Use TileDB Core 2.20, TileDB-Py 0.26, TileDB-R 0.24

[johnkerl]

[sc-41030]

[shortcut-integration]

This pull request has been linked to Shortcut Story #41030: Update projects to TileDB 2.20.

[codecov]

Codecov Report

Merging #2150 (2b93c63) into main (3f64022) will decrease coverage by 13.69%.
The diff coverage is n/a.

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #2150       +/-   ##
===========================================
- Coverage   81.15%   67.46%   -13.69%     
===========================================
  Files          84       50       -34     
  Lines        6341     2536     -3805     
  Branches      215      215               
===========================================
- Hits         5146     1711     -3435     
+ Misses       1096      726      -370     
  Partials       99       99               

Flag	Coverage Δ
libtiledbsoma	67.46% <ø> (-0.16%)	⬇️
python	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	∅ <ø> (∅)
libtiledbsoma	48.75% <ø> (ø)

[eddelbuettel]

This may have to be on hold for the R side of things until 0.24.0 is actually i) at CRAN, ii) merged into main, iii) tagged as a release, iv) built everywhere we care about (r2u, conda, ...)

We are waiting for a human override at CRAN as the package is held for an issue outside the package, and our control.

[johnkerl]

All good @eddelbuettel -- and thank you -- this PR is "up and ready to poke the retry button" whenever (and by whomever, although realistically I'll mostly likely be the one pushing the retry button when that's ready)

[eddelbuettel]

As just commented in another issue, it is a little different 'this time' and at least now as we have a release, binaries where we make them ... but no CRAN release (yet at least).

[johnkerl]

https://github.com/single-cell-data/TileDB-SOMA/actions/runs/7981175554/job/21792363225?pr=2150 shows that we are getting core 2.20.1 for TileDB-SOMA-R but 2.20.0 via TileDB-Py 0.26.0:

Run Rscript -e 'tiledbsoma::show_package_versions()'
tiledbsoma:    1.7.99.3
tiledb-r:      0.2[4](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/7981175554/job/21792363225?pr=2150#step:11:5).0.1
tiledb core:   2.20.1
libtiledbsoma: 2.20.1
R:             R version 4.3.2 (2023-10-31)
OS:            Ubuntu 22.04.3 LTS

Run python -c 'import tiledbsoma; tiledbsoma.show_package_versions()'
tiledbsoma.__version__        1.5.0rc0.post214.dev362487835
TileDB-Py tiledb.version()    (0, 26, 0)
TileDB core version           2.20.0
libtiledbsoma version()       libtiledb=2.20.1
python version                3.10.13.final.0
OS version                    Linux 6.2.0-1019-azure
tiledbsoma.__version__    1.5.0rc0.post214.dev362487835
tiledb.version()          0.26.0
core version              2.20.0
anndata.__version__  (ad) 0.10.5.post1
numpy.__version__    (np) 1.26.4
pandas.__version__   (pd) 2.2.0
pyarrow.__version__  (pa) 15.0.0
scanpy.__version__   (sc) 1.9.8
scipy.__version__    (sp) 1.[12](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/7981175554/job/21792363225?pr=2150#step:15:13).0
python__version__         3.10.[13](https://github.com/single-cell-data/TileDB-SOMA/actions/runs/7981175554/job/21792363225?pr=2150#step:15:14)

cc @ihnorton

[johnkerl]

Dependencies as discussed in Slack with @ihnorton