Tiledbsoma

* [r] TileDB-SOMA 1.12.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2759

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.12.0...1.12.1

Bug fixes

* [Backport release-1.15] [python] Fix `update_obs` semantics for some remote configurations by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3627
* [c++] Fix some build errors for Docker by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3620
* [r] TileDB-SOMA 1.15.5 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3628

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.15.4...1.15.5

New features added

* [Backport release-1.15] [python] Change `from_visium` to create `obs` presence matrix by default in 3596
* [Backport release-1.15][python] Set `soma_joinid` to always be an index column in the `PointCloudDataFrame` class in 3575
* [Backport release-1.15] [python] On is-not-context error, show type in 3584
* [Backport release-1.15] [python] Make `region_key` a categorical when exporting to SpatialData in 3589
* [Backport release-1.15] [python] Update warning on unsupported version in 3600
* [Backport release-1.15] [python] Add spatial I/O functions to readthedocs in 3604
* [Backport release-1.15][python] Add the spatial-encoding version to `Scene` and `PointCloudDataFrame` objects in 3603
* [Backport release 1.15][python/c++] Add C++ `SOMACoordinateSpace` and use it to push `Scene` metadata down to C++ in 3602
* [Backport release-1.15] [python] Add Unicode metadata support in 3607

Breaking changes

Upcoming deprecation notices

Bug fixes

* [Backport release-1.15] [c++] Handle add/drop/re-add of enumerated types in 3572
* [Backport release-1.15] [python] Throw error in `SOMAVFSFilebuf.open` on file-not-found in 3569
* [Backport release-1.15] [python] Fix search in `readthedocs` in 3576
* [Backport release-1.15] [python] More `readthedocs` search fix in 3579
* [Backport release-1.15] [python] Pass more context in `io/shaping.py` in 3587
* [Backport release-1.15] [python] Fix rendering of spatial docs in 3606
* [Backport release-1.15] [python] Iterate on spatial + readthedocs in 3610
* [Backport release-1.15] [python] More readthedocs fixes for spatial in 3613
* [Backport release-1.15] [c++] Correct Arrow offsets for enumeration and boolean columns in 3615

Minor changes

* [Backport release-1.15] [python] Release GIL in VFS bindings in 3564
* Fix 3569 backport to `release-1.15` in 3571
* [Backport release-1.15] [python] Merge `_axisp_get_array` and `_axism_get_array` into a single function in 3574
* [Backport release-1.15] [python] Remove `AxisName.getattr_from` from `ExperimentAxisQuery` in 3577
* [Backport release-1.15] [python] Update copyright header in `*.py` source files in 3593
* [Backport release-1.15] [r] [CI] Use binaries for packages on macOS in 3601
* [c++] Downgrade C++20isms to C++17isms for `release-1.15` branch in 3609
* [Backport release-1.15] [c++] Remove some compiler warnings in 3616
* [r] TileDB-SOMA 1.15.4 in 3617

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.15.3...1.15.4

New features added

* [Backport release-1.15] [python] Add region columns and metadata to SpatialData by github-actions in 3556
* [Backport release-1.15] [python] Handle non-list/non-tuple input in `tiledbsoma.io` registration by github-actions in 3520
* [Backport release-1.15] [c++] When a group has no type info, say its name by github-actions in 3532
* [Backport release-1.15] [c++] Show which coordinate is out of range in `fastercsx` error messages by github-actions in 3541
* [Backport release-1.15] [python] Add support for Visium v1 by github-actions in 3550

Bug fixes

* [Backport release-1.15] [python] Link lifetimes of `SOMAArray` and `ManagedQuery` by github-actions in 3522
* [Backport release-1.15] [python] Fix casting bug in `IntIndexer` by github-actions in 3527
* [Backport release-1.15] [python] Account for missing end-rows in shape-upgrader by github-actions in 3540
* [Backport release-1.15] [python] Implement `read`, `seek`, and `tell` for `SOMAVFSFilebuf` by github-actions in 3547
* [Backport release-1.15] [C++] Fix `ManagedQuery` segv: ctor/dtor order fix by github-actions in 3549
* [Backport release-1.15] [python] Validate byteorder on `fastercsx` argument arrays by github-actions in 3521

Minor changes

* [Backport release-1.15] [python] Fix and clean up basic `Scene` test by github-actions in 3523
* [Backport release-1.15] [python] Unpin `scipy` by github-actions in 3528
* [Backport release-1.15] [c++] Bump `spdlog` to 1.15 and remove patch by github-actions in 3531
* [c++] Fix backport on 3541 by johnkerl in 3542
* [Backport release-1.15] Bump jinja2 from 3.1.4 to 3.1.5 in /doc by github-actions in 3546
* [Backport release-1.15] [python] Inline `_read` and `AxisQueryResult` to `to_anndata` by github-actions in 3555
* [r] TileDB-SOMA 1.15.3 by johnkerl in 3551

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.15.2...1.15.3

New features added

* [Backport release-1.15] [python] Update `add_new_collection` method to support `Scene` collections by github-actions in 3499

Bug fixes

* [Backport release-1.15] [python] Make `ExperimentAxisQuery` inherit `somacore`, restore its `.close` by github-actions in 3500

Minor changes

* [Backport release-1.15] [c++] Use const references and `std::string_view` in `create` function by github-actions in 3483
* [Backport release-1.15] [c++] Make destructors of base classes virtual by github-actions in 3487
* [Backport release-1.15] [python] Fix a test deprecation warning by github-actions in 3488
* [Backport release-1.15] [python] `tiledbsoma.__init__.py`: restore lint checks by github-actions in 3498
* [r] TileDB-SOMA 1.15.2 by johnkerl in 3497
* [Backport release-1.15] [c++, python] `fastercsx`: improved duplicate coordinate handling by github-actions in 3485
* [Backport release-1.15] [c++] Set overriding user-provided prefix to be off by default by github-actions in 3489
* [Backport release-1.15] [c++/ci] Disable leak detection and add ASAN CI job to all C++ PRs by github-actions in 3492
* [Backport release-1.15] [python] Filter spatial disclaimer from pytest by github-actions in 3496

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.15.1...1.15.2

The primary bugfix for this release is 3479, which is a backport of 3476. This releases fixes the error message


TypeError: ExperimentAxisQuery() takes no arguments


Bug fixes

* [Backport release-1.15] [python] Re-enable `tiledbsoma.ExperimentAxisQuery` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3479
* [docs] Fix broken tutorial-doc symlinks in `release-1.15` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3466
* [Backport release-1.15] [python/c++] Fix invalid memory read in `fastercsx` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3464
* [Backport release-1.15] [python] Fix stochastic failure of `to_spatialdata` method by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3477
* [Backport release-1.15] [python] Add extra asserts for SpatialData tests by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3474
* [Backport release-1.15][r] Write group-level string metadata as `TILEDB_STRING_UTF8`; 1.15.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/3481

Minor changes

* [Backport release-1.15] [python/c++] Deprecate `config_options_from_schema` in favor of new function by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3465
* [Backport release-1.15] [c++, r, python] `read_next` clean-up by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3480
* [Backport release-1.15] [python] Convert from `Optional[Foo]` to `Foo | None` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/3467

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.15.0...1.15.1