TileDB-SOMA 0.5.0a8

Bugfixes

• [python] Depend on somacore 0.0.0a8] by @johnkerl in #809

Full Changelog: 0.5.0a7...0.5.0a8

TileDB-SOMA 0.5.0a7

New features added

• [r] Additional matrix readers for NDArrays by @eddelbuettel in #720
• [python] Make add-X-layer logic friendlier by @johnkerl in #793

Breaking changes

• [python] Stateful (open/close) objects by @mlin in #730

Minor changes

• [python] Replace flake8 & isort with ruff by @gsakkis in #751
• [r] Prevent one test script from failing under rcmdcheck by @eddelbuettel in #796
• [python] Create an isort (now ruff) config at the root of the repository by @thetorpedodog in #782
• [r] Allow use pbmc3k data package in test by @eddelbuettel in #798
• More unit tests, plus partial fix for #801 by @bkmartinjr in #802
• [python] Propagate context rather than parent.context by @johnkerl in #803
• [python] Do more is-Arrow checks on create and write by @johnkerl in #797
• Import somacore v0.0.0a7, without making any functional changes. by @thetorpedodog in #808
• [python] Pin to specific TileDB core major+minor by @johnkerl in #807

Bug fixes

• [python] Fix pip-install instructions by @johnkerl in #795

Full Changelog: 0.5.0a6...0.5.0a7

TileDB-SOMA 0.5.0a6

New features added

• [python] Enable Unicode non-indexed columns by @bkmartinjr in #777

Minor changes

• [r/python] Rename sidf to sdf [trivial] by @johnkerl in #776
• [python] Change _CachedElement._TdbInfo.type from str to type by @gsakkis in #775
• [python] A bit more deadstrip by @johnkerl in #781
• [python] Enhance value filter unit tests by @bkmartinjr in #785
• [python] Additional experiment-query unit tests by @bkmartinjr in #789
• [python] refactor SOMAReader construction into TileDBArray base helper method by @mlin in #787
• Simplify to_tiledb_supported_array_type by @gsakkis in #790

Bug fixes

• [python] Undo AWS_DEFAULT_REGION workaround by @johnkerl in #771

TileDB-SOMA 0.5.0a5

New features added

• [r/python/c++] Depend on core 2.14, tiledb-r 0.18, tiledb-py 0.20 by @johnkerl in #770

Breaking changes

• [python] Depend on somacore 0.0.0a5 by @johnkerl in #765

Minor changes

• [python] Add pre-commit hook for mypy and remove explicit mypy step from python-ci by @gsakkis in #743
• Remove pre-main spec file by @johnkerl in #758
• [python] Set up caching for packages downloaded with Pip by @thetorpedodog in #757
• [r/python/c++] Expand tabs that are immediately following spaces by @johnkerl in #754
• [python] Do not export QueryCondition by @johnkerl in #759
• [python] Remove ndims/ndim temp mod, given somacore 0.0.0a4 by @johnkerl in #762
• [python] Cache builds of libtiledbsoma in Python CI by @thetorpedodog in #760
• [python] Cache pre-commit environments by @thetorpedodog in #756
• [python] Replace bare assert with typed exceptions by @johnkerl in #746
• [python] Add test for to_anndata column_names by @bkmartinjr in #763
• [python] Add GHA workflow for minimal CI jobs by @atolopko-czi in #750
• [python] Add pandas-stubs for mypy and fix uncovered typing issues by @gsakkis in #772
• [python] Remove unnecessary steps from lint job by @thetorpedodog in #767
• [python] Add test case for issue 768 -- existence of ExperimentAxisQuery.get_indexer() by @bkmartinjr in #769
• [r] Simple R UTF-8 test by @johnkerl in #773

Full Changelog: 0.5.0a4...0.5.0a5

TileDB-SOMA 0.5.0a4

Breaking changes

• [python] Import somacore by @johnkerl in #678
• [python] Update to version 0.0.0a3 of somacore. by @thetorpedodog in #732
• [r] ids to coords as read args by @johnkerl in #748
• [python] Add SomaSessionContext to all SOMA objects by @atolopko-czi in #681
• [python] Prep for ExperimentAxisQuery perf work in somacore by @bkmartinjr in #745

