Tiledbsoma

What's Changed

This release is procedural. It ensures that we have version 1.4.2 for both Python and R, which was not the case in 1.4.1.

* [r] Backport 1596 to release-1.4 branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1597

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.4.1...1.4.2

What's Changed

This release is Python-only

* [backport release-1.4] [python] Make `tiledbsoma.io._create_or_open_coll` compatible with 1.2.7 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1593

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.4.0...1.4.1

TileDB-SOMA R General Availability

**This 1.4.0 release of the multi-language TileDB-SOMA package serves as the General Availability release for TileDB-SOMA-R.**

Installation guidance: https://github.com/single-cell-data/TileDB-SOMA/blob/main/apis/r/README.md

Major changes
* [r] Release 1.4.0 by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1574

New features added

* [r] Add SOMA Experiment Query -> SingleCellExperiment outgestor by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1279
* [python] Improve guidance on non-ingestible NaN data in categorical-int obs/var columns by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1568
* [python] Add parameters to `ExperimentAxis` query methods by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1553
* [python] Generalize `add_X_layer` URI handling by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1548

Minor changes

* [r] Temporarily install tiledb-r from r-universe by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1570
* [r] Docs and NAMESPACE cleanup by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1566
* [r] Experiments for r-universe dependencies on Mac by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1571
* Update to on core 2.16.2, TileDB-Py 0.22.2, and TileDB-R 0.20.3 by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1579
* Update to core 2.16.1, tiledb-py 0.22.1, tiledb-r 0.20.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1561
* [python] Replace dataclasses with attrs by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1557
* [python] Append-mode pre-check logic by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1554
* [python] Usability improvements to profiler by atolopko-czi in https://github.com/single-cell-data/TileDB-SOMA/pull/1516
* [c++] Add new constructor, factor validation helper by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1560
* [c++] Addition of `SOMACollection`, `SOMAMeasurement`, `SOMAExperiment` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1541
* [c++] Addition of `SOMA{Dense,Sparse}NDArray` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1529

Bug fixes

* [r] Ensure numeric axis query coordinates are converted by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1540
* [python] Adding missing context in ingest uns ndarray by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1552
* [python] Add a missing log-line for uns ndarray ingest by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1551

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.3.0...1.4.0

Highlights

This release serves as the release candidate for the TileDB-SOMA R package. For the moment, this appears in the
`DESCRIPTION` file as 0.99.1. Once we go to GA for the TileDB-SOMA R package, the `DESCRIPTION` file will have
1.4.0 in it, matching the GitHub release tag.

Additionally, this release brings in TileDB Core 2.16, along with TileDB-Py 0.22 and TileDB-R 0.20.

New features added

* [r] Restore `SOMASparseNDArray$read_sparse_matrix()` by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1414
* [r] Adjust vignette to change in zero-based access and views by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1417
* [r] Add iterator classes by pablo-gar in https://github.com/single-cell-data/TileDB-SOMA/pull/1274
* [c++,r] Use knowing whether read is initial or not when reading 'next' result set by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1422
* [r] Return empty arrow table on empty results set by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1426
* [r] Config and context support for `SOMACollection`'s `add_new_*()` methods by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1448
* [r] Support timestamps (in READ mode) by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1429
* [r] Refactoring of files in src/ by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1467
* [r] Add `to_sparse_matrix()` method to `SOMAExperimentAxisQuery` by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1478
* [r] Accommodate arrow vector as input vector for `soma_array_reader` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1480
* [r] Improve handling of arrays with with domains greater than 2^31 - 1 by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1504
* [r] Adjust `SOMAExperimentAxisQuery$to_sparse_matrix()` to handle gapped matrices by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1501
* [r] Refactor `SOMAExperimentAxisQuery` `obs()` `var()` and `X()` to allow for iteration by pablo-gar in https://github.com/single-cell-data/TileDB-SOMA/pull/1505
* [r] Update README.md installation instructions in preparation for 1.0[rc] by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1502
* [r] Optimize export of obsm/varm arrays to Seurat by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1521
* [r] Fix bug found on nested close by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1524
* [r] Check dimension domain when setting dim points and ranges by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1526
* [r] Add `axis_query()` method to `SOMAExperiment` by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1539
* [python] Ingest `anndata.layers` by default in `tiledbsoma.io` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1459
* [r/python] Clarify online docs re shape-as-capacity by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1446
* [python] Use 31-bit-friendly default shape for ingest by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1440
* [python] Don't re-write `uns` NDArrays when in resume mode by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1509
* [docs] Update install/quick-start notes by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1464
* [docs] Some doc-link updates by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1469
* Use core 2.16, tiledb-py 0.22, tiledb-r 0.20 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1535

