[r] Prepare for TileDB-SOMA R GA

[johnkerl]

​​Prerequsites

• ​​Obtain CZI sign-off on proceeding with R general availability release

​​Dependencies

• ​​TileDB core 2.16.1
  • ​​Release tag and GitHub artifacts https://github.com/TileDB-Inc/TileDB/releases/tag/2.16.1 — note 2.16.1 has a bugfix which is a release-blocker for TileDB-SOMA R GA
• ​​TileDB-Py 0.22.1
  • ​​Release tag and GitHub artifacts https://github.com/TileDB-Inc/TileDB-Py/releases/tag/0.22.1
  • ​​Artifacts on PyPI https://pypi.org/project/tiledb/#history
• ​​TileDB-R 0.20.2
  • Release tag and GitHub artifacts https://github.com/TileDB-Inc/TileDB-R/releases/tag/0.20.2
  • Artifacts available on r-universe https://tiledb-inc.r-universe.dev/tiledb -- artifacts not yet available on CRAN as we are one week into a two-week CRAN organizational break that ends August 7th

​​Release Preparation

• ​​Merge https://github.com/single-cell-data/TileDB-SOMA/tree/aaronwolen/docs-cleanup to reduce cross-section of exported namespace
• Temporarily change r-universe build cadence to release-only so users can obtain 0.22.1 builds from there until the update is available on CRAN Update tiledb-r to track releases TileDB-Inc/tiledb-inc.r-universe.dev#2
• ​​Depend on 2.16.1, 0.22.1, and 0.20.2 in Python, R, and C++ dependency files: [c++, python, r] Update to core 2.16.1, tiledb-py 0.22.1, tiledb-r 0.20.2 #1561
• ​​Update CI to install tiledb-r​ from R-universe due to the CRAN hiatus noted above
  • Step 1: Update tiledb-r to track releases TileDB-Inc/tiledb-inc.r-universe.dev#2
  • Step 2: [r] Temporarily install tiledb-r from r-universe #1570
• ​​Regenerate docs
• Verify no errors in R CMD check locally, and submit to rhub
  • Verifies that builds succeed in different CRAN-like environments — this is an efficient way to test/safety-check the package on a variety environments
• Revert Update tiledbsoma-r to track commits, only for today TileDB-Inc/tiledb-inc.r-universe.dev#3
• ​​Release PR [r] Release 1.4.0 #1574 for tiledbsoma-r​
  • ​​Update Version​ field in DESCRIPTION​ file to 1.4.0​
  • ​​Update top header in NEWS.md​ file to # TileDB-SOMA 1.4.0​
• https://github.com/single-cell-data/TileDB-SOMA/wiki/Branches-and-releases including but not limited to the following:
  • Create release branch release-1.4 from main on single-cell-data/TileDB-SOMA
  • Absolute necessity to do the Conda pre-check step shown in that wiki before tagging 1.4.0 in single-cell-data/TileDB-SOMA
  • Tag 1.4.0 in single-cell-data/TileDB-SOMA

​​Conda Packages

Dependencies

• tiledb​ 2.16.1 available on conda-forge anaconda channel (https://anaconda.org/conda-forge/tiledb/labels)
• ​​tiledb-py​ 0.22.1 available on conda-forge anaconda channel (https://anaconda.org/conda-forge/tiledb-py/labels)
• ​​r-tiledb​ 0.20.2 available on conda-forge anaconda channel (https://anaconda.org/conda-forge/r-tiledb/labels)

​​Update steps

​​

• Create PR to update tiledbsoma-feedstock​ tiledbsoma 1.4.0 TileDB-Inc/tiledbsoma-feedstock#39
  • ​​Update version​/version_r​ fields in recipe/meta.yaml​ to 1.4.0
    ​​

Validation

• ​​tiledbsoma​ 1.4.0 available on conda-forge anaconda channel
  • ​​https://anaconda.org/tiledb/libtiledbsoma/labels
  • ​​https://anaconda.org/tiledb/tiledbsoma-py/labels
  • ​​https://anaconda.org/tiledb/r-tiledbsoma/labels
    ​​

TileDB Cloud Updates

Internal

CRAN submission, which will be 1.4.1

• ​​Add/update CRAN comments -- tracked in [r] Prepare for CRAN [long-term tracker] #1582
• ​​Submit to R-hub builder and verify no errors (prep for release to CRAN, not a GA blocker) -- tracked in [r] Prepare for CRAN [long-term tracker] #1582

[johnkerl]

CRAN items (1.4.1) split out on #1582