by @github-actions in #3480
  • [Backport release-1.15] [python] Convert from Optional[Foo] to Foo | None by @github-actions in #3467

Full Changelog: 1.15.0...1.15.1

Contributors

johnkerl
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TileDB-SOMA 1.15.0

17 Dec 16:17
@johnkerl johnkerl
1.15.0
e5d19d0
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TileDB-SOMA 1.15.0

Summary

This release contains several important developments:

  • Spatial transcriptomics: alpha version of the feature.
  • Performance improvements: particularly for tiledbsoma.io.to_anndata / tiledbsoma.io.to_h5ad
  • Seurat I/O: incremental work for Seurat v5
  • New shape feature
  • Documentation infrastructure: more thorough class coverage, and more clickable links in the Python docs
  • The TileDB-Py package is no longer a required dependency.

New features added

Spatial transcriptomics

  • [python] Add to_spatial_data method to ExperimentAxisQuery #3431
  • [python] Export full experiment to SpatialData #3409
  • [python] Fix typos and import order in the spatial outgest #3381
  • [python] Fix output type when exporting PointCloudDataFrame to SpatialData points #3408
  • [python] Update Scene create method in the Python API #3356
  • [python] Change import experimental -> io.spatial in test #3394
  • [python] Add support for exporting to SpatialData without transform #3392
  • [python] Rename to_spatial_data -> to_spatialdata #3449
  • [python] Move experimental module to io.spatial #3384
  • [python] Add export for MultiscaleImage to SpatialData by @jp-dark in #3355
  • [python] Add PointCloudDataFrame to SpatialData points model by @jp-dark in #3357
  • [python] Add MultiscaleImage level SpatialData exporter by @jp-dark in #3342
  • [python] Spatial changes required for somacore 1.0.24 by @jp-dark in #3333
  • [python] Fix and test SpatialData transformation exporter by @jp-dark in #3330
  • [python] Rewrite Xarray support to use dask arrays by @jp-dark in #3325
  • [python] Return identity for MultiscaleImage transform to/from level 0 by @jp-dark in #3323
  • [python] Add MultiscaleImage methods to access level URI by @jp-dark in #3322
  • [python] Add export for PointCloudDataFrame to SpatialData shapes by @jp-dark in #3298
  • [python] Create xarray backend for DataArray types by @jp-dark in #3243
  • [python] Update spatial API to match somacore 1.0.23 by @jp-dark in #3274
  • [c++] Cast vertex list to WKB by @XanthosXanthopoulos in #3222
  • [c++] Geometry Dataframe by @XanthosXanthopoulos in #3212

Performance improvements

  • [python] Remove double open For SOMAArray reads #3293
  • [python,c++] Improve error handling in IntIndexer #3441
  • [python] Some memory-reduction for append mode #3404
  • [python] Extend #3354 to categoricals of arbitrary value type #3415
  • [python] Protect against huge enum-of-strings input #3354
  • [python] Optimization of ExperimentAxisQuery to_anndata by @bkmartinjr in #3359
  • [python] Fix incorrect type handling in ExperimentAxisQuery sparse reader by @bkmartinjr in #3375
  • [python/C++] Release GIL in IntIndexer C++ code by @bkmartinjr in #3344
  • [python] Partition sparse matrix reads in tiledbsoma.io.to_anndata by @bkmartinjr in #3328
  • [python/c++] COO to CSX conversion optimization by @bkmartinjr in #3304
  • [python] Performance improvement for experiment-level resize by @johnkerl in #3308
  • [python] Add ManagedQuery bindings by @nguyenv in #3281
  • [python] Ingest somacore classes by @ryan-williams in #3307
  • [c++] Fix heap management in fastercsx by @johnkerl in #3365
  • [c++] Add ManagedQuery constructor that takes SOMAArray by @nguyenv in #3279
  • [c++] Add ManagedQuery::set_layout by @nguyenv in #3278
  • [c++] Use schema from tiledb::Array instead of ManagedQuery by @nguyenv in #3277
  • [c++] Move casting from SOMAArray to ManagedQuery by @nguyenv in #3275

