Tiledbsoma

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/actionsv3 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**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a1...0.5.0a2

First stamp of `main`, which is a dev branch -- `main-old` has releasables on PyPI using 0.1.*.

What's Changed

This is all iterative dev work -- no major release, just a pypi-installable progress point people can use as a reference while collaborating forward.

* Split tiledbsc and tiledbsoma into separate branches by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/282
* Check for errors on scripts/setup by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/283
* Make __getattr__ Pythonic on key-not-found by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/288
* C++ SOMA pre-release by gspowley in https://github.com/single-cell-data/TileDB-SOMA/pull/286
* Error-check types on from_anndata/from_h5ad by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/294
* Support zero-sized arrays by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/295
* Improve C++ build by gspowley in https://github.com/single-cell-data/TileDB-SOMA/pull/304
* Optimize __repr__ by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/303
* MacOS findings by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/314
* Document C++ build options by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/316
* Update C++ CLI example by gspowley in https://github.com/single-cell-data/TileDB-SOMA/pull/317
* Enable option for enhancing debug-log visibility by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/319
* Propagate ctx through reprs and member-constructs by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/318
* Propagate ctx through reprs and member-constructs, continued by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/323
* improve column_name handling in dataframe read operations by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/327
* add missing double backtick by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/332
* quality of life: add venv to gitignore by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/334
* Depend on TileDB-Py 0.17.4 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/336
* NdArray implementation work (create, props) by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/339
* No readthedocs build on main for now by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/342
* Initial R API by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/321
* README.md updates, main branch by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/345
* revise version API to match spec by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/333
* Replace array->timestamp() with array->open_timestamp_end() by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/350
* NdArray refinement, part 2 by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/343
* Enable conda build and release by gspowley in https://github.com/single-cell-data/TileDB-SOMA/pull/348
* Fix MacOS build with local TileDB core by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/354
* SOMACollection: fix loose check in create logic by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/357
* Third tranche of NdArray refinement. by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/347
* Add initial C++ support for the R package by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/352
* Deduplicate C++ source files by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/364
* Publish main-branch pre-releases to pypi.org by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/366

New Contributors
* eddelbuettel made their first contribution in https://github.com/single-cell-data/TileDB-SOMA/pull/350

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.1.11...0.5.0a1

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 https://github.com/single-cell-data/TileDB-SOMA/pull/733

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.1.21...0.1.22

What's Changed

Nothing new from [0.1.20](https://github.com/single-cell-data/TileDB-SOMA/releases/tag/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 https://github.com/single-cell-data/TileDB-SOMA/pull/705

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.1.19...0.1.21

-- **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 https://github.com/single-cell-data/TileDB-SOMA/pull/627
* [python] Resume-ingest mode [main-old] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/628

Dependency updates:

* Update to TileDB 2.13 [main-old branch] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/586
* [r] TileDB-R 0.17.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/670
* [python] Update to schema-only mode for subsequent single-soma ingests [main-old] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/546

Minor

* [r] Release 0.1.19 by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/621
* [python] Update to setuptools 65.5.1 [main-old] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/631
* [r] Regularize test-file naming [main-old] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/554
* [python] No more memory reduction [main-old] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/687
* [python] Improve resume-mode/schema-only testing [main-old] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/666

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.1.19...0.1.20

What's Changed

* Do not rewrite pre-creation URI to post-creation URI by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/557
* Allow soma.query with X/data not in X_layer_names by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/567
* Parameterize dataframe capacities by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/565

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.1.18...0.1.19