New features added

• [r] Add SOMAMeasurement and SOMAExperiment classes by @aaronwolen in #729

Minor changes

• [ci/python] Don't build wheels on each PR push by @johnkerl in #697
• [ci/python] Include missing doc link in wheels YAML by @johnkerl in #703
• [python] build wheels only for CPython (not PyPy) to save CI time by @mlin in #702
• [ci/python] Dedupe PyPI stubs by @johnkerl in #704
• Apply black/isort/flake8/mypy to all repo .py files by @gsakkis in #711
• Add pull_request_template.md by @johnkerl in #712
• Add quote marks around a few strings in C++ errors. by @thetorpedodog in #721
• [python] Update pyarrow dependency by @johnkerl in #714
• [python] Separate pip installation of prereqs and tiledbsoma itself. by @thetorpedodog in #717
• [python] Stronger type checking by @gsakkis in #726
• Add CZI to the license and modify to include 2023 by @maniarathi in #727
• [python] Audit for bare Exception by @johnkerl in #742
• [python] Take ndim accessor from somacore by @johnkerl in #747

Bug fixes

• [python] Correct incorrect object-type metadata on storage by @johnkerl in #709

Upcoming deprecation notices

New Contributors

• @maniarathi made their first contribution in #727
• @atolopko-czi made their first contribution in #681

Full Changelog: 0.1.20...0.5.0a4

TileDB-SOMA 0.1.22

What's Changed

This simply loosens the version dependency on tiledb-py, while still preferring the most recent version.

• tiledbsoma 0.1.22 by @johnkerl in #733

Full Changelog: 0.1.21...0.1.22

TileDB-SOMA 0.1.21

What's Changed

Nothing new from 0.1.20, except 0.1.20 was missing a wheel at PyPI. This release fixes that.

• tiledbsoma 0.1.21 [main-old] by @johnkerl in #705

Full Changelog: 0.1.19...0.1.21

TileDB-SOMA 0.5.0a3

Breaking changes

Major query improvement:

• [python] ExperimentAxisQuery by @bkmartinjr in #632

Improved names for read methods:

• [python] Fluent API changes for read methods by @bkmartinjr in #663

New features added

Minor query improvements:

• [c++] Support empty range query by @gspowley in #618
• [c++] Support empty range query and Arrow nullable fields by @gspowley in #622
• [python] Support indexing by [] -> empty results in Python by @johnkerl in #623
• [python] DataFrame count accessor by @johnkerl in #637
• [python] Add len(dataframe) by @johnkerl in #649

Ingestion-UX improvements:

• [python] Less-in-core ingest from H5AD [main] by @johnkerl in #640
• [python] Resume mode [main] by @johnkerl in #664
• [python] More memory-reduction for ingest [main] by @johnkerl in #682

