TileDB-SOMA 1.0.0rc5

Key features of this release are #1053 and #1061.

New features added

• [python] Support ingest of H5AD dense X as SOMA sparse X by @johnkerl in #1061
• [r] Expand developer instructions in apis/r/README.md by @eddelbuettel in #1054
• [r] Add index_column_names() (as an aliases to dimnames()) by @eddelbuettel in #1056
• [r] Test-drive apis/r/README.md on a fresh EC2 instance by @johnkerl in #1060

Breaking changes

• [python] Ingestor must return readable result by @johnkerl in #1053

Minor changes

• [docs] Convert docstrings in _collection.py to Google style by @ebezzi in #1044
• [r] Refactor arrow export by @eddelbuettel in #1052
• [python] Run packaging workflow nightly by @mlin in #1059
• [python] Polish version.py by @mlin in #1057
• [python] Constrain numba & numpy versions for compatibility with old pip solver by @mlin in #1058
• [python] Code-neaten follow-up for #1061 by @johnkerl in #1065
• [python] Depend on somacore 1.0.0rc5 by @johnkerl in #1067

New Contributors

• @ebezzi made their first contribution in #1044

Full Changelog: 1.0.0rc4...1.0.0rc5

TileDB-SOMA 1.0.0rc4

Bug fixes

• [python] Depend on attrs package >= 22.2 by @johnkerl in #1050

Full Changelog: 1.0.0rc3...1.0.0rc4

TileDB-SOMA 1.0.0rc3

New features added

• [r] SOMA Experiment query API by @aaronwolen in #1030
• [r] Implement PlatformConfig and SOMATileDBContext for R by @mojaveazure in #1026
• [python] Allow all operations on a collection to share a timestamp by @thetorpedodog in #1001
• [python] Explicit shaping for DataFrame by @johnkerl in #1027
• [python] Add result_order support to sparse NDArray reads by @thetorpedodog in #1047
• [c++] Update C++ sandbox-build instructions by @johnkerl in #1025

Breaking changes

• [python] Improve spec/impl consistency on cls/type/kind parameters by @atolopko-czi in #1045

Minor changes

• [python] Unmark experiment_query xfailures since they pass now by @thetorpedodog in #1018
• [python] Pin stub versions used in type checking by @thetorpedodog in #1024
• [python] Lifecycle maturity tags by @bkmartinjr in #1028
• [r] Fix test for X-layer assertions by @aaronwolen in #1033
• [r] Revert #1026 by @johnkerl in #1037
• [python] Start adding errors to docstrings by @bkmartinjr in #1036
• [python] Adding more docstring info on error handling by @bkmartinjr in #1039
• [python] Depend on somacore 1.0.0rc4 by @thetorpedodog in #1048

Bug fixes

• [c++/python] Correctly handle all four timestamp types by @johnkerl in #1029
• [python] Return False on various .exists() by @johnkerl in #1040

Full Changelog: 1.0.0rc2...1.0.0rc3

TileDB-SOMA 1.0.0rc2

Bug fixes

• [python] Make the default timestamp in SOMATileDBContext be None by @thetorpedodog in #998

Minor changes

• Don't run R CI jobs on pre-commit changes by @thetorpedodog in #993
• [python] Remove an extraneous print statement by @johnkerl in #996
• [python] Raise TypeError on unsupported index type bool by @johnkerl in #1002
  • Note: this is a non-breaking change since this was already unsupported
• [r] Make SparseNDArray$write arg name match Python/spec by @johnkerl in #1004
• [python] Depend on somacore 1.0.0rc3 by @johnkerl in #1012

Full Changelog: 1.0.0rc1...1.0.0rc2

TileDB-SOMA 1.0.0rc1

New features added

• [python] Handle DataFrame index types beyond int/string -- except timestamps and bools by @johnkerl in #968
• [python] Handle timestamp index types for DataFrame by @johnkerl in #985
• [python] Include key–value pairs in metadata repr by @thetorpedodog in #987

Breaking changes

• [python] Use the same timestamp across read and write operations by @thetorpedodog in #981

Minor changes

• [python] Depend upon somacore v1.0.0rc0 by @thetorpedodog in #982
• [python] Depend on somacore 1.0.0rc2 by @johnkerl in #992
• [python] Move options implementations modules to private by @thetorpedodog in #979
• [python] Add regression test for bug #919 by @mlin in #983
• [c++] Improved bounds-detection for Arrow array data by @johnkerl in #986
• [python] A few minor readthedocs-related neatens by @johnkerl in #980

Bug fixes

• [c++] Support nnz when allow_duplicates=True by @johnkerl in #989

Full Changelog: 1.0rc0...1.0.0rc1

TileDB-SOMA 1.0rc0

New features

• [r] Return schema information as an Arrow schema by @eddelbuettel in #978

Full Changelog: 0.5.0a13...1.0rc0

TileDB-SOMA 0.5.0a13

New features added

• [r] Extend SOMADataFrame to writes to RecordBatch by @eddelbuettel in #963
• [r] Add shape(), ndim(), and nnz() by @eddelbuettel in #966
• [python] Improve docstring content by @bkmartinjr in #951
• [r] Update documentation by running roxygen2 by @eddelbuettel in #967
• [python] Expose ResultOrder in top-level namespace by @johnkerl in #973

Breaking changes

• [python] Mutable-X mods, and .shape as explicit SparseNDArray capacity by @johnkerl in #952

Minor changes

• [python] Add comments on why we expect replace tests to fail by @thetorpedodog in #964
• [python] Use setuptools_scm to get TileDB-SOMA-Py version by @nguyenv in #962
• [r] Adjust (vendored) r-ci.sh script by @eddelbuettel in #970

Bug fixes

• [python] Fixing PyPI packaging by @mlin in #969

Full Changelog: 0.5.0a12...0.5.0a13

TileDB-SOMA 0.5.0a12

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 #845
• [python] Allow slicing with any type and with negative values by @thetorpedodog in #948

Breaking changes

• [r/python] Rename stats_* to tiledbsoma_stats_* by @johnkerl in #944

Minor changes

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

Full Changelog: 0.5.0a11...0.5.0a12

TileDB-SOMA 0.5.0a11

Breaking changes

• [python] Explicitly remove support for slice steps by @thetorpedodog in #918
• [python] Upgrade to somacore==0.0.0a13 by @thetorpedodog in #923
• [python] Check to ensure we're not doing partitioned reads by @thetorpedodog in #917

Minor changes

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

Full Changelog: 0.5.0a10...0.5.0a11

TileDB-SOMA 0.5.0a10

What's Changed

This is a minor bump on top of 0.5.0a10.

• [python] Add replace method to SOMATileDBContext by @bkmartinjr in #908
• [python] Minor Python fixes: slots, delinting, removing duplicate code by @thetorpedodog in #902
• [python] Update to mypy 1.0.0 and FINALLY use Self! by @thetorpedodog in #905
• [python] Add and improve documentation for many public-facing methods by @thetorpedodog in #898
• [r] Update man/ directory by running roxygenize (closes #906) by @eddelbuettel in #907

Full Changelog: 0.5.0a9...0.5.0a10