Tiledbsoma

Summary

This release contains several important developments:

* [Spatial transcriptomics](https://tiledbsoma.readthedocs.io/en/latest/notebooks/tutorial_spatial.html): 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](https://documentation.cloud.tiledb.com/academy/structure/life-sciences/single-cell/tutorials/shapes)
* Documentation infrastructure: more thorough class coverage, and more clickable links in the [Python docs](https://tiledbsoma.readthedocs.io/en/1.15.0/)
* The [TileDB-Py package](https://github.com/TileDB-Inc/TileDB-Py) 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

* [docs] Fix Sphinx issue with linkless summaries by johnkerl in 3284
* [docs] Add new things to `.rst` files by johnkerl in 3283
* [python] Misc. formatting fix-ups by johnkerl in 3287
* [python] `_multiscale_image`: add missing docstrings, typo fixes by ryan-williams in 3312

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

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](https://github.com/single-cell-data/TileDB-SOMA/blob/main/apis/python/notebooks/tutorial_soma_shape.ipynb); Academy docs to be shipped by the time of 1.15.0
* Documentation infrastructure: please see the [pre-release docs](https://tiledbsoma.readthedocs.io/en/latest/) (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](https://github.com/TileDB-Inc/TileDB-Py) 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

* [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 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

* [docs] Fix Sphinx issue with linkless summaries by johnkerl in 3284
* [docs] Add new things to `.rst` files by johnkerl in 3283
* [python] Misc. formatting fix-ups by johnkerl in 3287
* [python] `_multiscale_image`: add missing docstrings, typo fixes by ryan-williams in 3312

C++20

* [ci] Change `manylinux` version for sdist&wheels CI (C++ 20) by XanthosXanthopoulos in 3351
* [c++] Another C++ 20 doc-spot by johnkerl in 3352
* [python] Update `README.md` to remove `fmt` reference by nguyenv in 3347
* [c++] Use `std::format` in `spdlog` (C++ 20) by XanthosXanthopoulos in 3343
* [c++/python] Switch to `std::span` by XanthosXanthopoulos in 3340
* [c++/python/r] Migrate to C++20 by XanthosXanthopoulos in 3331
* [python/docs] Use `ubuntu-24.04` (C++ 20) for `readthedocs` by ryan-williams in 3339

Packaging and CI

* [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

Miscellaneous internals

* [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

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 https://github.com/single-cell-data/TileDB-SOMA/pull/3248
* [Backport release-1.15] [python] Use `typeguard==4.4.0`, `somacore==1.0.22` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3254
* [Backport release-1.15] [python] Rename `set_reader_coords` to `set_coords` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3255
* File add/removes for bulk-sync from `main` to `release-1.15` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3258
* Bulk-sync `main` to `release-1.15` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3251
* Bulk sync `main` -> `release-1.15` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3256
* [r] Prepare for 1.15.0rc3 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3257

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.15.0rc2...1.15.0rc3

**See also**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.15.0rc2...main

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

Breaking changes

* [python] Drop support for Python 3.8 by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3021
* [python] Remove more Python 3.8 references by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3073

Bug fixes

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

Minor changes

* [python] Add `--maxfail=50` to GHA `pytest` invocations by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3034
* [python] Replace deprecated `wheel.bdist_wheel` with `setuptools.command.bdist_wheel` by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3076
* [python] `setuptools>=70.1` in sdist GHA by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3106
* [c++/python] Check `arrow_is_string_type` in `_update_dataframe` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/3111
* [python] Fix deprecation warnings [`main`] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3014
* [python] One more rename in prep for domainish pushdown by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3026
* [python] Use `somacore` 1.0.16 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3035
* [python] Use `somacore` 1.0.17 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3070
* [python/r] Use pushdown domainish accessors at the Python/R UX level by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3027
* [python] Use same default max domain between Python and R by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3088
* [python/r] `DataFrame` resizer by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3091
* [python] Use `somacore` 1.0.20 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3120
* [c++/python] Push `update_dataframe_schema` down to `libtiledbsoma` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3113
* [c++/python/r] Use `libtiledbsoma` for R schema evolution by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3100
* [c++/python/r] Rename a helper function by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3127
* [r] Address some pkgdown GHA warnings by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3077
* [r] Post-1.14 version for `main` branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3009
* [r] Run `clang-format` on `apis/r/src` (except autogen code) by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3048
* [r] Remove the unused `fragment_count` accessor by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3054
* [r] Push `ndim` down to C++ by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3066
* [r] Fix up doc blocks and re-run roxygenise by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3071
* [r] Improve test-case field names for `DataFrame` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3067
* [r] Push `dimnames` down to C++ by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3065
* [r] Run `devtools::document()` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3084
* [r] Implement missing `domain` argument to `DataFrame` `create` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3032
* [r] Make `DataFrame` objects shapeable at ingest by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3089
* [r] Push `attrnames` down to C++ by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3121
* [r] `DESCRIPTION` and `NEWS.md` for 3121 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3122
* [r] Push `schema` accessor down to `libtiledbsoma` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3079
* [c++] Pre-neatens for polymorphic domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3011
* [c++] Update dataframe unit-test writes in prep for polytype domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3017
* [c++] Readback-testing pieces for polytype domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3018
* [c++] Have a `DataFrame` test case with `soma_joinid` not first by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3019
* [c++] Be a bit more careful testing dim-max vs shape by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3020
* [c++] Implementation and unit testing for domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3012
* [c++] Fix bad merge from 3012 and 3020 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3025
* [c++] Fix a `valgrind` issue in unit-test code by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3029
* [c++] Fix memory-management issues in new domainish helpers by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3030
* [c++] Improve current-domain signaling for string dims by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3028
* [c++] Extend some unit-test cases for new shape by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3068
* [c++] Expose custom `DataFrame` domain for `libtiledbsoma` unit-test cases by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3069
* [c++] Add can-resize helpers in prep for experiment-level resize by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3095
* Use core 2.26.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3096
* Minor update to `.gitignore` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3103
* [c++] Fail earlier if `n_buffers` is not as expected by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3107
* [c++] Fix a minor typo in logging statements by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3099
* [c++] Trivial name-shortens in unit-test code by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3125
* [c++] Propagate Python/R function names to C++ for upgrade/resize methods by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3130

