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

TileDB-SOMA 1.11.0rc0

What's Changed

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

Full Changelog: 1.10.2...1.11.0rc0

TileDB-SOMA 1.10.2

Features

• [r] Backport resume-mode for R to the release-1.10 branch, and R 1.10.2 by @johnkerl in #2490
• [Backport release-1.10] [python] Allow obs_query=None/var_query=None in ExperimentAxisQuery by @github-actions in #2478

Minor/internal changes

• [Backport release-1.10] [r,ci] Run coverage only on workflow_dispatch events by @github-actions in #2489
• [Backport release-1.10] [r,ci] Update r-ci.sh, remove unneeded entries from r-ci.yml by @github-actions in #2477

Full Changelog: 1.10.1...1.10.2

1.10.1

This release contains a single Python bugfix.

• [Backport release-1.10] [python]Robust URI handling for Ingestion-performance improvement by @github-actions in #2459
• [r] TileDB-SOMA-R 1.10.1 by @johnkerl in #2458

Full Changelog: 1.10.0...1.10.1

TileDB-SOMA 1.10.0

New features added

• [python] Add back deprecated function tiledbsoma_build_index by @jp-dark in #2344
• [python/ci] typeguard==4.2.1, make requirements_dev.txt canonical by @ryan-williams in #2314
• [python] tiledbsoma.io.from_h5ad: document new additional_metadata param by @ryan-williams in #2360
• [python] Ingestion performance by @johnkerl in #2434
• [r] Add obsm, varm, obsp, and varp to SOMAExperimentAxisQuery by @mojaveazure in #2351
• [r] Port blockwise iterator/reader to R by @mojaveazure in #2152
• [r] Add $reopen() to TileDBObject by @mojaveazure in #2372

Minor changes

• Use core 2.22.0, TileDB-Py 0.28.0, TileDB-R 0.26.0 on main branch by @johnkerl in #2448
• [python/ci] Typofix from #2305 by @johnkerl in #2326
• [python/ci] Unbreak wheel builds, main by @johnkerl in #2341
• [python] Remove no-longer-necessary _query_condition import by @ryan-williams in #2286
• [c++/python] Add soma_type argument for SOMAObject::open by @nguyenv in #2350
• [python] Skip writing empty arrow_tables by @ryan-williams in #2357
• [python] isort: tiledbsoma before tiledb by @ryan-williams in #2381
• [c++,r,python] Move nanoarrow to src/external by @eddelbuettel in #2383
• [python/ci] Run SO copying workflow on macos-13 to avoid SIP by @jdblischak in #2435
• [python] Code-review-feedback follow-up from #2434 by @johnkerl in #2441
• [r] Bump DESCRIPTION version for main past 1.9 by @johnkerl in #2328
• [r] Additional nanoarrow refactor followup by @eddelbuettel in #2376
• [r] TileDB-SOMA R 1.10 (release-1.10 branch) by @johnkerl in #2452
• [r/ci] Continue #2275 by @johnkerl in #2395
• [c++, r] Update and refactor nanoarrow by @eddelbuettel in #2188
• [c++] Set nanoarrow.c to use CMAKE_CXX_COMPILER by @nguyenv in #2366
• [c++] Address final valgrind issue by @eddelbuettel in #2403
• [c++] Refactor metadata and create to respect timestamps by @nguyenv in #2180
• Do not include nanoarrow files in clang-format by @nguyenv in #2449

Bug fixes

• [python] Expand coverage for registration of multi-region S3-backed H5ADs by @johnkerl in #2369
• [python] More nan_append checks: not-all-NaN, non-dupe IDs by @ryan-williams in #2364
• [python] Check for uniqueness of registration obs/var field-name inputs by @johnkerl in #2380
• [python] Enforce if-not-exists semantics for append/registration by @johnkerl in #2384
• [python] Pass more context in registrar by @johnkerl in #2411
• [python] verify_core_versions() during import tiledbsoma by @ryan-williams in #2437
• [r] Check that TileDB Core library versions match by @eddelbuettel in #2410
• [r/ci] Unbreak wheel builds by @johnkerl in #2398

