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

TileDB-SOMA 1.9.5rc0

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

TileDB-SOMA 1.9.4

New features added

• [Backport release-1.9] [python] tiledbsoma.io.from_h5ad: document new additional_metadata param by @github-actions in #2361
• [Backport release-1.9] [r] Add obsm, varm, obsp, and varp to SOMAExperimentAxisQuery by @johnkerl in #2365

Minor changes

• [Backport release-1.9] [c++, r] Update and refactor nanoarrow by @github-actions in #2363
• [Backport release-1.9] [python] Remove no-longer-necessary _query_condition import by @github-actions in #2348
• [Backport release-1.9] [c++] Set nanoarrow.c to use CMAKE_CXX_COMPILER by @github-actions in #2371
• [r/ci] Controlled downgrade for TileDB-R 0.25 by @johnkerl in #2373
• [Backport release-1.9] [r] Additional nanoarrow refactor followup by @github-actions in #2377
• [Backport release-1.9] [python] isort: tiledbsoma before tiledb by @github-actions in #2382
• [r/ci] Backport of #2395 to the release-1.9 branch by @johnkerl in #2396
• [r] TileDB-SOMA-R 1.9.4 by @johnkerl in #2399

Bug fixes

• [Backport release-1.9] [python] Skip writing empty arrow_tables by @github-actions in #2358
• [Backport release-1.9] [python] Check for uniqueness of registration obs/var field-name inputs by @github-actions in #2385
• [Backport release-1.9] [python] Enforce if-not-exists semantics for append/registration by @github-actions in #2387
• [Backport release-1.9] [python] Expand coverage for registration of multi-region S3-backed H5ADs by @github-actions in #2370
• [Backport release-1.9] [python] More nan_append checks: not-all-NaN, non-dupe IDs by @github-actions in #2378
• [Backport release-1.9] [r/ci] Unbreak wheel builds by @github-actions in #2401

Full Changelog: 1.9.3...1.9.4

TileDB-SOMA 1.9.3

What's Changed

This release contains a single Python performance improvement.

• [Backport release-1.9] [c++/python] Add soma_type argument for SOMAObject::open by @github-actions in #2354
• [r] TileDB-SOMA 1.9.3 by @johnkerl in #2355

Full Changelog: 1.9.2...1.9.3

TileDB-SOMA 1.9.2

What's Changed

• [Backport release-1.9] [python] Add back deprecated function tiledbsoma_build_index by @github-actions in #2346
• [r] tiledbsoma-r 1.9.2 by @johnkerl in #2349

Full Changelog: 1.9.1...1.9.2

TileDB-SOMA 1.9.1

This release fixes a wheel-build issue with 1.9.0.

• [python/ci] Unbreak wheel builds by @johnkerl in #2339
• [r] tiledbsoma-r 1.9.1 by @johnkerl in #2342

Full Changelog: 1.9.0...1.9.1

1.9.0

Note: PyPI wheels are missing due to #2337 so there will be an immediate 1.9.1.

New features added

• [python] Let ingest accept additional_metadata: dict[str, Metadatum] by @ryan-williams in #2258
• [c++/python] Use a shared threadpool for the reindexer by @beroy in #2148
• [c++] Optimizing indexer for pandas and pyarrow by @beroy in #2159

Breaking changes

• [Backport release-1.9] [python/ci] typeguard==4.2.1, make requirements_dev.txt canonical by @github-actions in #2332
• [python] Drop support for Python 3.7 by @johnkerl in #2181

Bug fixes

• [python] Fix race in SOMADataFrame schema with multiple enumerated columns by @johnkerl in #2194
• [python] Fix context-type for tiledbsoma_build_index by @johnkerl in #2224
• [python] Fix an ingestion corner case with empty chunks by @johnkerl in #2283
• [python] Fix registration path with non-standard obs/var index names by @johnkerl in #2281
• [c++] Match delete[] with new[] by @johnkerl in #2259
• [c++] Fix display of Arrow schema for enum of bytes datatype by @johnkerl in #2305
• [c++] Use std::future::get() instead of ::wait() by @eddelbuettel in #2320

