This is a sibling of #1632. Its sole job is to link-track, at the GitHub Issues level, smaller issues which will be split out as individual GitHub Issues.

Some sequencings:

• [r] Push schema accessor down to libtiledbsoma #3079 is the last spot R/TileDBArray.R needs the .tiledb_array / self$object TileDB-R array handle
• That in turn (as narrated on that PR) is blocked by [r] Use libtiledbsoma for schema evolution #3057
• Once 3057 and 3079 are merged then we can do [r] Use libtiledbsoma handles for arrays #3059
• Then [r] Use libtiledbsoma for the mode accessor #3060
• [r] Port QueryCondition from tiledb-r to tiledbsoma-r [WIP] #3083 appears somewhat orthogonal to that list just now
• Likewise [r] Use libtiledbsoma for schema/filter specification #3056

Status quo and to-do items as of 2025-02-03:

• Many tiledbsoma-r unit-test cases call into tiledb-r and should not.
  • Some assertions can be removed as no longer needed (they were needed during initial bring-up but are now redundant).
  • Some assertions will need to be ported to use tiledbsoma-r.
  • [r] Remove TileDB-R accesses within tests/testthat #3124
• The persistent underlying array handle opened at soma open and closed at soma close is a tiledb-r handle. These need to go away.
• All the calls into libtiledbsoma pass in URI and context, doing open-use-close.
  • These libtiledbsoma handles need to be opened persistently as soma array open and closed at soma array close.
  • All the calls into libtiledbsoma need to then be modified to take in an open handle.
  • [r] Use libtiledbsoma for array handles #3061
• This will require passing around SOMATileDBContext without breaking unit-test cases.
  • On discussion with @mojaveazure we need to:
    • Retain the existing under-the-hood SOMATileDBContext
    • For the user-facing API, replace the complex user-facing context object with a simple named list.
  • [r] Remove all references to tiledb-r context #3052