Seurat I/O

  • [r] Add initial support for ragged array writing for Seurat v5 by @mojaveazure in #2523

New shape

  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 4/n #3372
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 3 of 4 #3371
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 2/n #3370
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 1 of 4 #3369
  • [c++] Use valid ASCII for wide-as-possible string current domain #3367
  • [c++] Match zero-basing for old/new sparse-array shapes #3439
  • [r] Add check_only support for domain/shape updates #3400
  • [python/r] Update docstrings for domain argument to create #3396
  • [r] Vignette for new-shape feature #3302
  • [c++] Fix upgrade-soma-joinid-shape for dataframes having non-standard dimensions #3416
  • [python/r] Docstring audit for new shape #3399
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 4 of 4 by @johnkerl in #3372
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 3 of 4 by @johnkerl in #3371
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 2 of 4 by @johnkerl in #3370
  • [python/r] Remove 2.27-related feature flag by @johnkerl in #3368
  • [r/python] Revert #3300 by @johnkerl in #3358
  • [python/r] Enforce dataframe domain lower bound == 0 by @johnkerl in #3300
  • [c++] Use valid ASCII for wide-as-possible string current domain by @johnkerl in #3367
  • [python] Use new shape in one more spot by @johnkerl in #3321
  • [python] Fix bad merge of soma-shapes notebook by @johnkerl in #3309
  • [python] Tutorial notebook for the new-shape feature by @johnkerl in #3294
  • [r] Data refresh for new shapes by @johnkerl in #3303
  • [python/r] Move beyond the new-shape feature flag by @johnkerl in #3301
  • [python] Fix dense example data for core 2.27 by @johnkerl in #3296
  • [python/docs] Replace experiment directories with .tgz files in source control by @johnkerl in #3295
  • [python] Doc updates for new-shape feature by @johnkerl in #3285
  • [python] Run upgrade-shapes on notebook example experiments by @johnkerl in #3289
  • [python] Include tiledbsoma_upgrade_shape for DenseNDArray by @johnkerl in #3288
  • [python] More auto-detect of function_name_for_messages by @johnkerl in #3286
  • [r] More fixes for unit-test cases with dense + core 2.27 by @johnkerl in #3280
  • [python] Fix last 2.27+Python+dense failing test case by @johnkerl in #3269
  • [r] Fixes for dense+2.27 by @johnkerl in #3270
  • [python] Fix 3D/4D cases with core 2.27 by @johnkerl in #3268
  • [c++] Apply subarrays for dense reads and writes by @johnkerl in #3263
  • [python] Fix some dense+2.27 failing test cases by @johnkerl in #3265
  • [python] Centralize sparse/dense pybind11 shape methods by @johnkerl in #3261
  • [python] Re-run, and update, example notebooks with new shape feature by @johnkerl in #3290

Upcoming deprecation notices

  • The .used_shape accessor for SparseNDArray and DenseNDArray is scheduled for removal in 1.16: as of 1.15 the .shape accessor replaces it.

Bug fixes

  • [python] ExperimentAxisQuery: to_anndata obsp/varp as sparse matrices #3387
  • [python] Fix conditional fall-through in SOMAObject.open #3446
  • [c++] Fix bug with sliced Arrow-table writes, with string columns #3433
  • [python, c++] Fix misleading DoesNotExistErrors in open factory #3402
  • [c++] ManagedQuery::set_condition should not reset entire instance state #3418
  • [r] Update changelog and develop version for #3395 #3401
  • [r] Adjust blockwise + re-indexer to return condensed matrix, not full domain #3395
  • [python] Re-introduce tiledb_ctx for SOMATileDBContext #3335