Minor changes

• [r] Add SOMACollection class by @aaronwolen in #606
• [r] Rename NdArray -> NDArray by @johnkerl in #609
• [python] Shorten class constants using Final typing feature by @thetorpedodog in #616
• [c++] Add clang-format check to CI by @gspowley in #617
• Add wiki link to README.md by @johnkerl in #619
• [c++] Add SOMAReader reset for stateful API changes by @gspowley in #624
• [r/ci] Fix and re-enable CI macOS builds by @aaronwolen in #629
• [python] Update to setuptools 65.5.1 [main] by @johnkerl in #630
• [r] Adjust SparseNDArray test to renamed soma_data method by @eddelbuettel in #634
• Python 3.7 CI by @johnkerl in #620
• [r] Regularize test-file naming [main] by @johnkerl in #553
• [python] Add some docstrings by @johnkerl in #635
• [python] Deadstrip some old code by @johnkerl in #647
• [r] Correct handling of soma_joinid and soma_rowid by @aaronwolen in #642
• [r] Enhancements to SparseNDArray by @eddelbuettel in #645
• [python] Temp pin to TileDB-Py 0.19.0 by @johnkerl in #651
• [python] Typofix by @johnkerl in #648
• [python] Fixing typing_extensions dependency by @johnkerl in #650
• [python] setup.* typing-extensions vs import typing_extensions by @johnkerl in #655
• [python] Remove _indent by @johnkerl in #658
• [python] Trivial io-module function-reorder by @johnkerl in #662
• [python] Complete basic anndata I/O tests by @johnkerl in #667
• [python] Use RNA not mRNA in examples/tests by @johnkerl in #665
• [python] Simplify setup by @gsakkis in #674
• [python/ci] Fix setup.py to play well with cibuildwheel by @gsakkis in #677
• [python] Trivial comments for wheel-build by @johnkerl in #676
• [python] Prep for import somacore by @johnkerl in #673
• [python] Remove duplicate test_general_utilities.py file. by @thetorpedodog in #680
• [python] Add a few hints so mypy knows what type things are. by @thetorpedodog in #683
• Remove bdist_egg command & unused names from setup.py by @gsakkis in #691
• [python] Bump versions of precommit hooks by @gsakkis in #692
• [r] Additional sparse test code by @eddelbuettel in #690
• [ci] Use paths-ignore to avoid R CI for Python commits and vice versa by @johnkerl in #694

Bug fixes

• [python] Honor AWS_DEFAULT_REGION if no overriding ctx is specified by @johnkerl in #625
• [r] Fix storage of int64 values by SOMADataFrame by @aaronwolen in #639
• [python] Do not use extent 2048 on 8-bit index types by @johnkerl in #653
• [r] Fix creation of SOMADataFrames with non-int32 dimensions by @aaronwolen in #657
• [python] Unbreak editable install from clean by @johnkerl in #689

Upcoming deprecation notices

• Experiment-level open and close, including open-at-timestamp support
• ids in some methods vs coords in others to be aligned (#686)
• Add explicit context to the API (#644)

Full Changelog: 0.5.0a2...0.5.0a3

TileDB-SOMA 0.1.20 (do not use)

-- DO NOT USE -- CREATED IN ERROR --

This was tagged from main when it should have been tagged from main-old.

This has been yanked from https://pypi.org/project/tiledbsoma

Major

Ingestion UX:

• [python] Less-in-core ingest from H5AD [main-old] by @johnkerl in #627
• [python] Resume-ingest mode [main-old] by @johnkerl in #628

Dependency updates:

• Update to TileDB 2.13 [main-old branch] by @johnkerl in #586
• [r] TileDB-R 0.17.1 by @johnkerl in #670
• [python] Update to schema-only mode for subsequent single-soma ingests [main-old] by @johnkerl in #546

Minor

• [r] Release 0.1.19 by @aaronwolen in #621
• [python] Update to setuptools 65.5.1 [main-old] by @johnkerl in #631
• [r] Regularize test-file naming [main-old] by @johnkerl in #554
• [python] No more memory reduction [main-old] by @johnkerl in #687
• [python] Improve resume-mode/schema-only testing [main-old] by @johnkerl in #666

Full Changelog: 0.1.19...0.1.20

TileDB-SOMA 0.5.0a2

This is for development on the main branch, in contrast to 0.1.x releases which track development on the main-old branch.

