Tiledbsoma

One of the main reasons for this release is to bring https://tiledbsoma.readthedocs.io/en/stable/ up to date.

New features added

* [Backport release-1.11] [c++/python] Enable optional global-order writes for sparse arrays by github-actions in 2598
* [Backport release-1.11] Tutorial: TileDB-SOMA append-mode by github-actions in 2600
* [Backport release-1.11] [python] Append-mode tutorial: "atlas model" by github-actions in 2606

Minor changes

* [Backport release-1.11] [c++/python] Address C++ warnings in Python build by github-actions in 2611
* [Backport release-1.11] [c++] Allow `row-major` and `col-major` in `SOMArray::create` by github-actions in 2562
* [Backport release-1.11] [c++] Correct `platform_config` to `tiledb_config` by github-actions in 2601
* [Backport release-1.11] [c++] Handle 32-bit string and binary in writes by github-actions in 2604
* [Backport release-1.11] [c++] `PlatformConfig` refactoring by github-actions in 2572
* [Backport release-1.11] [c++] Fix nightly build failure on `formattable` of `json` type by github-actions in 2614
* [Backport release-1.11] [c++] Also map "NONE" to `TILEDB_FILTER_NONE` (2599) by johnkerl in 2612
* [Backport release-1.11] [python/c++] Typo fixes / nits by johnkerl in 2613
* [Backport release-1.11] [python] Document build improvements, unshallow clone (fix dev builds) by github-actions in 2566
* [Backport release-1.11] [python] Trivial neaten by github-actions in 2568
* [Backport release-1.11] [r] Fix builds against current TileDB Embedded by github-actions in 2574
* [Backport release-1.11] [r] Switch 'UNORDERED' cell order to 'ROW_MAJOR' on schema creation by github-actions in 2576
* [Backport release-1.11] [python/ci] Use `macos-11` -> `macos-12` for `python-packaging.yml` by github-actions in 2595
* [Backport release-1.11] [python] Better version numbers during development by github-actions in 2570
* [Backport release-1.11] [ci] Move Python wheel-builds from `macos-11,macos-12` to `macos-12,macos-latest` by github-actions in 2607
* [Backport release-1.11] [python] `version.py`: guard `git` calls during wheel builds (sans `.git`) by johnkerl in 2602
* [Backport release-1.11] [r] Better handling of timestamps in `$reopen()` by johnkerl in 2610
* [Backport release-1.11] [python/ci] Build wheel from sdist outside of Git repository by johnkerl in 2605
* [r] TileDB-SOMA 1.11.2 by johnkerl in 2615

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.11.1...1.11.2

This release is identical to 1.11.0. The sole job of this release is to provide PyPI artifacts to work around an issue documented here:

https://github.com/single-cell-data/TileDB-SOMA/issues/2556#issuecomment-2110422212

What's Changed

* [r] tiledbsoma 1.11.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2558

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.11.0...1.11.1

New features added

* [python]Robust URI handling for Ingestion-performance improvement by johnkerl in 2457
* [python] Allow `obs_query=None`/`var_query=None` in `ExperimentAxisQuery` by johnkerl in 2476
* [python] Export `tiledbsoma.SparseNDArrayRead`, include in module doc site by ryan-williams in 2544
* [r] Port resume-mode to R by mojaveazure in 2405

Minor changes


* [python] Use C++ `DataFrame` bindings for create and writes by nguyenv in 2431
* [python] Remove arbitrary dimension limit in `used_shape` by thetorpedodog in 2479
* [python/c++] Use C++ bindings for `SparseNDArray` write path by nguyenv in 2446
* [python,c++] Use C++ `DenseNDArray` bindings in Python API by nguyenv in 2494
* [c++,python] Remove tiledb-py for all arrays by nguyenv in 2498
* [python/ci] Add CI job to test building wheel from sdist by jdblischak in 2506
* [python] Continue 2516 by johnkerl in 2522
* [python] Clarify `test_update_dataframe.py` and `_arrow_types.py` by johnkerl in 2521
* [python] Raise `NotImplementedError` for `DataFrame.shape` by nguyenv in 2533
* [python] Update `doc/` README/deps, fix warnings, `from_h5ad` formatting by ryan-williams in 2538
* [r] Set default create options during `TileDBCreateOptions$new()` by mojaveazure in 2483
* [r] Always return filters in `TileDBCreateOptions` by mojaveazure in 2486
* [r,ci] Run coverage only on `workflow_dispatch` events by eddelbuettel in 2488
* [r] Silence missing command logs warning by mojaveazure in 2507
* [r] Ensure `SOMADataFrame$shape()` throws a not-yet-implemented error by mojaveazure in 2531
* [r/ci] Utilize pin of tiledb-r during install by mojaveazure in 2540
* [r/ci] Add check to disable BSPM in R CI by mojaveazure in 2546
* [c++] Addition of `ArrowSchema` to TileDB `ArraySchema` Converter by nguyenv in 2418
* [c++] Fix Windows build regressions and stop using deprecated TileDB APIs by teo-tsirpanis in 2445
* [c++] Write data in `ArrowArray` to `SOMAArray` by nguyenv in 2425
* [c++] Pass `ColumnIndexInfo` as `ArrowTable` by nguyenv in 2472
* [c++] Add documentation and better checking to `PlatformConfig` by nguyenv in 2481
* [c++] Pass Boolean to indicate sparse or dense in ArraySchema by nguyenv in 2487
* [c++] Support `cmake-verbose` flag in `Makefile` by johnkerl in 2495
* [c++] Do not add dimensions for dense array queries if not requested by johnkerl in 2453
* [c++] Remove extraneous print statements by johnkerl in 2527
* [c++] Explicitly set `ArrowSchema` flag to 0 by nguyenv in 2525
* Bump jinja2 from 3.1.3 to 3.1.4 in /doc by dependabot in 2514
* [ci] Restrict R/Python GHAs from running on irrelevant `{.github,doc}` changes by ryan-williams in 2543
* [r] Bump `DESCRIPTION` version past 1.10 (`main` branch) by johnkerl in 2451
* [r] Prep for 1.11.0 by johnkerl in 2553
* Use core 2.23.0, TileDB-Py 0.29.0, TileDB-R 0.27.0 by johnkerl in 2548