Minor changes

Documentation infastructure

Packaging and CI

  • [python] Pin dask version 2024.11.2 to unblock CI #3403
  • [python] Pre-emptively avoid SciPy 1.15, pending a bugfix #3445
  • [c++] Use core 2.27.0 #3421
  • [c++] Use core 2.27.0.rc5 #3410
  • [c++/python/r] Use core 2.27.0-rc3 by @johnkerl in #3366
  • [packaging] More failure info in update-tiledb-versions.py by @johnkerl in #3363
  • [python] Run pre-commit autoupdate by @johnkerl in #3326
  • [r/python] Note on dev installs and spdlog failures by @johnkerl in #3324
  • [r/ci] Remove tiledb-r specific install by @mojaveazure in #3319
  • [r/ci] Try to unbreak r-valgrind CI by @johnkerl in #3318
  • [r/ci] Avoid log truncation with "Last 13 lines of output" by @johnkerl in #3313
  • [r] Run tests in closer to internal-dependency order by @johnkerl in #3311
  • [python] Unbreak CI with anndata==0.11 by @johnkerl in #3305
  • [python] Fix some warnings at anndata==0.11 by @johnkerl in #3306

Remove TileDB-Py as a required dependency

  • [python] Update README.md to remove tiledb-py by @nguyenv in #3346

Other internals

  • [python] Remove use of deprecated schema-display function #3380
  • [r] Use standard name zzz.R for init code by @johnkerl in #3332
  • [r] Address two more compiler warnings by @johnkerl in #3320
  • [c++] Fix a compiler warning by @johnkerl in #3310
  • [python] Consolidate all _set_coords methods into single _util function by @nguyenv in #3292
  • [python] Rename set_reader_coords to set_coords by @johnkerl in #3253
  • [python] Use somacore 1.0.26 #3460
  • [python] Use somacore 1.0.25 #3455
  • [c++] Add ASAN run of CI to weekly CI job #3434

Contributors

ryan-williams, johnkerl, and 5 other contributors
Assets 2
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TileDB-SOMA 1.15.0rc4

22 Nov 22:16
@johnkerl johnkerl
1.15.0rc4
684cd69
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TileDB-SOMA 1.15.0rc4 Pre-release
Pre-release

This is a release candidate for 1.15.0 which we anticipate releasing in earlly December 2024. It contains several important developments.

  • Spatial transcriptomics: alpha version of the feature.
  • Performance improvements: particularly for tiledbsoma.io.to_anndata / tiledbsoma.io.to_h5ad
  • Seurat I/O: incremental work for Seurat v5
  • New shape feature: Python tutorial here; Academy docs to be shipped by the time of 1.15.0
  • Documentation infrastructure: please see the pre-release docs (note latest in the URL)
  • For developers only: We now build our C++ library using C++ 20. This doesn't affect non-developer installs, which will get artifacts from PyPI/r-universe/Conda.
  • The TileDB-Py package is no longer a required dependency.

Upcoming deprecation notices

  • The .used_shape accessor for SparseNDArray and DenseNDArray is scheduled for removal in 1.16: as of 1.15 the .shape accessor replaces it.

Spatial transcriptomics

  • [python] Add export for MultiscaleImage to SpatialData by @jp-dark in #3355
  • [python] Add PointCloudDataFrame to SpatialData points model by @jp-dark in #3357
  • [python] Add MultiscaleImage level SpatialData exporter by @jp-dark in #3342
  • [python] Spatial changes required for somacore 1.0.24 by @jp-dark in #3333
  • [python] Fix and test SpatialData transformation exporter by @jp-dark in #3330
  • [python] Rewrite Xarray support to use dask arrays by @jp-dark in #3325
  • [python] Return identity for MultiscaleImage transform to/from level 0 by @jp-dark in #3323
  • [python] Add MultiscaleImage methods to access level URI by @jp-dark in #3322
  • [python] Add export for PointCloudDataFrame to SpatialData shapes by @jp-dark in #3298
  • [python] Create xarray backend for DataArray types by @jp-dark in #3243
  • [python] Update spatial API to match somacore 1.0.23 by @jp-dark in #3274
  • [c++] Cast vertex list to WKB by @XanthosXanthopoulos in #3222
  • [c++] Geometry Dataframe by @XanthosXanthopoulos in #3212

Performance improvements

Seurat I/O

  • [r] Add initial support for ragged array writing for Seurat v5 by @mojaveazure in #2523