Full Changelog: 1.9.5...1.10.0rc0

TileDB-SOMA 1.10.0rc0

New features added

• [python] Add back deprecated function tiledbsoma_build_index by @jp-dark in #2344
• [python/ci] typeguard==4.2.1, make requirements_dev.txt canonical by @ryan-williams in #2314
• [python] tiledbsoma.io.from_h5ad: document new additional_metadata param by @ryan-williams in #2360
• [python] Ingestion performance by @johnkerl in #2434
• [r] Add obsm, varm, obsp, and varp to SOMAExperimentAxisQuery by @mojaveazure in #2351
• [r] Port blockwise iterator/reader to R by @mojaveazure in #2152
• [r] Add $reopen() to TileDBObject by @mojaveazure in #2372

Minor changes

• Use core 2.22.0, TileDB-Py 0.28.0, TileDB-R 0.26.0 on main branch by @johnkerl in #2448
• [python/ci] Typofix from #2305 by @johnkerl in #2326
• [python/ci] Unbreak wheel builds, main by @johnkerl in #2341
• [python] Remove no-longer-necessary _query_condition import by @ryan-williams in #2286
• [c++/python] Add soma_type argument for SOMAObject::open by @nguyenv in #2350
• [python] Skip writing empty arrow_tables by @ryan-williams in #2357
• [python] isort: tiledbsoma before tiledb by @ryan-williams in #2381
• [c++,r,python] Move nanoarrow to src/external by @eddelbuettel in #2383
• [python/ci] Run SO copying workflow on macos-13 to avoid SIP by @jdblischak in #2435
• [python] Code-review-feedback follow-up from #2434 by @johnkerl in #2441
• [r] Bump DESCRIPTION version for main past 1.9 by @johnkerl in #2328
• [r] Additional nanoarrow refactor followup by @eddelbuettel in #2376
• [r] TileDB-SOMA R 1.10 (release-1.10 branch) by @johnkerl in #2452
• [r/ci] Continue #2275 by @johnkerl in #2395
• [c++, r] Update and refactor nanoarrow by @eddelbuettel in #2188
• [c++] Set nanoarrow.c to use CMAKE_CXX_COMPILER by @nguyenv in #2366
• [c++] Address final valgrind issue by @eddelbuettel in #2403
• [c++] Refactor metadata and create to respect timestamps by @nguyenv in #2180
• Do not include nanoarrow files in clang-format by @nguyenv in #2449

Bug fixes

• [python] Expand coverage for registration of multi-region S3-backed H5ADs by @johnkerl in #2369
• [python] More nan_append checks: not-all-NaN, non-dupe IDs by @ryan-williams in #2364
• [python] Check for uniqueness of registration obs/var field-name inputs by @johnkerl in #2380
• [python] Enforce if-not-exists semantics for append/registration by @johnkerl in #2384
• [python] Pass more context in registrar by @johnkerl in #2411
• [python] verify_core_versions() during import tiledbsoma by @ryan-williams in #2437
• [r] Check that TileDB Core library versions match by @eddelbuettel in #2410
• [r/ci] Unbreak wheel builds by @johnkerl in #2398

Full Changelog: 1.9.5...1.10.0rc0

TileDB-SOMA 1.9.5

What's Changed

This release contains a bugfix in the form of #2416.

• [Backport release-1.9] [python] Pass more context in registrar by @github-actions in #2416
• [Backport release-1.9] [c++] Address final valgrind issue by @github-actions in #2404
• [Backport release-1.9] [r] Check that TileDB Core library versions match by @github-actions in #2417
• [r] TileDB-SOMA 1.9.5 by @johnkerl in #2432

Full Changelog: 1.9.4...1.9.5