Minor changes and bugfixes

* [r] Refactor `matrixZeroBasedView` by pablo-gar in https://github.com/single-cell-data/TileDB-SOMA/pull/1411
* [r] Minor arrow refactor ensuring ext pointers use for struct cols by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1407
* [r] Vignette follow-up from 1417 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1418
* [r] Respect global log level by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1419
* [r] Expose two more arguments for `sr_setup` and enable tests by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1428
* [r] Address issues identified by `R CMD check` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1444
* [r] Run coverage in parallel instead of sequentially after test by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1442
* [r] Remove now redundant dependency on `dplyr` (given `arrow`) by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1457
* [r] Additional cleanup after dropping dplyr by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1461
* [r] Fix example error in sr_setup docs by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1462
* [r] Trivial typofix by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1465
* [r] Remove defunct query code from `TileDBArray` by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1481
* [r] Add `SOMANDArrayBase` class by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1523
* [r] Run R/interop CI on release branches as well as main by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1543
* [python] Make `TileDBCreateOptions` suitable for human consumption by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1408
* [python] Update lifecycle tags by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1405
* [python] Export `TileDBCreateOptions` at the top level, and add to docs by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1431
* [python] Depend on somacore 1.0.3 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1430
* [python] Improve stack traces on collection create/open in the ingestor by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1438
* [python] Wire obs/var ID options to `devtools/outgestor` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1435
* [python] Raise on `add_X_layer` if collection not open by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1460
* [python] Skip ingest of zero-cell uns arrays by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1468
* [python] Add 3.11 to `classifiers=` in `setup.py` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1471
* [python] Update numba/numpy versions for Python 3.11 by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1472
* [python] Early version of the generic profiler by beroy in https://github.com/single-cell-data/TileDB-SOMA/pull/1290
* [python] Generic profiler fixes by atolopko-czi in https://github.com/single-cell-data/TileDB-SOMA/pull/1473
* [python] Simplify internal ingestion API via `IngestionParams` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1474
* [python] Minor function-extract in ingestion logic by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1500
* [python] Trivial extract-method in uns ingestor by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1508
* [python] Ingest uns string arrays as single-attr SOMADataFrame by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1514
* [c++/python] Fix new pybind11 capsule build error by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1533
* [c++] Reformat C++ code post 1429 by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1451
* [c++] Add Unit Test for `SOMAArray::read_next` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1452
* [c++] Addition of `SOMAArray::create` and `SOMAArray::write` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1439
* [c++] Addition of `SOMAObject` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1475
* [c++] `SOMAArray::write` Modified To Take in `ArrayBuffers` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1476
* [c++] `ColumnBuffer` Constructor Should Call `alloc` Method by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1499
* [c++] Addition of `SOMADataFrame` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1449
* [ci] Initial experiments with backport-bot by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1506
* [ci] Backport-bot Ubuntu-image update by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1510
* [ci] Remove GitHub Python 3.7 build workaround. by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1517
* [r/docs] Fine-tune article display in pkgdown setup by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1415
* [r/docs] Update README.md to current build setup by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1413
* [docs][python] Add autosummary by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1392
* [ci/python] Run full CI on merges to `release-i.j` branches by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1490

New Contributors

* beroy made their first contribution in https://github.com/single-cell-data/TileDB-SOMA/pull/1290

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.2.4...1.3.0

This is a cherry-pick of a few Python-only bugfix items from main. The bulk of current development work at present is on the R and C++ fronts, most likely to be delivered in an upcoming 1.3.0 release.

Note: there is no 1.2.6.

* [python] Backport 1471 from `main` to `release-1.2` branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1483
* [python] Backport 1472 from `main` to `release-1.2` branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1484
* [python] Backport 1468 from `main` to `release-1.2` branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1485
* [python] Backport 1459 from `main` to `release-1.2` branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1486


**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.2.5...1.2.6

This is a cherry-pick of a few items from `main`, branched from 1.2.4. The main goal is getting the `lifecycle: maturing` tags released into GitHub and PyPI.

What's Changed

* [python] 1.2.5 backports by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1432

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.2.4...1.2.5