TileDB-SOMA 0.5.0a9

New features added / breaking changes

For this alpha release, many changes are breaking. This is a step toward 1.0rc0 in which we will
try to isolate the (hopefully zero) remaining opportunities for breaking changes before 1.0rc0.

• [python] Export open function, to universally open everything by @thetorpedodog in #896
• [python] Add add_new_collection implementation by @thetorpedodog in #837
• [python] Add add_new_dataframe and _sparse/_dense_ndarray by @thetorpedodog in #848
• [python] Create and open objects using Thing.create() and Thing.open() by @thetorpedodog in #824
• [python] Add static exists method to TileDBObject by @thetorpedodog in #890
• [python] Generalize tiledbsoma.io.add_X_layer to obsm, varp, etc. by @johnkerl in #814
• [python] Add timestamp slots in SOMATileDBContext and apply throughout by @mlin in #892
• [python] Document newly-created platform_config options by @thetorpedodog in #897
• [python] Re-export somacore's AxisColumnNames at top level by @johnkerl in #881
• [python] Support indices of type bytes by @johnkerl in #861
• [r] Support iterated sparse and dense matrix reads by @eddelbuettel in #835
• [r] Support remotes::install_github use by @eddelbuettel in #826
• [r] Add iterated readers for SOMA classes by @eddelbuettel in #811
• [python] Add user-level stats hooks, to reach parity with tiledbsoma-r by @johnkerl in #871
• [r] Add stats API accessors by @eddelbuettel in #865
• Use show_package_versions in bug-report issue template by @johnkerl in #868
• [r,python] Add show_package_versions for bug-report use by @johnkerl in #855
• Create bug-report and feature-request templates by @maniarathi in #728

Internal support for features

• [python] Refactor processing of URIs for collection creation/setting by @thetorpedodog in #889
• [python] Add additional create-time platform_config hooks for schema mods by @bkmartinjr in #888
• [python] Pull in somacore==0.0.0a12 and associated improvements by @thetorpedodog in #882
• [python] Keep only the read or write TileDB handles open long-term by @thetorpedodog in #863
• [python] Track ownership of accessed and added collection members. by @thetorpedodog in #847
• [python] Create ReadWriteHandle to manage TileDB handles by @thetorpedodog in #823
• [python] Switch to somacore 0.0.0a10 by @thetorpedodog in #825
• [c++] SOMAReader open-at-timestamp support by @mlin in #788

Minor changes

• [python] Move io into submodule and organize various util_ files. by @thetorpedodog in #899
• [python] Capture stdout/stderr from stats_dump output by @thetorpedodog in #887
• [python] Un-xfail some tests which are now passing by @thetorpedodog in #891
• [r] Validate no allow-duplicates for sparse N-d arrays and dataframes by @johnkerl in #879
• [python] string_dim_zstd_level -> int64_dim_zstd_level by @johnkerl in #883
• [python] Schema validation for DataFrame by @johnkerl in #880
• [python] Directly use backend TileDB dimension names for DataFrame by @thetorpedodog in #870
• [python] Use the array we already have open to generate the Arrow schema by @thetorpedodog in #869
• [python] Unexpose TileDBArray and TileDBObject by @johnkerl in #856
• Update LICENSE to make the years the same. by @maniarathi in #852
• [python] Make typeguard_ignore decorator play nice with Pylance by @thetorpedodog in #849
• [python] Remove __eq__ method from base TileDBObject class by @thetorpedodog in #846
• [python] Pull the common parts of NDArrays into the base NDArray class by @thetorpedodog in #836
• [python] Fix legacy misuse ofurllib.parse.urljoin by @johnkerl in #832
• [r] Limit builds to unix operating systems by @eddelbuettel in #831
• [r] Add lifecycle-maturity tags to Roxygen blocks by @johnkerl in #829
• [python] Use the contents of bld, not setup.py, for binary cache by @thetorpedodog in #827
• [python] Add lifecycle maturity tags to public API docstrings by @atolopko-czi in #818
• [python] Move test data to testdata folder by @thetorpedodog in #817
• [python] Refactor factory._construct_member by @gsakkis in #815

Bug fixes

• [python] Fix and test over-indexing semantics by @johnkerl in #901
• [python] No allow-duplicates for sparse N-d arrays by @johnkerl in #878
• [python] Improve detection of nonexistent-array errors from TileDB Cloud by @johnkerl in #873
• [python] Fix __del__ error when improperly constructing a TileDB object by @thetorpedodog in #864
• [python] Modify setup.py to find system-installed libtiledbsoma on POSIX by @nguyenv in #838
• [python] Fix use_relative_uri for tiledbsoma.io [post-824] by @johnkerl in #833
• [python] Fix #822 re small tile extents by @johnkerl in #830

New Contributors

• @nguyenv made their first contribution in #838

Full Changelog: 0.5.0a8...0.5.0a9

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