TileDB-SOMA 1.7.0

TileDB-SOMA uses Tile-DB Core 2.19, TileDB-Py 0.25, and Tile-R 0.23.

New features added

• [Backport release-1.7] [python] Using optimized reindexer in blockwise iterators by @johnkerl in #2093
• [Backport release-1.7] [python] Reindexer external python API by @johnkerl in #2092
• [Backport release-1.7] [python] Save off ingest-time obs/var index names for use at outgest by @github-actions in #2072
• [python] Allow specification of X names on ingest by @johnkerl in #1993
• [r] Arrays should remain open after write by @aaronwolen in #1947
• [r] Add support for registering arrays with write_soma() by @mojaveazure in #2013
• [r] Add write_soma.character() by @mojaveazure in #2021
• [r] Update documentation on g++ requirement for R package by @CharlesBordet in #2031
• [r] Support cross compiling on MacOS with R by @jeroen in #2034

Minor changes

• [Backport release-1.7] [c++] Handling edge cases for C++ re-indexer (#2098) (#2100)
• [Backport release-1.7] [python] Elaborate docstring re relativity for add-new by @github-actions in #2089
• [Backport release-1.7] [python] Rename utils.py to _index_util.py by @github-actions in #2058
• [Backport release-1.7] [python] Add common.h to MANIFEST.in by @github-actions in #2043
• [Backport release-1.7] [python] Update unit tests for pandas 2.2 and scipy 1.12 by @github-actions in #2044
• [Backport release-1.7] [r] Enable opt-in use of 'catchsegv', enable in CI on Linux by @github-actions in #2046
• [Backport release-1.7] [python] Silence a unit-test warning by @github-actions in #2070
• [Backport release-1.7] [c++/ci] Fix a pkgdown CI error about unnecessary semicolons by @github-actions in #2051
• Depend on TileDB core 2.19, TileDB-Py 0.25, TileDB-R 0.23 by @johnkerl in #2002
• Update to use somacore==1.0.7. by @thetorpedodog in #2000
• Bump jinja2 from 3.0.0 to 3.1.3 in /doc by @dependabot in #2007
• [python] Depend on somacore 1.0.6 by @johnkerl in #1940
• [python] Add unit tests for obsm, obsp, and to_anndata by @ebezzi in #1934
• [python] QueryCondition should error out if given empty set by @nguyenv in #1967
• [python] Dataframe read path by @nguyenv in #1793
• [r] tiledbsoma-r 1.7.0 by @johnkerl in #2041
• [r/ci] Show CPU info in R CI as well as Python CI by @johnkerl in #1956
• [r] Apply PR 1943 to main by @johnkerl in #1957
• [r] Tweak coverage data generation by @eddelbuettel in #1990
• [r] Bump apis/r/DESCRIPTION for main past current latest release by @johnkerl in #2005
• [r] Add a helper function to determine max value per int type by @eddelbuettel in #2022
• [c++] Modify ManagedQuery to perform async queries by @nguyenv in #1953
• [c++] Have tiledbsoma-cli link to tiledbsoma by @teo-tsirpanis in #1965
• [c++] Extend codecov to cover tiledbsoma library by @beroy in #1970
• [c++] Append TILEDBSOMA_COVERAGE to cmake flags by @nguyenv in #2019
• [c++] Reindexer overrides and fast COO/CSR by @beroy in #1728
• [Backport release-1.7] Use core 2.19.1 by @github-actions in #2085

Bug fixes

• [Backport release-1.7] [c++] Fix for error when the key array size is smaller than thread count by @github-actions in #2097
• [Backport release-1.7] [python] Fix some docstring typos by @johnkerl in #2095
• [Backport release-1.7] [python] Pass config options to DataFrame.read by @github-actions in #2059
• [Backport release-1.7] [c++] Fix zero-size lookup chunk size for the C++ re-indexer by @github-actions in #2062
• [Backport release-1.7] [python] Chunked writes for DataFrame; byte-caps for Arrow-table writes by @github-actions in #2064
• [python] Fix from_anndata() to respect var_id_name by @aaronwolen in #1963
• [python] Fix data loss for multiple writes with Enumeration extend by @nguyenv in #1978
• [python] Error if extending enum past index type limit by @nguyenv in #1986
• [r] Ensure factors are releveled before appending w/ expanded levels by @eddelbuettel in #1983
• [r] Ensure addition of factor levels does not overflow capacity of index type by @eddelbuettel in #2008

Ongoing progress

• [python] Add Windows support for the Python API by @teo-tsirpanis in #1811 (Note: this is still a WIP)
• [python] Revert "Add Windows support for the Python API" by @johnkerl in #1959
• [python] Add back Windows support for the Python API, but without CI by @teo-tsirpanis in #1961

New Contributors

• @teo-tsirpanis made their first contribution in #1811
• @dependabot made their first contribution in #2007
• @CharlesBordet made their first contribution in #2031
• @jeroen made their first contribution in #2034

Full Changelog: 1.6.2...1.7.0