TileDB-SOMA 0.5.0a9

New features added / breaking changes

For this alpha release, many changes are breaking. This is a step toward 1.0rc0 in which we will
try to isolate the (hopefully zero) remaining opportunities for breaking changes before 1.0rc0.

• [python] Export open function, to universally open everything by @thetorpedodog in #896
• [python] Add add_new_collection implementation by @thetorpedodog in #837
• [python] Add add_new_dataframe and _sparse/_dense_ndarray by @thetorpedodog in #848
• [python] Create and open objects using Thing.create() and Thing.open() by @thetorpedodog in #824
• [python] Add static exists method to TileDBObject by @thetorpedodog in #890
• [python] Generalize tiledbsoma.io.add_X_layer to obsm, varp, etc. by @johnkerl in #814
• [python] Add timestamp slots in SOMATileDBContext and apply throughout by @mlin in #892
• [python] Document newly-created platform_config options by @thetorpedodog in #897
• [python] Re-export somacore's AxisColumnNames at top level by @johnkerl in #881
• [python] Support indices of type bytes by @johnkerl in #861
• [r] Support iterated sparse and dense matrix reads by @eddelbuettel in #835
• [r] Support remotes::install_github use by @eddelbuettel in #826
• [r] Add iterated readers for SOMA classes by @eddelbuettel in #811
• [python] Add user-level stats hooks, to reach parity with tiledbsoma-r by @johnkerl in #871
• [r] Add stats API accessors by @eddelbuettel in #865
• Use show_package_versions in bug-report issue template by @johnkerl in #868
• [r,python] Add show_package_versions for bug-report use by @johnkerl in #855
• Create bug-report and feature-request templates by @maniarathi in #728

Internal support for features

• [python] Refactor processing of URIs for collection creation/setting by @thetorpedodog in #889
• [python] Add additional create-time platform_config hooks for schema mods by @bkmartinjr in #888
• [python] Pull in somacore==0.0.0a12 and associated improvements by @thetorpedodog in #882
• [python] Keep only the read or write TileDB handles open long-term by @thetorpedodog in #863
• [python] Track ownership of accessed and added collection members. by @thetorpedodog in #847
• [python] Create ReadWriteHandle to manage TileDB handles by @thetorpedodog in #823
• [python] Switch to somacore 0.0.0a10 by @thetorpedodog in #825
• [c++] SOMAReader open-at-timestamp support by @mlin in #788

Minor changes

• [python] Move io into submodule and organize various util_ files. by @thetorpedodog in #899
• [python] Capture stdout/stderr from stats_dump output by @thetorpedodog in #887
• [python] Un-xfail some tests which are now passing by @thetorpedodog in #891
• [r] Validate no allow-duplicates for sparse N-d arrays and dataframes by @johnkerl in #879
• [python] string_dim_zstd_level -> int64_dim_zstd_level by @johnkerl in #883
• [python] Schema validation for DataFrame by @johnkerl in #880
• [python] Directly use backend TileDB dimension names for DataFrame by @thetorpedodog in #870
• [python] Use the array we already have open to generate the Arrow schema by @thetorpedodog in #869
• [python] Unexpose TileDBArray and TileDBObject by @johnkerl in #856
• Update LICENSE to make the years the same. by @maniarathi in #852
• [python] Make typeguard_ignore decorator play nice with Pylance by @thetorpedodog in #849
• [python] Remove __eq__ method from base TileDBObject class by @thetorpedodog in #846
• [python] Pull the common parts of NDArrays into the base NDArray class by @thetorpedodog in #836
• [python] Fix legacy misuse ofurllib.parse.urljoin by @johnkerl in #832
• [r] Limit builds to unix operating systems by @eddelbuettel in #831
• [r] Add lifecycle-maturity tags to Roxygen blocks by @johnkerl in #829
• [python] Use the contents of bld, not setup.py, for binary cache by @thetorpedodog in #827
• [python] Add lifecycle maturity tags to public API docstrings by @atolopko-czi in #818
• [python] Move test data to testdata folder by @thetorpedodog in #817
• [python] Refactor factory._construct_member by @gsakkis in #815

Bug fixes

• [python] Fix and test over-indexing semantics by @johnkerl in #901
• [python] No allow-duplicates for sparse N-d arrays by @johnkerl in #878
• [python] Improve detection of nonexistent-array errors from TileDB Cloud by @johnkerl in #873
• [python] Fix __del__ error when improperly constructing a TileDB object by @thetorpedodog in #864
• [python] Modify setup.py to find system-installed libtiledbsoma on POSIX by @nguyenv in #838
• [python] Fix use_relative_uri for tiledbsoma.io [post-824] by @johnkerl in #833
• [python] Fix #822 re small tile extents by @johnkerl in #830

New Contributors

• @nguyenv made their first contribution in #838

Full Changelog: 0.5.0a8...0.5.0a9