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.14.2...1.15.0rc2

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

Breaking changes

* [python] Drop support for Python 3.8 by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3021
* [python] Remove more Python 3.8 references by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3073

Bug fixes

* [Backport release-1.15] Do not fatal on 1.15-related assertions by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3138
* [python] Fix retrieval of named levels from a MultiscaleImage by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/3119
* [python] Fix f-strings in multiscaleimage error messages by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/3118
* [c++] Fix bug in `nnz` of variant-indexed dataframes by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2990

Minor changes

* [python] Add `--maxfail=50` to GHA `pytest` invocations by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3034
* [python] Replace deprecated `wheel.bdist_wheel` with `setuptools.command.bdist_wheel` by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3076
* [python] `setuptools>=70.1` in sdist GHA by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3106
* [c++/python] Check `arrow_is_string_type` in `_update_dataframe` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/3111
* [python] Fix deprecation warnings [`main`] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3014
* [python] One more rename in prep for domainish pushdown by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3026
* [python] Use `somacore` 1.0.16 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3035
* [python] Use `somacore` 1.0.17 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3070
* [python/r] Use pushdown domainish accessors at the Python/R UX level by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3027
* [python] Use same default max domain between Python and R by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3088
* [python/r] `DataFrame` resizer by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3091
* [python] Use `somacore` 1.0.20 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3120
* [c++/python] Push `update_dataframe_schema` down to `libtiledbsoma` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3113
* [c++/python/r] Use `libtiledbsoma` for R schema evolution by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3100
* [c++/python/r] Rename a helper function by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3127
* [r] Address some pkgdown GHA warnings by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/3077
* [r] Post-1.14 version for `main` branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3009
* [r] Run `clang-format` on `apis/r/src` (except autogen code) by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3048
* [r] Remove the unused `fragment_count` accessor by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3054
* [r] Push `ndim` down to C++ by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3066
* [r] Fix up doc blocks and re-run roxygenise by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3071
* [r] Improve test-case field names for `DataFrame` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3067
* [r] Push `dimnames` down to C++ by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3065
* [r] Run `devtools::document()` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3084
* [r] Implement missing `domain` argument to `DataFrame` `create` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3032
* [r] Make `DataFrame` objects shapeable at ingest by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3089
* [r] Push `attrnames` down to C++ by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3121
* [r] `DESCRIPTION` and `NEWS.md` for 3121 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3122
* [r] Push `schema` accessor down to `libtiledbsoma` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3079
* [c++] Pre-neatens for polymorphic domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3011
* [c++] Update dataframe unit-test writes in prep for polytype domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3017
* [c++] Readback-testing pieces for polytype domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3018
* [c++] Have a `DataFrame` test case with `soma_joinid` not first by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3019
* [c++] Be a bit more careful testing dim-max vs shape by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3020
* [c++] Implementation and unit testing for domainish accessors by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3012
* [c++] Fix bad merge from 3012 and 3020 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3025
* [c++] Fix a `valgrind` issue in unit-test code by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3029
* [c++] Fix memory-management issues in new domainish helpers by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3030
* [c++] Improve current-domain signaling for string dims by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3028
* [c++] Extend some unit-test cases for new shape by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3068
* [c++] Expose custom `DataFrame` domain for `libtiledbsoma` unit-test cases by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3069
* [c++] Add can-resize helpers in prep for experiment-level resize by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3095
* Use core 2.26.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3096
* Minor update to `.gitignore` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3103
* [c++] Fail earlier if `n_buffers` is not as expected by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3107
* [c++] Fix a minor typo in logging statements by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3099
* [c++] Trivial name-shortens in unit-test code by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3125
* [c++] Propagate Python/R function names to C++ for upgrade/resize methods by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3130

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.14.2...1.15.0rc0

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 https://github.com/single-cell-data/TileDB-SOMA/pull/3225
* [r] Prepare for 1.14.5 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3226

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.14.4...1.14.5