Tiledbsoma

New features added

* [python] MacOS arm64 wheel-builds for PyPI by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1385

Ongoing development toward 1.0 R release

* [r] SOMASparseNDArray: sparseMatrix zero-based shim to facilitate soma_joinid lookup by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1313
* [r] Port notebooks to R vignettes by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1337
* [r] Put like with like in test-helpers by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1349
* [r] Add some whitespace for improved readability by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1350
* [r] Unit-test failure on Mac M1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1357
* [r] Re-order methods in `ephemeral.R` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1359
* [r] Allow default `index_column_names=c("soma_joinid")` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1363
* [r] Refactor build by as-needed rebuilding libtiledbsoma by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1361
* [r] Update MacOS build for developer-with-local-core corner case by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1368
* [r] Split up large `test-SeuratOutgest.R` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1373
* [r] Provide reference to `libtiledbsoma` source via soft-link by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1372
* [r] Implement stateful open/close by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1325
* [r] Set a define so that spdlog uses REprintf by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1381
* [r] Remove two debug statements by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1382
* [r] Address remaining two R CMD check nags by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1384
* [r] Update mode semantics for implicit open by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1383
* [r] Update Seurat ingestor to skip the data slot when it's identical to counts by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1389

Ongoing C++ development

* [c++] Move installed header files one level deeper by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1338
* [c++] Adjust two more include paths by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1341
* [c++] Remove unused references to removed R_BUILD option by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1344
* [c++] Remove remaining traces of BUILD_R from library CMakeLists.txt by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1345
* [c++] Addition of `SOMAGroup` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1339
* [c++] Make `SOMA{Array,Group}` Changes According To Review in 1339 by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1352

Minor changes

* [python] Update `platform_config` usage advice by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1371
* [python] Reduce default `goal_chunk_nnz` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1393
* [python] Auto-consolidate fragment metadata and commits by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1284
* [python] Add run-time type checks to `PlatformConfig` on ingest/create by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1370
* [r/docs] Clean up documentation by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1379
* [docs] Added two badges (and ensure consistent two break before sections) by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1375

Bug fixes

* [python] Update obsm-chunking logic by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1380
* [python] PyPI-publish workflow by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1388
* [python] Improve resume-mode experience by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1396
* [docs] Fix signup link for TileDB Community Slack by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1369

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.2.3...1.2.4

Overview

* Improve Seurat I/O
* Add support for unsigned/public AWS/S3 URIs
* Fix query conditions for boolean attributes in R

New features added

* [r] Seurat <> SOMA Integration Improvements by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1305

Minor changes

C++

* [c++] Rename `SOMAArrayReader` to `SOMAArray` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1283
* [c++] Add Array metadata methods by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1323
* [c++] Add `cstring` Header to `util.cc` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1309
* [c++] Do not install source files by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1319
* [c++] Install span header by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1311
* [c++] Move two headers and adjust two include statements by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1318
* [c++] Reorganize directory to separate public and private headers by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1301

R

* [r] Add new example dataset and methods for accessing example datasets by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1298
* [r] Additional neatification of src/Makevars{,.in} by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1321
* [r] Build against shared library `libtiledbsoma` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1302
* [r] Condition on more test on SeuratObject by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1320
* [r] Remove all (already unused) cases of the R_BUILD define by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1304
* [r/python] Seurat to AnnData test by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1316

Python

* [python] Depend on somacore 1.0.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1292
* [python] Add a run-time type check on contexts provided to `tiledbsoma.io` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1297
* [python] Mark `tiledbsoma` as containing type annotations for users by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1324
* [ci/python] Publish to TestPyPI on nightly or manual run by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1291
* [docs/python] Expand docstrings for `Experiment` and `Measurement` by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1230

Bug fixes

* [c++/r/python] Update to core 2.15.2, TileDB-Py 0.21.3, TileDB-R 0.19.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1303
* [python] Require TileDB-Py >= 0.21.2 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1296
* [python] Tighten TileDB pypi dependency to be a 0.21.x version. by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1299

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.2.2...1.2.3

Highlights

* R Seurat I/O
* Full support for Python 3.11

New features added

* [r] Add Seurat -> SOMA Ingestor by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1146
* [r] Provide `context()` accessor by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1205
* [r] Return lists of Arrow 'Table' objects in `read(iterated=TRUE)` by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1214
* [r] Seurat outgestors expect sparse arrays in `obsm` and `varm` by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1225