Bug fixes

* [python] Append-mode enum bit-width mods by johnkerl in 2455
* [python] Fix unbound-local error by johnkerl in 2516
* [python] Fix `failed to convert buffer` on `update_obs`/`update_var` by johnkerl in 2518
* [python] Error on registration of multi-modal experiment with distinct var field names by johnkerl in 2535
* [python] Fix write from array that is not row or column order by jp-dark in 2542
* [r,ci] Update `r-ci.sh`, remove unneeded entries from `r-ci.yml` by eddelbuettel in 2475

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.10.2...1.11.0

What's Changed
* [r] Bump `DESCRIPTION` version past 1.10 (`main` branch) by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2451
* [c++] Addition of `ArrowSchema` to TileDB `ArraySchema` Converter by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2418
* [c++] Fix Windows build regressions and stop using deprecated TileDB APIs by teo-tsirpanis in https://github.com/single-cell-data/TileDB-SOMA/pull/2445
* [c++] Write data in `ArrowArray` to `SOMAArray` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2425
* [python]Robust URI handling for Ingestion-performance improvement by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2457
* [python] Use C++ `DataFrame` bindings for create and writes by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2431
* [r,ci] Update `r-ci.sh`, remove unneeded entries from `r-ci.yml` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/2475
* [c++] Pass `ColumnIndexInfo` as `ArrowTable` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2472
* [python] Allow `obs_query=None`/`var_query=None` in `ExperimentAxisQuery` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2476
* [r] Port resume-mode to R by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/2405
* [c++] Add documentation and better checking to `PlatformConfig` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2481
* [r] Set default create options during `TileDBCreateOptions$new()` by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/2483
* [r] Always return filters in `TileDBCreateOptions` by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/2486
* [c++] Pass Boolean to indicate sparse or dense in ArraySchema by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2487
* [r,ci] Run coverage only on `workflow_dispatch` events by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/2488
* [c++] Support `cmake-verbose` flag in `Makefile` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2495
* [python] Remove arbitrary dimension limit in `used_shape` by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/2479
* [c++] Do not add dimensions for dense array queries if not requested by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2453
* [r] Silence missing command logs warning by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/2507
* [python/c++] Use C++ bindings for `SparseNDArray` write path by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2446
* [python] Append-mode enum bit-width mods by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2455
* [python,c++] Use C++ `DenseNDArray` bindings in Python API by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2494
* [c++,python] Remove tiledb-py for all arrays by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2498
* [python] Fix unbound-local error by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2516
* [python/ci] Add CI job to test building wheel from sdist by jdblischak in https://github.com/single-cell-data/TileDB-SOMA/pull/2506
* [python] Continue 2516 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2522
* [c++] Remove extraneous print statements by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2527
* [c++] Explicitly set `ArrowSchema` flag to 0 by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2525
* Bump jinja2 from 3.1.3 to 3.1.4 in /doc by dependabot in https://github.com/single-cell-data/TileDB-SOMA/pull/2514
* [python] Clarify `test_update_dataframe.py` and `_arrow_types.py` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2521
* [r] Ensure `SOMADataFrame$shape()` throws a not-yet-implemented error by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/2531
* [python] Fix `failed to convert buffer` on `update_obs`/`update_var` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2518
* [python] Raise `NotImplementedError` for `DataFrame.shape` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/2533
* [python] Error on registration of multi-modal experiment with distinct var field names by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2535
* [r/ci] Utilize pin of tiledb-r during install by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/2540
* [python] Fix write from array that is not row or column order by jp-dark in https://github.com/single-cell-data/TileDB-SOMA/pull/2542
* [ci] Restrict R/Python GHAs from running on irrelevant `{.github,doc}` changes by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/2543
* [python] Update `doc/` README/deps, fix warnings, `from_h5ad` formatting by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/2538
* [r/ci] Add check to disable BSPM in R CI by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/2546
* Use core 2.23.0, TileDB-Py 0.29.0, TileDB-R 0.27.0 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2548
* [python] Export `tiledbsoma.SparseNDArrayRead`, include in module doc site by ryan-williams in https://github.com/single-cell-data/TileDB-SOMA/pull/2544
* [r] Prep for 1.11.0 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2553


**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.10.2...1.11.0rc0

Features

* [r] Backport resume-mode for R to the `release-1.10` branch, and R 1.10.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2490
* [Backport release-1.10] [python] Allow `obs_query=None`/`var_query=None` in `ExperimentAxisQuery` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2478

Minor/internal changes

* [Backport release-1.10] [r,ci] Run coverage only on `workflow_dispatch` events by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2489
* [Backport release-1.10] [r,ci] Update `r-ci.sh`, remove unneeded entries from `r-ci.yml` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2477

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.10.1...1.10.2

This release contains a single Python bugfix.

* [Backport release-1.10] [python]Robust URI handling for Ingestion-performance improvement by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/2459
* [r] TileDB-SOMA-R 1.10.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2458

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.10.0...1.10.1