Tiledbsoma

Superseded

**This release has no installable PyPI wheels and has been marked as pre-release. [Release 1.1.1](https://github.com/single-cell-data/TileDB-SOMA/releases/tag/1.1.1) fixes these issues.**

Main goal

This release brings in [TileDB Embedded 2.15.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.15.0), along with [TileDB-Py 0.21.1](https://github.com/TileDB-Inc/TileDB-Py/releases/tag/0.21.1) and [TileDB-R 0.19.0](https://github.com/TileDB-Inc/TileDB-R/releases/tag/0.19.0). It also brings in updates for Conda installs.

New features added

* [python] Support Conda builds on POSIX by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1043

Minor changes

* [c++,r,python] Update to core version 2.15.0 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1066
* [c++/r/python] Add libtiledbsoma info to `show_package_versions()` by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1101
* [c++/python/r] Add `shape` to C++ `SOMAReader` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1083
* [r] Add test for nnz() when duplicates==TRUE by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1107

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0...1.1.0

What's Changed

The sole modification in this bugfix update to 1.0.0 is to update the library version of TileDB Embedded. The 1.1.1 release and above is appropriate for general-purpose use.

* [c++] Have TileDB-SOMA 1.0 depend on TileDB Embedded 2.14.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1145


**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0...1.0.1

This is the 1.0.0 release for the TileDB-SOMA Python API. A 1.0 release for the R version is forthcoming.

Feedback, questions, comments, and concerns are all welcomed at [https://github.com/single-cell-data/TileDB-SOMA/issues](https://github.com/single-cell-data/TileDB-SOMA/issues).

New features added

* [docs] Update `README.md` to include API docsites by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1103
* [python] Get `readthedocs` going by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1098
* [docs][python] Add experiment-query example notebook by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1104
* [docs] [python] Notebook - Read from a SparseNDArray by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1093
* [r] Publish TileDB-SOMA-R `pkgdown` docs to GitHub Pages by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1095
* [r] Add four `add_new_*` setters to `SOMACollectionBase` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1091
* [r] Implement `PlatformConfig` and `SOMATileDBContext` for R by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1038

Minor changes

* [r] Switch four internal functions to noRd by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1096
* [docs] Update `README.md` with more contextual and onboarding info by pablo-gar in https://github.com/single-cell-data/TileDB-SOMA/pull/1069
* [python] Trivial doc-neatens in prep for web publishing by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1042
* [docs] Add `pip upgrade` in readthedocs pipeline by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1094
* [python] Depend on somacore 1.0.0 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1105

New Contributors
* pablo-gar made their first contribution in https://github.com/single-cell-data/TileDB-SOMA/pull/1069

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0rc6...1.0.0

New features added

* [r/c++] Add mode flag to `is_complete()` and add `total_num_cells()` accessor by gspowley in https://github.com/single-cell-data/TileDB-SOMA/pull/1071

* [python] Tutorial notebook for SOMA objects by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1063
* [python] Add optional shape parameter to `SparseNDArrayRead .coos()` by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1081

* [docs] Add SparseNDArray section in tutorial notebook by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1074
* [docs] Convert all the modules to Google-style docstrings by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1070
* [docs] Fix documentation bug for from_h5ad by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1075
* [docs] Add SOMA reading tutorial notebook (part 1) by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1079

Minor changes

* [c++/r/python] Push down stats to `libtiledbsoma`; pass config not context to `sr_setup` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1072
* [r] Implement `tiledbsoma:::tiledb_embedded_version` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1077
* [r] A bit more dev advice for R by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1080
* [r] Don't doubly specify in a unit-test case by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1084
* [r] Handle config in non-iterated readers by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1085
* [python] Depend on somacore 1.0.0rc6 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1092

Bug fixes

* [r] Support callers not having done `library(tiledb)` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1082
* [r] Avoid "Error: Can't convert input object to pointer" by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1078

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0rc5...1.0.0rc6

Key features of this release are 1053 and 1061.

New features added

* [python] Support ingest of H5AD dense X as SOMA sparse X by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1061
* [r] Expand developer instructions in `apis/r/README.md` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1054
* [r] Add `index_column_names()` (as an aliases to `dimnames()`) by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1056
* [r] Test-drive `apis/r/README.md` on a fresh EC2 instance by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1060

Breaking changes

* [python] Ingestor must return readable result by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1053

Minor changes

* [docs] Convert docstrings in `_collection.py` to Google style by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1044
* [r] Refactor arrow export by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1052
* [python] Run packaging workflow nightly by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1059
* [python] Polish `version.py` by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1057
* [python] Constrain numba & numpy versions for compatibility with old pip solver by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1058
* [python] Code-neaten follow-up for 1061 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1065
* [python] Depend on somacore 1.0.0rc5 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1067

New Contributors
* ebezzi made their first contribution in https://github.com/single-cell-data/TileDB-SOMA/pull/1044

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0rc4...1.0.0rc5

Bug fixes
* [python] Depend on attrs package >= 22.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1050


**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.0.0rc3...1.0.0rc4