TileDB-SOMA 1.7.0rc1

What's Changed

In addition to https://github.com/single-cell-data/TileDB-SOMA/releases/tag/1.7.0rc0:

• [Backport release-1.7] [c++/ci] Fix a pkgdown CI error about unnecessary semicolons by @github-actions in #2051
• [Backport release-1.7] [python] Rename utils.py to _index_util.py by @github-actions in #2058
• [Backport release-1.7] [python] Pass config options to DataFrame.read by @github-actions in #2059
• [Backport release-1.7] [c++] Fix zero-size lookup chunk size for the C++ re-indexer by @github-actions in #2062
• [Backport release-1.7] [python] Chunked writes for DataFrame; byte-caps for Arrow-table writes by @github-actions in #2064

Full Changelog: 1.7.0rc0...1.7.0rc1

TileDB-SOMA 1.7.0rc0

TileDB-SOMA uses Tile-DB Core 2.19, TileDB-Py 0.25, and Tile-R 0.23.

New features added

• [python] Allow specification of X names on ingest by @johnkerl in #1993
• [r] Arrays should remain open after write by @aaronwolen in #1947
• [r] Add support for registering arrays with write_soma() by @mojaveazure in #2013
• [r] Add write_soma.character() by @mojaveazure in #2021
• [r] Update documentation on g++ requirement for R package by @CharlesBordet in #2031
• [r] Support cross compiling on MacOS with R by @jeroen in #2034

Minor changes

• [Backport release-1.7] [python] Add common.h to MANIFEST.in by @github-actions in #2043
• [Backport release-1.7] [python] Update unit tests for pandas 2.2 and scipy 1.12 by @github-actions in #2044
• [Backport release-1.7] [r] Enable opt-in use of 'catchsegv', enable in CI on Linux by @github-actions in #2046
• Depend on TileDB core 2.19, TileDB-Py 0.25, TileDB-R 0.23 by @johnkerl in #2002
• Update to use somacore==1.0.7. by @thetorpedodog in #2000
• Bump jinja2 from 3.0.0 to 3.1.3 in /doc by @dependabot in #2007
• [python] Depend on somacore 1.0.6 by @johnkerl in #1940
• [python] Add unit tests for obsm, obsp, and to_anndata by @ebezzi in #1934
• [python] QueryCondition should error out if given empty set by @nguyenv in #1967
• [python] Dataframe read path by @nguyenv in #1793
• [r] tiledbsoma-r 1.7.0 by @johnkerl in #2041
• [r/ci] Show CPU info in R CI as well as Python CI by @johnkerl in #1956
• [r] Apply PR 1943 to main by @johnkerl in #1957
• [r] Tweak coverage data generation by @eddelbuettel in #1990
• [r] Bump apis/r/DESCRIPTION for main past current latest release by @johnkerl in #2005
• [r] Add a helper function to determine max value per int type by @eddelbuettel in #2022
• [c++] Modify ManagedQuery to perform async queries by @nguyenv in #1953
• [c++] Have tiledbsoma-cli link to tiledbsoma by @teo-tsirpanis in #1965
• [c++] Extend codecov to cover tiledbsoma library by @beroy in #1970
• [c++] Append TILEDBSOMA_COVERAGE to cmake flags by @nguyenv in #2019
• [c++] Reindexer overrides and fast COO/CSR by @beroy in #1728

Bug fixes

• [python] Fix from_anndata() to respect var_id_name by @aaronwolen in #1963
• [python] Fix data loss for multiple writes with Enumeration extend by @nguyenv in #1978
• [python] Error if extending enum past index type limit by @nguyenv in #1986
• [r] Ensure factors are releveled before appending w/ expanded levels by @eddelbuettel in #1983
• [r] Ensure addition of factor levels does not overflow capacity of index type by @eddelbuettel in #2008

Ongoing progress

• [python] Add Windows support for the Python API by @teo-tsirpanis in #1811 (Note: this is still a WIP)
• [python] Revert "Add Windows support for the Python API" by @johnkerl in #1959
• [python] Add back Windows support for the Python API, but without CI by @teo-tsirpanis in #1961

New Contributors

• @teo-tsirpanis made their first contribution in #1811
• @dependabot made their first contribution in #2007
• @CharlesBordet made their first contribution in #2031
• @jeroen made their first contribution in #2034

Full Changelog: 1.6.2...1.7.0-rc0

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