Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[r] Remove TileDB-R accesses within tests/testthat #3124

Open
johnkerl opened this issue Oct 3, 2024 · 0 comments
Open

[r] Remove TileDB-R accesses within tests/testthat #3124

johnkerl opened this issue Oct 3, 2024 · 0 comments

Comments

@johnkerl
Copy link
Member

johnkerl commented Oct 3, 2024

grep tiledb:: tests/testthat | cat -n shows over 200 spots which are relying on tiledb-r for various assertions. These need to be worked off.

Inventory:

tests/testthat/test-SOMASparseNDArray.R     68
tests/testthat/test-SOMADataFrame.R         68
tests/testthat/test-SOMADenseNDArray.R      57
tests/testthat/test-Arrow-utils.R           14
tests/testthat/helper-test-soma-objects.R   6
tests/testthat/helper-test-tiledb-objects.R 5
tests/testthat/test-TileDBGroup.R           2
tests/testthat/test-SOMATileDBContext.R     2
tests/testthat/test-OrderedAndFactor.R      2
tests/testthat/test-example-datasets.R      1
tests/testthat/test-TileDBArray.R           1
tests/testthat/test-SOMAExperiment-query.R  1
tests/testthat/test-SOMACollection.R        1

Categorizing:

  • A few of these are is-array or is-group checks which can be just as easily done using tiledbsoma-r
  • The massive line-counts of occurrences of tiledb:: on test-SOMASparseNDArray.R, test-SOMADenseNDArray.R, and test-SOMADataFrame.R are due mainly to using tiledb-r to introspect on compression filters etc. that we written using tiledbsoma-r and platform_config but for which we lack a way to read back and verify in tiledbsoma-r -- or tiledbsoma-py for that matter -- please see https://github.com/single-cell-data/TileDB-SOMA/pull/3129/files#r1787917405

Context: #2406

[sc-56845]

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant