1.12.1

What's Changed

• Use core 2.24.1 on release-1.12 branch by @johnkerl in #2757
  • https://github.com/TileDB-Inc/TileDB/releases/tag/2.24.1
• [r] TileDB-SOMA 1.12.1 by @johnkerl in #2759

Full Changelog: 1.12.0...1.12.1

TileDB-SOMA 1.12.1rc0

What's Changed

• Use core 2.24.1 on release-1.12 branch by @johnkerl in #2757

Full Changelog: 1.12.0...1.12.1rc0

TileDB-SOMA 1.12.0rc1

This is a quick pre-check for the release-tagging process itself (pkgdown, wheel build/publish, etc.) before tagging 1.12.0 -- which I expect to happen today.

What's Changed

• [Backport release-1.12] [python] Deprecate tiledb_ctx usage in TileDBSOMAContext by @github-actions in #2724
• [Backport release-1.12] [c++] Fix a nightly-build issue by @github-actions in #2725
• [Backport release-1.12] [c++] Fix enum-of-bool leveling by @github-actions in #2727
• [Backport release-1.12] [python] Support tiledbsoma.io.update_obs with post-nullable non-string attributes by @github-actions in #2728
• [Backport release-1.12] [python] Pin to numpy < 2.0 for 1.12 release by @github-actions in #2746
• [Backport release-1.12] [r] Connect re-indexer to blockwise iterator by @github-actions in #2748
• [r] TileDB-SOMA 1.12 by @johnkerl in #2747

Full Changelog: 1.12.0rc0...1.12.0rc1

TileDB-SOMA 1.12.0

New features added

• [Backport release-1.12] [r] Connect re-indexer to blockwise iterator by @github-actions in #2748
• [r] Port re-indexer to the R API by @mojaveazure in #2637
• [python] Append-mode tutorial: "atlas model" by @ryan-williams in #2582
• [python] TileDB-SOMA append-mode tutorial by @ryan-williams in #2571
• [c++/python] Enable optional global-order writes for sparse arrays by @nguyenv in #2564
• [python] Include guidance for older CPU architectures by @johnkerl in #2643
• [r] Better handling of timestamps in $reopen() by @mojaveazure in #2497
• [c++] Improve default buffer sizes by @johnkerl in #2681
• Update to core 2.24, tiledb-py 0.30, tiledb-r 0.28 by @johnkerl in #2715

Breaking changes

• [Backport release-1.12] [python] Deprecate tiledb_ctx usage in TileDBSOMAContext by @github-actions in #2724

Minor changes

• [Backport release-1.12] [python] Pin to numpy < 2.0 for 1.12 release by @github-actions in #2746
• [python] Document build improvements, unshallow clone (fix dev builds) by @ryan-williams in #2560
• [python] Trivial neaten by @johnkerl in #2567
• [python] Better version numbers during development by @ryan-williams in #2563
• [python] version.py: guard git calls during wheel builds (sans .git) by @ryan-williams in #2590
• [python/ci] Build wheel from sdist outside of Git repository by @jdblischak in #2589
• [python/ci] Use macos-11 -> macos-12 for python-packaging.yml by @johnkerl in #2594
• [python/c++] Typo fixes / nits by @ryan-williams in #2596
• [c++/python] Address C++ warnings in Python build by @jp-dark in #2581
• [python/ci] Stop wheel-smoke-test failures for MacOS > 11 by @johnkerl in #2620
• [r] Prep on main for release-1.11 branch by @johnkerl in #2550
• [r] Fix builds against current TileDB Embedded by @johnkerl in #2573
• [r] Correct four \link{} references in help pages by @eddelbuettel in #2626
• [r] Update changed URL in three vignette files by @eddelbuettel in #2632
• [r] Set minimum version of Arrow to 15.0.1 by @mojaveazure in #2678
• [r] Use arrow minimum 14, not 15 by @johnkerl in #2690
• [r/ci] Adjust file download timeout to 300 seconds by @mojaveazure in #2649
• [r] Fix dependency of a test on fixed buffer sizes by @johnkerl in #2685
• [r/ci] Unbreak pkgdown CI by @johnkerl in #2703
• [r,py,c++] Support data frame write path by @eddelbuettel in #2704
• [r/ci] Unbreak r-valgrind CI by @johnkerl in #2711
• [c++] Allow row-major and col-major in SOMArray::create by @johnkerl in #2561
• [c++] PlatformConfig refactoring by @nguyenv in #2541
• [c++] Correct platform_config to tiledb_config by @nguyenv in #2597
• [c++] Also map "NONE" to TILEDB_FILTER_NONE by @nguyenv in #2599
• [ci] Move Python wheel-builds from macos-11,macos-12 to macos-12,macos-latest by @johnkerl in #2491
• [c++] Fix nightly build failure on formattable of json type by @johnkerl in #2609
• version.py: prevent Git version computation from raiseing by @ryan-williams in #2624
• Restore/add wheel smoke-tests, parallelize wheel builds by @ryan-williams in #2640
• [c++] Pass in a shared_ptr<Context> to _create_dim_aux by @nguyenv in #2645
• [ci] Switch from 16MB to 32MB buffer sizes for tiny GHA runners by @johnkerl in #2688
• [doc] Update README.md badge for Python CI (closes #2694) [ci skip] by @eddelbuettel in #2695
• [r] TileDB-SOMA 1.12 by @johnkerl in #2747
• [Backport release-1.12] [c++] Fix a nightly-build issue by @github-actions in #2725

