Tiledbsoma

What's Changed

1.6.1 delivers a Python-only bugfix on the `release-1.6` branch. R is not affected, other than our commitment to keep Python and R API versions synchronized.

* [Backport release-1.6] [python] Fix `from_anndata()` to respect `var_id_name` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1964
* [r] Update `DESCRIPTION` and `NEWS.md` for 1.6.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1974


**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.6.0...1.6.1

New features added

* [python] Add unit tests for obsm, obsp, and to_anndata 1942
* [python] Depend on `somacore` 1.0.6 (1940) (1941) which brings in https://github.com/single-cell-data/SOMA/pull/179 which add `obsm`, etc. to `ExperimentAxisQuery`

Minor changes

* [python/r/c++] Depend on core 2.18.2, tiledb-py 0.24.0, tiledb-r 0.22.0 (1936)
* [python] Avoid a double log statement on debug-mode ingest (1918)
* [python] Update pyarrow dependency (1925)
* [python] Fix `pyarrow.compute` for version 12 (1908)
* [python] Normalize unit-test exception coverage (1909)
* [python] Use `numba<0.58` on `release-1.6` branch (1939)
* [r] `tiledbsoma-r` 1.6.0 (1943)
* [r/ci] Show CPU info in R CI as well as Python CI (1956) (1958)
* [r] No longer show 'libtiledb=' before core library version triplet (1929)
* [r] Update tests (1928)
* [r] Future-proof one assertion for an upcoming change in R 4.4.0 (1914)
* [r] Condition one more test file on 'extended mode' (1907)
* [r] Restore `expect_no_condition()` tests in `Seurat` object outgestion (1906)

Bug fixes

* [python] Append-mode ingestion with disjoint measurement names (1919)
* [python] Work around apparent AWS ABI clash with pyarrow on MacOS (1938)
* [r] Arrays should remain open after write (1947) (1949)
* [c++] Modify `ManagedQuery` to perform async queries (1953) (1954)

1.5.3 delivers a Python-only bugfix on the `release-1.5` branch. R is not affected, other than our commitment to keep Python and R API versions synchronized.

Bug fixes

* [python] Allow specification of X names on ingest [release-1.5] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1995
* [python] Minor update to `from_h5ad` online help (backport release-1.5) by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2003
* TileDB-SOMA 1.5.3 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/2004

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.5.2...1.5.3

1.5.2 delivers a Python-only bugfix on the `release-1.5` branch. R is not affected, other than our commitment to keep Python and R API versions synchronized.

Bug fixes

* [Backport release-1.5] [python] Append-mode ingestion with disjoint measurement names by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1922
* [Backport release-1.5] [python] Fix `from_anndata()` to respect `var_id_name` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1968

Minor changes

* [Backport release-1.5] [python] Fix `pyarrow.compute` import for version 12 by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1910
* [Backport release-1.5] [python] Normalize unit-test exception coverage by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1911
* [Backport release-1.5] [python] Avoid a double log statement on debug-mode ingest by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1920
* [Backport release-1.5] [r] Condition one more test file on 'extended mode' by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1913
* [Backport release-1.5] [r] Restore `expect_no_condition()` tests in `Seurat` object outgestion by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1912
* [Backport release-1.5] [r] Future-proof one assertion for an upcoming change in R 4.4.0 by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1921
* [r] Update `DESCRIPTION` and `NEWS.md` for 1.5.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1972

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.5.1...1.5.2

Bug fixes

This is a minor bug-fix release immediately following 1.5.0. Feature deliveries previously scheduled for 1.5.1 will be in 1.5.2.

* [Backport release-1.5] [c++] Set `result_order_` in `SOMAArray` constructor initializer list by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1889
* [Backport release-1.5] `ResultOrder` validation in `SOMAArray::reset` by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1902
* [Backport release-1.5] [python] Fix an f-string by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1893
* [Backport release-1.5] [python] Fix performance regression in bounding-box calculation by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1899
* [Backport release-1.5] [r] Install SeuratObject from source on macOS, rely on update r2u binary on linux by github-actions in https://github.com/single-cell-data/TileDB-SOMA/pull/1901

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.5.0...1.5.1

New features added

* [python] Blockwise SciPy sparse and Arrow Table iterator (1792) (1858)
* [python] Outgest `uns` (1770) (1801)
* [python] Handle string columns with all-NaN values (1834) (1859)
* [python] Support default-coord reads of corner-written dense ND arrays (1810) (1812)
* [python] Allow uns-key restriction for ingest and outgest (1815) (1826)
* [python] Allow `X_layer_name=None` for outgest of X-free experiments (1830) (1832)
* [r] Write string attrs as UTF-8 (Python compatibility) (1843) (1850)

Minor changes

* [r] Set the package version to 1.5.0, and update NEWS.md (1856) (1860)
* [r] Unit-test queryability of enumerated columns (1884) (1885)
* [r] Depend on TileDB-R 0.21.3 (1882) (1883)
* [r] Install required tiledb package version from r-universe (1863) (1881)
* [r] Suppress deprecation warnings in `write_soma.DataFrame()` (1876) (1878)
* [r] Force exporting v3 assays with SeuratObject v5 installed (1809) (1841)
* [ci/r] No more "Last 13 lines of output:" in CI (1871) (1873)
* [ci/python] Make Python blockwise tests less resource-intensive (1877) (1879)
* [ci/python] Excess `pytest` duration (1866) (1868)
* [c++/python] Depend on core 2.17.3 and TileDB-Py 0.23.2 (1838) (1842)
* [c++] Remove `spdlog` requirement (1852) (1857)
* [c++/python] Expose `uri`, `result_order`, and `column_names` for `SOMAArray` (1814) (1827)
* [c++/python/r] Depend on core 2.17.4, tiledb-py 0.23.4, and tiledb-r 0.21.2 (1854) (1855)

Bug fixes

* [python] Enumerations-API refinement (1755) (1844)
* [python] Non-default measurement propagation on `from_anndata` (1820) (1821)
* [python/c++] Support enumerations with Pandas 2.0+
* [python/c++] Expanded enumeration support in `ArrowAdapter::to_arrow` (1848) (1861)
* [ci/python] Enable more verbose python unit test logging (1870) (1872)
* [r] Update `SOMADataFrame` creation and writes (1835) (1847)
* [c++] Correct `results_complete` (1816) (1831)
* [ci/c++] Avoid intermittent CI fail building `catch2` (1828) (1833)