Minor changes

• Use core 2.21.1 by @johnkerl in #2301
• Use TileDB core 2.21.0, TileDB-Py 0.27.0, TileDB-R 0.25.0 by @johnkerl in #2294
• [python] Expose tiledbsoma.io.ExperimentAmbientLabelMapping by @johnkerl in #2175
• [c++] Address issues related to reindexer advanced features by @beroy in #2186
• [ci] Fix scripts/bld typo (aarch64 opts) by @ryan-williams in #2193
• [python] Fix a lint fail on main by @johnkerl in #2200
• [python] Fix and test setup.py flags to external shared objects by @jdblischak in #2221
• [python] Typo fixes, broken README link by @ryan-williams in #2235
• [python] Attempt to repro #1565 by @ryan-williams in #2236
• [python] Verify pa.{Chunked,Integer}Array args to SparseNDArray.read by @ryan-williams in #2234
• [python/ci] Restore pre-merge lint checks by @ryan-williams in #2247
• [python] Factor io/ingest.py, create io/{_common,outgest}.py by @ryan-williams in #2246
• [python] Bump somacore to 1.0.9 by @ryan-williams in #2251
• [ci/python] Use Python 3.11 for single version CI runs by @jp-dark in #2255
• [python] Remove deprecated Python 3.7 AST types by @jp-dark in #2271
• [python/ci] Complete 3.8 -> 3.11 work by @johnkerl in #2278
• [python] Neaten registration-mapping test code by @johnkerl in #2285
• [python] Extract fs wrapper to util file by @johnkerl in #2290
• [python] Fix many typeguard warnings by @johnkerl in #1960
• [python/ci] Factor pytest.fixtures, verify #1988 by @ryan-williams in #2299
• [python] Make _util.read_h5ad a @contextmanager by @ryan-williams in #2291
• [python] Make test_empty_categorical_query work with TileDB<2.21 by @ryan-williams in #2308
• [python/ci] Pin typeguard==4.1.5 by @ryan-williams in #2313
• [python] Implement IntIndexer as class that wraps around clib.IntIndexer by @jp-dark in #2310
• [Backport release-1.9] [python/ci] Typofix from #2305 by @github-actions in #2331
• [r] Call array schema evolution after loop setting up enums by @eddelbuettel in #2201
• [ci] Updated hard-coded core version in another file by @johnkerl in #2207
• [ci] Add MacOS job to test shared object copying by @jdblischak in #2220
• Append LD_LIBRARY_PATH for census by @johnkerl in #2218
• [ci] Only run build tests when build files are modified by @jdblischak in #2229
• Needed changes for census profiling by @beroy in #2074
• [r] Correct parenthesis in covr() call activate quiet=FALSE by @eddelbuettel in #2243
• [c++] Fix building TileDB if a CMake toolchain is not specified by @teo-tsirpanis in #2244
• [r/ci] Set options(pkgType = "binary") for MacOS by @mojaveazure in #2257
• [r/ci] Point at correct TileDB-R location by @johnkerl in #2275
• ingest.py cleanups, doc nits by @ryan-williams in #2256
• [r] Add tests for enum value filters in SOMAExperimentAxisQuery by @mojaveazure in #2316
• [r] R version for release-1.9 branch by @johnkerl in #2329

New Contributors

• @jdblischak made their first contribution in #2220

Full Changelog: 1.8.1...1.9.0

1.8.1

Bug fixes

• [Backport release-1.8] [python] Fix an ingestion corner case with empty chunks by @github-actions in #2284
• [Backport release-1.8] [python] Fix registration path with non-standard obs/var index names by @github-actions in #2288

Minor changes

• [Backport release-1.8] [python] Verify pa.{Chunked,Integer}Array args to SparseNDArray.read by @github-actions in #2263
• [Backport release-1.8] [python] Bump somacore to 1.0.9 by @github-actions in #2264
• [Backport release-1.8] [python] Factor io/ingest.py, create io/{_common,outgest}.py by @github-actions in #2266
• [Backport release-1.8] [python] Remove deprecated Python 3.7 AST types by @github-actions in #2272
• [Backport release-1.8] [python] Needed changes for census profiling by @github-actions in #2261
• [Backport release-1.8] [ci/python] Use Python 3.11 for single version CI runs by @github-actions in #2267
• [Backport release-1.8] [python/ci] Restore pre-merge lint checks by @johnkerl in #2268
• [Backport release-1.8] [python/ci] Complete 3.8 -> 3.11 work by @github-actions in #2280
• [Backport release-1.8] [python] Neaten registration-mapping test code by @github-actions in #2287
• [r] Prepare for tiledbsoma 1.8.1 by @johnkerl in #2289
• [Backport release-1.8] [r/ci] Point at correct TileDB-R location by @github-actions in #2276
• [Backport release-1.8] [r/ci] Set options(pkgType = "binary") for MacOS by @github-actions in #2265
• [Backport release-1.8] [r] Correct parenthesis in covr() call activate quiet=FALSE by @github-actions in #2262
• [Backport release-1.8] [c++] Match delete[] with new[] by @github-actions in #2260
• [Backport release-1.8] [c++] Fix building TileDB if a CMake toolchain is not specified by @johnkerl in #2274
• [Backport release-1.8] [ci] Only run build tests when build files are modified by @johnkerl in #2232
• [Backport release-1.8] [docs] Typo fixes, broken README link by @github-actions in #2273

Full Changelog: 1.8.0...1.8.1