Tiledbsoma

New features added

* [r] Extend `SOMADataFrame` to writes to `RecordBatch` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/963
* [r] Add `shape()`, `ndim()`, and `nnz()` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/966
* [python] Improve docstring content by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/951
* [r] Update documentation by running roxygen2 by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/967
* [python] Expose `ResultOrder` in top-level namespace by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/973

Breaking changes

* [python] Mutable-X mods, and `.shape` as explicit `SparseNDArray` capacity by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/952

Minor changes

* [python] Add comments on why we expect replace tests to fail by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/964
* [python] Use `setuptools_scm` to get `TileDB-SOMA-Py` version by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/962
* [r] Adjust (vendored) r-ci.sh script by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/970

Bug fixes

* [python] Fixing PyPI packaging by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/969

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a12...0.5.0a13

_Note: this release has no wheel artifacts at https://pypi.org/project/tiledbsoma/. That was fixed on PR #969 , and the next release 0.5.0a13 will have wheel artifacts._

New features added

* [c++] Create shared library for conda builds by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/845
* [python] Allow slicing with any type and with negative values by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/948

Breaking changes

* [r/python] Rename `stats_*` to `tiledbsoma_stats_*` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/944

Minor changes

* [python] Bring `SOMADataFrame` domain into spec compliance by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/932
* [python] Add names to `NDArray` tests, too by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/928
* [python] Typo-fix in `NDArray` `create` error message by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/934
* Make the pull-request template a little less shouty by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/945
* [python] Unify coordinate-parsing logic and use entire dimension for slicing by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/936
* [python] Remove matplotlib pin since scanpy is fixed by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/953
* [python] Add underscore prefix to internal submodules by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/955
* [c++/python] Use `py::print` in libtiledbsoma11 to print, not `cout` by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/958
* Fix duplicate-sentence typo in `README.md` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/959
* [python] Stop using the flush hack when writing metadata or group contents by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/957

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a11...0.5.0a12

Breaking changes

* [python] Explicitly remove support for slice steps by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/918
* [python] Upgrade to somacore==0.0.0a13 by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/923
* [python] Check to ensure we're not doing partitioned reads by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/917

Minor changes

* [docs] Harmonize `README.md` files by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/886
* [python] Use `**kwargs` and a function decorator to forward arguments by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/909
* [python] Minor cleanup to deduplicate some code by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/911
* [python] Allow passing 0-length lists of coordinates to `DataFrame` by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/910
* [python] Put more info in the `__repr__` of SOMA objects by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/912
* [r] Re-punctuate lifecycle tags by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/916
* Don't use shouty-caps in issue templates by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/894
* [r] Use dimension information when applying coords by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/920
* [python] Give dataframe tests descriptive names and columns by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/925
* [python] Exclude matplotlib 3.7 due to incompatible scanpy by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/929

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a10...0.5.0a11

What's Changed

This is a minor bump on top of 0.5.0a10.

* [python] Add `replace` method to `SOMATileDBContext` by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/908
* [python] Minor Python fixes: slots, delinting, removing duplicate code by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/902
* [python] Update to mypy 1.0.0 and FINALLY use `Self`! by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/905
* [python] Add and improve documentation for many public-facing methods by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/898
* [r] Update `man/` directory by running roxygenize (closes 906) by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/907


**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a9...0.5.0a10

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 of`urllib.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**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a8...0.5.0a9

Bugfixes

* [python] Depend on somacore 0.0.0a8] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/809

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/0.5.0a7...0.5.0a8