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Releases: single-cell-data/TileDB-SOMA

TileDB-SOMA 1.11.2

21 May 21:29
@johnkerl johnkerl
1.11.2
0381e8e
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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

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.11.1

14 May 16:51
@johnkerl johnkerl
1.11.1
78ff65f
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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

Full Changelog: 1.11.0...1.11.1

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.11.0

14 May 12:53
@johnkerl johnkerl
1.11.0
a955277
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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

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

Contributors

ryan-williams, eddelbuettel, and 8 other contributors
Assets 2
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TileDB-SOMA 1.11.0rc0

13 May 20:15
@johnkerl johnkerl
1.11.0rc0
a955277
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TileDB-SOMA 1.11.0rc0 Pre-release
Pre-release

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

Contributors

ryan-williams, eddelbuettel, and 8 other contributors
Assets 2
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TileDB-SOMA 1.10.2

29 Apr 16:59
@johnkerl johnkerl
1.10.2
b1f7fd5
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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

Contributors

johnkerl
Assets 2
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1.10.1

19 Apr 19:37
@johnkerl johnkerl
1.10.1
563a8b5
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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

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.10.0

17 Apr 15:56
@johnkerl johnkerl
1.10.0
de04c46
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TileDB-SOMA 1.10.0

New features added

Minor changes

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

Contributors

ryan-williams, eddelbuettel, and 5 other contributors
Assets 2
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TileDB-SOMA 1.10.0rc0

17 Apr 13:53
@johnkerl johnkerl
1.10.0rc0
de04c46
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TileDB-SOMA 1.10.0rc0 Pre-release
Pre-release

New features added

Minor changes

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

Contributors

ryan-williams, eddelbuettel, and 5 other contributors
Assets 2
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TileDB-SOMA 1.9.5

11 Apr 13:32
@johnkerl johnkerl
1.9.5
3ed7453
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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

Contributors

johnkerl
Assets 2
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TileDB-SOMA 1.9.5rc0

09 Apr 20:41
@johnkerl johnkerl
1.9.5rc0
d425839
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TileDB-SOMA 1.9.5rc0 Pre-release
Pre-release

What's Changed

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

Full Changelog: 1.9.4...1.9.5rc0

Assets 2
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