New shape

  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 4 of 4 by @johnkerl in #3372
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 3 of 4 by @johnkerl in #3371
  • [c++] Some use_current_domain unit-test/feature-flag teardown, part 2 of 4 by @johnkerl in #3370
  • [python/r] Remove 2.27-related feature flag by @johnkerl in #3368
  • [r/python] Revert #3300 by @johnkerl in #3358
  • [python/r] Enforce dataframe domain lower bound == 0 by @johnkerl in #3300
  • [c++] Use valid ASCII for wide-as-possible string current domain by @johnkerl in #3367
  • [python] Use new shape in one more spot by @johnkerl in #3321
  • [python] Fix bad merge of soma-shapes notebook by @johnkerl in #3309
  • [python] Tutorial notebook for the new-shape feature by @johnkerl in #3294
  • [r] Data refresh for new shapes by @johnkerl in #3303
  • [python/r] Move beyond the new-shape feature flag by @johnkerl in #3301
  • [python] Fix dense example data for core 2.27 by @johnkerl in #3296
  • [python/docs] Replace experiment directories with .tgz files in source control by @johnkerl in #3295
  • [python] Doc updates for new-shape feature by @johnkerl in #3285
  • [python] Run upgrade-shapes on notebook example experiments by @johnkerl in #3289
  • [python] Include tiledbsoma_upgrade_shape for DenseNDArray by @johnkerl in #3288
  • [python] More auto-detect of function_name_for_messages by @johnkerl in #3286
  • [r] More fixes for unit-test cases with dense + core 2.27 by @johnkerl in #3280
  • [python] Fix last 2.27+Python+dense failing test case by @johnkerl in #3269
  • [r] Fixes for dense+2.27 by @johnkerl in #3270
  • [python] Fix 3D/4D cases with core 2.27 by @johnkerl in #3268
  • [c++] Apply subarrays for dense reads and writes by @johnkerl in #3263
  • [python] Fix some dense+2.27 failing test cases by @johnkerl in #3265
  • [python] Centralize sparse/dense pybind11 shape methods by @johnkerl in #3261
  • [python] Re-run, and update, example notebooks with new shape feature by @johnkerl in #3290

Documentation infastructure

C++20

Packaging and CI

Remove TileDB-Py as a required dependency

  • [python] Update README.md to remove tiledb-py by @nguyenv in #3346

Miscellaneous internals

Contributors

ryan-williams, johnkerl, and 5 other contributors
Assets 2
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TileDB-SOMA 1.15.0rc3

30 Oct 14:27
@johnkerl johnkerl
1.15.0rc3
d41a025
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TileDB-SOMA 1.15.0rc3 Pre-release
Pre-release

Summary

  • NumPy 2 support
  • Python 3.12 support
  • Significant work on spatial transcriptomics
  • Progress on new shape (#2407) to be released with 1.15.0
  • The TileDB-Py package is no longer a dependency

Changes

  • [Backport release-1.15] [python] Support NumPy 2 by @github-actions in #3248
  • [Backport release-1.15] [python] Use typeguard==4.4.0, somacore==1.0.22 by @github-actions in #3254
  • [Backport release-1.15] [python] Rename set_reader_coords to set_coords by @github-actions in #3255
  • File add/removes for bulk-sync from main to release-1.15 by @johnkerl in #3258
  • Bulk-sync main to release-1.15 by @johnkerl in #3251
  • Bulk sync main -> release-1.15 by @johnkerl in #3256
  • [r] Prepare for 1.15.0rc3 by @johnkerl in #3257

Full Changelog: 1.15.0rc2...1.15.0rc3

See also: 1.15.0rc2...main

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.14.5

23 Oct 20:14
@johnkerl johnkerl
1.14.5
afca166
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TileDB-SOMA 1.14.5

This is a single-bug-fix release

  • [Backport release-1.14] [c++/python] Check arrow_is_string_type in _update_dataframe by @github-actions in #3225
  • [r] Prepare for 1.14.5 by @johnkerl in #3226

Full Changelog: 1.14.4...1.14.5

Contributors

johnkerl
Assets 2
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1.14.4

22 Oct 18:32
@johnkerl johnkerl
1.14.4
e3ec4de
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1.14.4

What's Changed

This release does not affect any Python code.

Full Changelog: 1.14.3...1.14.4

Contributors

johnkerl and mojaveazure
Assets 2
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