TileDB-SOMA 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 #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

• [python] Drop support for Python 3.8 by @ryan-williams in #3021
• [python] Remove more Python 3.8 references by @ryan-williams in #3073

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

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

Full Changelog: 1.14.2...1.15.0rc2