Bug fixes

• [Backport release-1.12] [python] Support tiledbsoma.io.update_obs with post-nullable non-string attributes by @github-actions in #2728
• [python] Correctly handle string vs large string in Enumerations by @nguyenv in #2668
• [r] Switch 'UNORDERED' cell order to 'ROW_MAJOR' on schema creation by @eddelbuettel in #2575
• [c++] Handle 32-bit string and binary in writes by @nguyenv in #2519
• [c++] Fix validity buffer bit unpacking by @nguyenv in #2650
• [c++] Fix indexer memory leak by @johnkerl in #2665
• [Backport release-1.12] [c++] Fix enum-of-bool leveling by @github-actions in #2727

Upcoming deprecation notices

Full Changelog: 1.11.4...1.12.0

1.12.0rc0

This is a draft release for 1.12.0. Release notes coming soon.

New features added

• [python] Append-mode tutorial: "atlas model" by @ryan-williams in #2582
• [python] TileDB-SOMA append-mode tutorial by @ryan-williams in #2571
• [c++/python] Enable optional global-order writes for sparse arrays by @nguyenv in #2564
• [python] Include guidance for older CPU architectures by @johnkerl in #2643
• [r] Better handling of timestamps in $reopen() by @mojaveazure in #2497
• [r] Port re-indexer to the R API by @mojaveazure in #2637
• Update to core 2.24, tiledb-py 0.30, tiledb-r 0.28 by @johnkerl in #2715
• [c++] Improve default buffer sizes by @johnkerl in #2681

