Tiledbsoma

What's Changed

* [Backport release-1.7] [r] Fix Seurat ingestion with missing command logs collection by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2155
* [r] tiledbsoma 1.7.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2156

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.7.1...1.7.2

New features added

* [Backport release-1.7] [r] Support ingestion of `SeuratCommands` in 2106
* [Backport release-1.7] [r] Support outgestion of `SeuratCommands` in 2114
* [Backport release-1.7] [python] `tiledbsoma.io.update_matrix` in 2130
* [Backport release-1.7] [python] Outgest additional X layers to AnnData in 2144
* [Backport release-1.7] [python] Add type checks to `obsm`, `obsp`, `varm` and `varp` early in ingestion in 2138

Breaking changes

Minor changes

* [r] TileDB-SOMA-R 1.7.1 in 2145
* [r] Fix quoting for a particular Docker-build environment (`release-1.7`) in 2102
* [Backport release-1.7] [r] Let `get_tarball.R` interop with `update-tiledb-version.py` in 2104
* [Backport release-1.7] [python] Reorganize `Reindexer` bindings into separate file in 2111
* [Backport release-1.7] [python] Relax numba dependency in 2127
* [Backport release-1.7] [python] Support Python 3.12 in 2135
* [Backport release-1.7] [python/ci] Leave 3.12 support provisional in 2142
* [Backport release-1.7] [python] Lint fix in 2143

Bug fixes

* [Backport release-1.7] [python] Do not mutate `adata.obs`/`adata.var` on ingest in 2105
* [Backport release-1.7] [python] Specially handle cast for object and category dtypes in 2107
* [Backport release-1.7] [python] Accumulate obs/var IDs across batched reads in `register_anndatas()` in 2113

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.7.0...1.7.1

TileDB-SOMA uses [Tile-DB Core 2.19](https://github.com/TileDB-Inc/TileDB/releases/tag/2.19.0), [TileDB-Py 0.25](https://github.com/TileDB-Inc/TileDB-Py/releases/tag/0.25.0), and [Tile-R 0.23](https://github.com/TileDB-Inc/TileDB-R/releases/tag/0.23.0).

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**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.6.2...1.7.0

What's Changed

In addition to https://github.com/single-cell-data/TileDB-SOMA/releases/tag/1.7.0rc0:

* [Backport release-1.7] [c++/ci] Fix a `pkgdown` CI error about unnecessary semicolons by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2051
* [Backport release-1.7] [python] Rename `utils.py` to `_index_util.py` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2058
* [Backport release-1.7] [python] Pass config options to `DataFrame.read` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2059
* [Backport release-1.7] [c++] Fix zero-size lookup chunk size for the C++ re-indexer by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2062
* [Backport release-1.7] [python] Chunked writes for DataFrame; byte-caps for Arrow-table writes by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2064

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.7.0rc0...1.7.0rc1

TileDB-SOMA uses [Tile-DB Core 2.19](https://github.com/TileDB-Inc/TileDB/releases/tag/2.19.0), [TileDB-Py 0.25](https://github.com/TileDB-Inc/TileDB-Py/releases/tag/0.25.0), and [Tile-R 0.23](https://github.com/TileDB-Inc/TileDB-R/releases/tag/0.23.0).

New features added


* [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] [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
* 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

Bug fixes

* [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**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.6.2...1.7.0-rc0

1.6.2 delivers a Python-only bugfix on the `release-1.6` branch. R is not affected, other than our commitment to keep Python and R API versions synchronized.

Bug fixes

* [python] Allow specification of X names on ingest [release-1.6] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1996
* [python] Minor update to `from_h5ad` online help by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1999
* [r] tiledbsoma 1.6.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2006

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.6.1...1.6.2