Ongoing development

• NdArray refinement - tranche 4 by @bkmartinjr in #367
• [python] Conform to spec by reading as pyarrow.Table not pyarrow.RecordBatch by @johnkerl in #355
• Correctly handle empty query results in SparseNdArray read operations by @bkmartinjr in #371
• Initial SOMADataFrame class by @aaronwolen in #377
• Fix for SOMAIndexedDataFrames with float dims by @aaronwolen in #379
• Initial SOMAIndexedDataFrame class by @aaronwolen in #378
• Prevent word splitting path in bld by @aaronwolen in #387
• [r] Enhance support for (partial) table extraction by @eddelbuettel in #389
• Python collections refinement by @bkmartinjr in #381
• [python] Use true ASCII attributes in dataframes by @johnkerl in #359
• [r] Support Query Condition objects, small other polishes by @eddelbuettel in #398
• Refine soma_ column handling in Python API by @bkmartinjr in #397
• [r] Add basic unit testing for SOMAReader interface by @eddelbuettel in #401
• [c++] Add fast nnz by @gspowley in #404
• fix index in pandas read all by @bkmartinjr in #408
• [python] Disambiguate bytes/ascii on tiledb schema -> arrow schema by @johnkerl in #406
• rename type to soma_type by @bkmartinjr in #409
• [python] Match SparseNdArray dim/attr names to spec by @johnkerl in #411
• [c++] Expose two functions from managed_query in soma_reader by @eddelbuettel in #412
• add unit tests for issues 415, 418, 419 by @bkmartinjr in #420
• [r] Provide nnz() accessor by @eddelbuettel in #422
• [c++,r] Simplify spdlog setup for use from R by @eddelbuettel in #421
• Refactor from_anndata support by @bkmartinjr in #416
• Use C++17 to ease build requirements by @eddelbuettel in #417
• [python] Disallow duplicates [main branch] by @johnkerl in #437
• [r] Add support for row selection by @eddelbuettel in #402
• [r] Add Continuous Integration for the R package by @eddelbuettel in #403
• [python/c++] Connect C++ nnz to Python by @johnkerl in #439
• [c++] Revert #439 by @johnkerl in #443
• [c++] Internal context-handling updates by @johnkerl in #444
• [python/ci] Run Python CI on 3.8 and 3.9 by @johnkerl in #445
• Correct configure by ensuring R_HOME is set early by @eddelbuettel in #449
• [python] Depend on TileDB Core 2.12.0 by @johnkerl in #448
• [c++] Do not require query condition columns in column_names by @gspowley in #393
• [python/c++] Connect C++ nnz to Python by @johnkerl in #446
• [c++] Add column name to the arrow schema by @gspowley in #452
• [c++] Support passing column_names as None by @gspowley in #451
• [r] Enhanced soma reader by @eddelbuettel in #454
• [c++] Add obs slice X test by @gspowley in #456
• [python/c++] Connect C++ reader for dataframes by @johnkerl in #400
• [python] Correctly handle zero-length dataframes with SOMAReader by @johnkerl in #459
• [python] More unit-test cases for #459 by @johnkerl in #460
• [c++] Expose is_complete predicate from managed_query in soma reader by @eddelbuettel in #461
• [python/c++] Connect C++ reader for SOMASparseNdArray by @johnkerl in #447
• [r] Initial support for iterated reads from SOMAReader by @eddelbuettel in #462
• [python] Unprefix SOMA names by @johnkerl in #464
• [r] Minor rearrangement demoting initial test function and renaming by @eddelbuettel in #468
• [python] Fix #471 by @johnkerl in #472
• [python] Update to TileDB-Py 0.18.0 [main] by @johnkerl in #476
• [python] Replace Exception with SOMA-specific exceptions by @johnkerl in #486
• [r] Expand iterated reader via refactored row/col selectors by @eddelbuettel in #480
• [r] Initial SOMADenseNDArray class by @aaronwolen in #488
• [c++] Accept dim_points as pyarrow.Array by @gspowley in #498
• [r] Add coverage reports in script and yaml by @eddelbuettel in #504
• [python] Depend on TileDB-Py 0.18.1 [main] by @johnkerl in #503
• [r] Arrow conversion utilities by @aaronwolen in #505
• [r] Use libtiledbsoma.a in build by @eddelbuettel in #510