* [python/ci] Include Python 3.11 in CI matrix by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/599
* [python] Store `obsm` and `varm` sparsely by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1246

* [docs/python] Add `tutorials.rst` by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1243

Minor changes

* [r] Coerce `obs_joinids()` and `var_joinids()` to vectors by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1281
* [r][python] Create an AnnData -> SOMA -> Seurat test by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1263
* [r] Refine group member caching behavior by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1272
* [r] More renames `SOMAReader` -> `SOMAArrayReader` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1191
* [r] Improve R query performance with obs and var both specified by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1195
* [r] Update result_order docs and defaults by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1196
* [r] Rerun roxygenise by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1204
* [r] Rename NdArray file names to match NDArray class names by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1218
* [r] Add `pbmc3k.tiledb` info to `apis/r/README.md` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1219
* [r] Static library is configured to install to `lib` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1221
* [r] Correct typo and minor edit to configure by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1231
* [r] Port ephemeral classes to R by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1212
* [r] Port `TileDBCreateOptions` from Python to R by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1216
* [r] Fix (venial) typo in R unit test by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1244
* [r] Upcast SOMADataFrame coords to int64 by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1254
* [r/ci] Update R MacOS CI, given R 4.3.0 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1275

* [c++] Final rename `SOMA_READER` -> `SOMA_ARRAY_READER` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1201
* [c++] Fix build on MacOS 13.3 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1206
* [c++] Omit no-longer-needed libtiledbsoma commit-hash info from `show_package_versions` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1207
* [c++] Ensure cmake parameters are used and passed from superbuild by Shelnutt2 in https://github.com/single-cell-data/TileDB-SOMA/pull/1208
* [c++] Update MacOS 13 check from 1206 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1235

* [docs] Update name of CZ CELLxGENE Census by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1211
* [docs] CZI Slack channel name change by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1213
* [docs/python] Remove `main-old` branch documentation by atolopko-czi in https://github.com/single-cell-data/TileDB-SOMA/pull/1187
* [docs/python] More doc links/styling by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1210
* [ci/python] Auto-create a GH issue on nightly CI fail by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1233
* [python/r] Always write TileDB Cloud–specific metadata to Experiments by aaronwolen in https://github.com/single-cell-data/TileDB-SOMA/pull/1286

* [python] Write TileDB Cloud–specific metadata to Experiments by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1260
* [python] Add tests for `*_dim_zstd_level` create options by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1215
* [python] Parse `TILEDB_PATH` and `TILEDBSOMA_PATH` in `setup.py` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1189
* [python] Include PyPI wheel-publish in release CI by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1190
* [python] Put `capacity` on the same footing as other `PlatformConfig` parameters by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1229
* [python] Support CLI config arguments in `devtools/ingestor` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1227
* [python] Put `allows_duplicates` on the same footing as other `PlatformConfig` parameters by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1234
* [python] Pin anndata to < 0.9 for Python 3.7 since it doesn't support Python 3.7 like we do by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1252
* [python] Flexible `--libtiledbsoma` specification in `setup.py` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1253

Bug fixes

* [r] Upcast axis query coords to integer64 by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1209
* [r] Error on incomplete (non-iterated) reads by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1194

* [python] Explicit casting of Numpy nulls to Arrow nulls by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1265
* [python] Unwrap numpy scalar values when importing `uns` data by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1268
* [python] Handle ingest of completely empty sparse arrays by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1267
* [python] Avoid context leak on group-set-timestamp operation; use TileDB Embedded 2.15.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1199
* [python] Wire `context` through `tiledbsoma.io.from_anndata` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1224

* [ci] Fix publish_to_pypi.yml parse error by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1236

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.2.1...1.2.2

Bug fixes

The primary purpose of this release is for Conda builds: https://github.com/TileDB-Inc/tiledbsoma-feedstock/pull/9#issuecomment-1486852905

* [python] Don't use `distro` in `show_package_versions` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1186
* [R] Fix `to_seurat()` cell-level meta data by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1179

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.2.0...1.2.1

Summary

* Support for ingesting `uns` data from AnnData files
* Steady progress toward R 1.0 release candidate
* Doc-site evolution

