Tiledbsoma

* [r] TileDB-SOMA 1.12.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2759

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.12.0...1.12.1

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

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

What's Changed

This release does not affect any Python code.

* [r] Backport sparse COO writer to 1.14 by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/3217
* [r] Prep for 1.14.4 release by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3219

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.14.3...1.14.4