• [c++] Fix macos build error by @gspowley in #513
• [c++] Enable internal TileDB stats collection by @gspowley in #515
• [python] Update slicing logic for SparseNdArray by @johnkerl in #485
• [r] Enable code coverage token use by @eddelbuettel in #521
• [c++] Improve build experience by @gspowley in #522
• [python] Update SOMAIndexedDataFrame indexing logic by @johnkerl in #483
• add temporary configuration to SOMAReader instances by @bkmartinjr in #527
• improving IndexedDataFrame test coverage by @mlin in #529
• [c++] Cmake bug fix and improvements by @gspowley in #525
• [python] Remove DataFrame in favor of IndexedDataFrame by @johnkerl in #538
• [r] Support logging via spdlog by @eddelbuettel in #530
• [python] Remove DataFrame::is_indexed by @johnkerl in #545
• [r] Remove DataFrame in favor of IndexedDataFrame by @johnkerl in #537
• [c++] Release Python GIL on reads by @gspowley in #550
• [r] Ignore directory with TileDB Core headers in coverage analysis by @eddelbuettel in #552
• [r] Update logging code utilizing templated interface by @eddelbuettel in #555
• [python] unit tests and error checking for #300 by @bkmartinjr in #559
• Add the platform_config parameter to create methods. by @thetorpedodog in #542
• [r] Extend iterated reader interface with platform_config by @eddelbuettel in #556
• DataFrame read result_order by @mlin in #528
• [c++] Map 8-bit TILEDB_BOOL to 1-bit Arrow boolean by @bekadavis9 in #561
• [r] Simplify logging via 'spdl' package by @eddelbuettel in #563
• Add documentation for platform_config to the Python README. by @thetorpedodog in #568
• [r] Make source build more robust by @eddelbuettel in #572
• [r] Tighten package by removing some initial exploratory code by @eddelbuettel in #577
• Fix #578 (tile-order/cell-order typo) by @johnkerl in #580
• [python] Support half-slices in indexed reads by @bekadavis9 in #582
• Fix DenseNdArray slicing by @johnkerl in #581
• Use C++ reader for SOMA.DenseNdArray by @johnkerl in #574
• Fix flaky unit test by @johnkerl in #585
• Update to TileDB 2.13 [main] by @johnkerl in #587
• Support value-filter on boolean columns [pending core 2.13 / tiledb-py 0.19] by @johnkerl in #579
• Un-xfail half-slice tests in DenseNdArray by @johnkerl in #589
• Extend indexing-related unit-test cases for DenseNdArray by @johnkerl in #588
• Use soma_reader in SOMADataFrame by @eddelbuettel in #590
• [r] Convert arrow::large_utf8() to ascii by @aaronwolen in #591
• Support string dims in soma.DataFrame by @johnkerl in #592
• Include Python 3.10 in CI matrix by @johnkerl in #597
• Use soma_reader in SOMADenseNdArray read method by @eddelbuettel in #598
• [python] Add tests for point indexing with ndarray by @bkmartinjr in #604
• [r] Tweak logging default value enabling easier use by @eddelbuettel in #607
• [python] Rename NdArray -> NDArray by @johnkerl in #608
• Support reading data that uses old NdArray name by @bkmartinjr in #610
• [r] Making package R CMD check clean by @eddelbuettel in #614

Continuous integration and build infrastructure

• [python] Pause PyPI publish on main by @johnkerl in #369
• [ci] Work around recent Mac GHA issue by @johnkerl in #370
• [ci] Fix scripts/test for MacOS by @johnkerl in #358
• [python] Depend on TileDB-Py 0.17.5 by @johnkerl in #394
• [r] Support build against external artifact and system library by @eddelbuettel in #388
• [ci] Use MacOS 12 for CI by @johnkerl in #413
• [ci] Update to checkout/actions@v3 to suppress nag about node.js 12 by @eddelbuettel in #455
• Build flow improvements by @gspowley in #496
• report pytest coverage to codecov by @mlin in #495
• Build python sdist & wheels by @mlin in #605
• py packaging: strike 'v' prefix from expected version numbers by @mlin in #613

New Contributors

• @mlin made their first contribution in #495
• @bekadavis9 made their first contribution in #561

Full Changelog: 0.5.0a1...0.5.0a2