TileDB-SOMA 1.6.2

1.6.2 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.

Bug fixes

• [python] Allow specification of X names on ingest [release-1.6] by @johnkerl in #1996
• [python] Minor update to from_h5ad online help by @johnkerl in #1999
• [r] tiledbsoma 1.6.2 by @johnkerl in #2006

Full Changelog: 1.6.1...1.6.2

TileDB-SOMA 1.5.3

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 #1995
• [python] Minor update to from_h5ad online help (backport release-1.5) by @johnkerl in #2003
• TileDB-SOMA 1.5.3 by @johnkerl in #2004

Full Changelog: 1.5.2...1.5.3

TileDB-SOMA 1.6.1

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 #1964
• [r] Update DESCRIPTION and NEWS.md for 1.6.1 by @johnkerl in #1974

Full Changelog: 1.6.0...1.6.1

TileDB-SOMA 1.5.2

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 #1922
• [Backport release-1.5] [python] Fix from_anndata() to respect var_id_name by @github-actions in #1968

Minor changes

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

Full Changelog: 1.5.1...1.5.2

TileDB-SOMA 1.6.0

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 single-cell-data/SOMA#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)

TileDB-SOMA 1.5.1

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 #1889
• [Backport release-1.5] ResultOrder validation in SOMAArray::reset by @github-actions in #1902
• [Backport release-1.5] [python] Fix an f-string by @github-actions in #1893
• [Backport release-1.5] [python] Fix performance regression in bounding-box calculation by @github-actions in #1899
• [Backport release-1.5] [r] Install SeuratObject from source on macOS, rely on update r2u binary on linux by @github-actions in #1901

Full Changelog: 1.5.0...1.5.1

TileDB-SOMA 1.5.0

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)

TileDB-SOMA 1.5.0rc3

New features added

• [Backport release-1.5] [python] Non-default measurement propagation on from_anndata by @github-actions in #1821
• [Backport release-1.5] [python] Allow uns-key restriction for ingest and outgest by @github-actions in #1826
• [Backport release-1.5] [python] Allow X_layer_name=None for outgest of X-free experiments by @github-actions in #1832
• [Backport release-1.5] [python] Support new set-membership query condition by @github-actions in #1788
• [Backport release-1.5] [python] Create separate set_condition by @github-actions in #1796
• [Backport release-1.5] [python] Outgest uns by @github-actions in #1801
• [Backport release-1.5] [python] Support default-coord reads of corner-written dense ND arrays by @github-actions in #1812

Minor changes

• [Backport release-1.5] [python] Use AnnData 0.10.1 by @github-actions in #1786
• [Backport release-1.5] [r] Articulate R version 1.4.4.1 by @github-actions in #1805
• [Backport release-1.5] [python] Add py.typed to package manifest by @github-actions in #1813
• [Backport release-1.5] [python/c++] Expose uri, result_order, and column_names for SOMAArray by @github-actions in #1827
• [Backport release-1.5] [c++] Correct results_complete by @github-actions in #1831
• [Backport release-1.5] [c++] Avoid intermittent CI fail building catch2 by @github-actions in #1833

Bug fixes

• [Backport release-1.5] [python] Update chunk-sizing estimator for chunked matrix write by @github-actions in #1800

Full Changelog: 1.5.0rc2...1.5.0rc3

TileDB-SOMA 1.4.4

This release is a single-bug-fix release affecting TileDB-SOMA Python. There are no changes for TileDB-SOMA R; however, it is our policy to stamp all implementation languages with the same release tag regardless of how many mods affect each given language. Thus, this is a no-op release for TileDB-SOMA R.

• Backport #1690 to release-1.4 by @johnkerl in #1794
• [r] Bump to 1.4.4 in apis/r/DESCRIPTON on release-1.4 by @johnkerl in #1802

Full Changelog: 1.4.3...1.4.4

TileDB-SOMA 1.5.0rc2

New features added

• [Backport release-1.5] [python] Support obs_id_name and var_id_name in tiledbsoma.io.from_anndata by @github-actions in #1750
• [Backport release-1.5] [python] Allow adata.X to be None by @github-actions in #1772
• [Backport release-1.5] [python] Ingest 2D uns string arrays (e.g. color labels) by @github-actions in #1773

Minor changes

• [Backport release-1.5] [ci/r] Use TileDB-R 0.21.1 binaries by @github-actions in #1751
• [Backport release-1.5] [ci] Update tools used in pre-commit testing by @github-actions in #1754
• [Backport release-1.5] [r] Remove duplicated step in workflow by @github-actions in #1760
• [Backport release-1.5] [r] Update installed packages in workflow by @github-actions in #1761
• [Backport release-1.5] [python] Temporarily pin to AnnData 0.9.* by @github-actions in #1771
• Manually backport #1757 by @johnkerl in #1781
• Manually backport #1779 by @johnkerl in #1782

Bug fixes

• [Backport release-1.5] [python] Check for downgraded categorical write by @github-actions in #1752
• [Backport release-1.5] [c++] Rework SOMAArray reader iterator sequence by @github-actions in #1753
• [Backport release-1.5] [python] Fix and auto-test notebook paths by @github-actions in #1780

Full Changelog: 1.5.0rc1...1.5.0rc2