Breaking changes

Minor changes

• [python] Document build improvements, unshallow clone (fix dev builds) by @ryan-williams in #2560
• [python] Trivial neaten by @johnkerl in #2567
• [python] Better version numbers during development by @ryan-williams in #2563
• [python] version.py: guard git calls during wheel builds (sans .git) by @ryan-williams in #2590
• [python/ci] Build wheel from sdist outside of Git repository by @jdblischak in #2589
• [python/ci] Use macos-11 -> macos-12 for python-packaging.yml by @johnkerl in #2594
• [python/c++] Typo fixes / nits by @ryan-williams in #2596
• [c++/python] Address C++ warnings in Python build by @jp-dark in #2581
• [python/ci] Stop wheel-smoke-test failures for MacOS > 11 by @johnkerl in #2620
• [r] Prep on main for release-1.11 branch by @johnkerl in #2550
• [r] Fix builds against current TileDB Embedded by @johnkerl in #2573
• [r] Correct four \link{} references in help pages by @eddelbuettel in #2626
• [r] Update changed URL in three vignette files by @eddelbuettel in #2632
• [r] Set minimum version of Arrow to 15.0.1 by @mojaveazure in #2678
• [r] Use arrow minimum 14, not 15 by @johnkerl in #2690
• [r/ci] Adjust file download timeout to 300 seconds by @mojaveazure in #2649
• [r] Fix dependency of a test on fixed buffer sizes by @johnkerl in #2685
• [r/ci] Unbreak pkgdown CI by @johnkerl in #2703
• [r,py,c++] Support data frame write path by @eddelbuettel in #2704
• [r/ci] Unbreak r-valgrind CI by @johnkerl in #2711
• [c++] Allow row-major and col-major in SOMArray::create by @johnkerl in #2561
• [c++] PlatformConfig refactoring by @nguyenv in #2541
• [c++] Correct platform_config to tiledb_config by @nguyenv in #2597
• [c++] Also map "NONE" to TILEDB_FILTER_NONE by @nguyenv in #2599
• [ci] Move Python wheel-builds from macos-11,macos-12 to macos-12,macos-latest by @johnkerl in #2491
• [c++] Fix nightly build failure on formattable of json type by @johnkerl in #2609
• version.py: prevent Git version computation from raiseing by @ryan-williams in #2624
• Restore/add wheel smoke-tests, parallelize wheel builds by @ryan-williams in #2640
• [c++] Pass in a shared_ptr<Context> to _create_dim_aux by @nguyenv in #2645
• [ci] Switch from 16MB to 32MB buffer sizes for tiny GHA runners by @johnkerl in #2688
• [doc] Update README.md badge for Python CI (closes #2694) [ci skip] by @eddelbuettel in #2695

Bug fixes

• [python] Correctly handle string vs large string in Enumerations by @nguyenv in #2668
• [r] Switch 'UNORDERED' cell order to 'ROW_MAJOR' on schema creation by @eddelbuettel in #2575
• [c++] Handle 32-bit string and binary in writes by @nguyenv in #2519
• [c++] Fix validity buffer bit unpacking by @nguyenv in #2650
• [c++] Fix indexer memory leak by @johnkerl in #2665

Upcoming deprecation notices

Full Changelog: 1.11.4...1.12.0rc0

TileDB-SOMA 1.11.4

New features added

• [Backport release-1.11] [python] Include guidance for older CPU architectures by @johnkerl in #2656
• [Backport release-1.11] [r] Port re-indexer to the R API by @johnkerl in #2648
  • Note: the reindexer will be integrated with the blockwise iterator in an upcoming release

Minor changes

• [Backport release-1.11] [r/ci] Adjust file download timeout to 300 seconds by @github-actions in #2651
• [r] tiledbsoma 1.11.4 by @johnkerl in #2670

Bug fixes

• [Backport release-1.11] [python] Correctly handle string vs large string in Enumerations by @github-actions in #2669
• [Backport release-1.11] [c++] Fix validity buffer bit unpacking by @github-actions in #2654
• [Backport release-1.11] [c++] Fix indexer memory leak by @github-actions in #2666

Full Changelog: 1.11.3...1.11.4

TileDB-SOMA 1.11.3

#2646 fixes an intermittent segfault introduced in 1.11.2.

Bug fixes

• [Backport release-1.11] [c++] Pass in a shared_ptr<Context> to _create_dim_aux by @github-actions in #2646

Minor changes

• [Backport release-1.11] [r] Correct four \link{} references in help pages by @github-actions in #2627
• [Backport release-1.11] [r] Update changed URL in three vignette files by @github-actions in #2633
• [Backport release-1.11] [python/ci] Stop wheel-smoke-test failures for MacOS > 11 by @github-actions in #2635
• [Backport release-1.11] version.py: prevent Git version computation from raiseing by @github-actions in #2636
• [Backport release-1.11] Restore/add wheel smoke-tests, parallelize wheel builds by @github-actions in #2642
• [r] TileDB-SOMA 1.11.3 by @johnkerl in #2647

Full Changelog: 1.11.2...1.11.3

TileDB-SOMA 1.11.2

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: 1.11.1...1.11.2

TileDB-SOMA 1.11.1

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:

#2556 (comment)

What's Changed

• [r] tiledbsoma 1.11.1 by @johnkerl in #2558

Full Changelog: 1.11.0...1.11.1

TileDB-SOMA 1.11.0

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: 1.10.2...1.11.0