New features added

* [r] Adding factory methods by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1123
* [r] Pass config through `shape()` and `nnz()` by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1138
* [r] Add general opener by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1141
* [r] Make obj$close() public by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1142
* [r] Add SOMA Experiment Query -> Seurat outgestors by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1119
* [r] Clarify status of DenseNDArray writes and matrices by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1160
* [r] Also show osVersion when displaying package versions by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1176

* [python] Ingest `uns` values from AnnData files by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1157
* [python] Allow `to_anndata` when `feature_id` not `var_id` is in `var` columns by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1136

Minor changes

* [r] Tweak CI on Ubuntu by taking advantage of newest bspm release by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1168
* [r] Rename `soma_reader` -> `soma_array_reader` within source code by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1174

* [python] Ensure that `libtiledbsoma_dir` is always a `pathlib.Path` by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1155
* [python] A round of cross-references by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1161
* [python] Depend on somacore 1.0.1 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1167
* [python] Include OS info in `show_package_versions` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1177

* [c++] Install cmake Target and Config for libtiledbsoma by Shelnutt2 in https://github.com/single-cell-data/TileDB-SOMA/pull/1159
* [c++] Pass TILEDBSOMA_ENABLE_TESTING and TILEDBSOMA_BUILD_CLI in INHERITED_CMAKE_ARGS by Shelnutt2 in https://github.com/single-cell-data/TileDB-SOMA/pull/1162

* [r/python] Support `bytes` metadata field + R `SOMA_ENCODING_VERSION` by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1149
* [r/python] R-Python roundtrip testing by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1139
* [r/python] DenseNDArray R-Python roundtrip testing by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1158
* [r/python] fix TestDenseNDArrayWriteRReadPython by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1163
* [r/python] SparseNDArray R-Python roundtrip testing by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1165
* [c++/r/python] Modify `SOMAReader` To `SOMAArrayReader` by nguyenv in https://github.com/single-cell-data/TileDB-SOMA/pull/1147
* Filenames `soma_reader` -> `soma_array_reader` by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1173

* [docs/python] Add more lifecycle-experimental indicators to docstrings [WIP] by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1153
* [docs] Add notebooks as tutorials to the docsite by ebezzi in https://github.com/single-cell-data/TileDB-SOMA/pull/1140
* [docs/python] Fix hyperlinks in Sphinx docs by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1152
* [docs/python] Add more external links for docsite by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1154
* [docs/python] Neaten Sphinx config by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1166

Bug fixes

* [r] Fix reading very sparse assays by mojaveazure in https://github.com/single-cell-data/TileDB-SOMA/pull/1156

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.1.1...1.2.0

Primary features

* This release brings in [TileDB Embedded 2.15.0](https://github.com/TileDB-Inc/TileDB/releases/tag/2.15.0), along with [TileDB-Py 0.21.1](https://github.com/TileDB-Inc/TileDB-Py/releases/tag/0.21.1) and [TileDB-R 0.19.0](https://github.com/TileDB-Inc/TileDB-R/releases/tag/0.19.0), in addition to updates for Conda installs
* Ongoing R development
* No significant changes for Python users

New features added

* Add examples to docstrings by bkmartinjr in https://github.com/single-cell-data/TileDB-SOMA/pull/1109

Bug fixes

* [python] Fix wheel builds given recent Conda-related changes by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1134
* [ci] Ensure macOS builds use clang instead of gcc by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1127
* [python] Pin typeguard to < 3.0 by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1115


Minor changes

* [r] `SOMASparseNDArray$read_sparse_matrix`: set dims on the returned `sparseMatrix` by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1110
* [r] `SOMASparseNDArray$read_sparse_matrix`: set dims on iterated `sparseMatrix` parts by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1125
* [r] Fix testing logic for iterated reads from `SOMASparseNDArray` by mlin in https://github.com/single-cell-data/TileDB-SOMA/pull/1112
* [r] Limit pkgdown runs to releases and manual triggers by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1131
* [r] Update documentation with roxygen2 by eddelbuettel in https://github.com/single-cell-data/TileDB-SOMA/pull/1133
* [python] Trivial typofix by johnkerl in https://github.com/single-cell-data/TileDB-SOMA/pull/1120
* [ci] Don't mark a run as failed if coverage upload fails. by thetorpedodog in https://github.com/single-cell-data/TileDB-SOMA/pull/1132

**Full Changelog**: https://github.com/single-cell-data/TileDB-SOMA/compare/1.1.0...1.1.1