Skip to content

[python][r] Update deprecation lifecycle#4431

Merged
jp-dark merged 31 commits intomainfrom
dark/deprecations
Apr 17, 2026
Merged

[python][r] Update deprecation lifecycle#4431
jp-dark merged 31 commits intomainfrom
dark/deprecations

Conversation

@jp-dark
Copy link
Copy Markdown
Collaborator

@jp-dark jp-dark commented Mar 13, 2026 •
edited
Loading

Issue and/or context: Closes SOMA-815

Changes:
R:

  • Change tiledbsoma_ctx parameter to be defunct.
  • Remove defunct warning for deleting in write mode and just throw the standard error.
  • Update argument types for domain/shape and throw an error if NULL.
  • Remove defunct method set_data_type.

Pythons:

  • Update argument types for domain/shape and throw an error if None.
  • Update somacore version to match a version with updated API.

@jp-dark jp-dark marked this pull request as draft March 16, 2026 13:59
@codecov
Copy link
Copy Markdown

codecov Bot commented Mar 16, 2026 •
edited
Loading

Codecov Report

❌ Patch coverage is 75.00000% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.21%. Comparing base (992b147) to head (e946052).
⚠️ Report is 2 commits behind head on main.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main    #4431      +/-   ##
==========================================
- Coverage   85.42%   85.21%   -0.21%     
==========================================
  Files         136      136              
  Lines       21442    21353      -89     
==========================================
- Hits        18317    18197     -120     
- Misses       3125     3156      +31
Flag Coverage Δ
python 88.27% <50.00%> (-0.10%) ⬇️
r 83.51% <84.37%> (-0.28%) ⬇️

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

Components Coverage Δ
python_api 88.27% <50.00%> (-0.10%) ⬇️
libtiledbsoma ∅ <ø> (∅)
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@jp-dark jp-dark marked this pull request as ready for review March 16, 2026 20:03
mojaveazure
mojaveazure requested changes Mar 17, 2026
View reviewed changes
Comment thread apis/r/R/SOMADataFrame.R
Comment thread apis/r/R/SOMADataFrame.R Outdated
Comment thread apis/r/R/SOMANDArrayBase.R
Comment thread apis/r/R/SOMAObject.R
Comment thread apis/r/R/utils.R
Comment thread apis/r/R/write_seurat.R Outdated
Comment thread apis/r/tests/testthat/test-03-SOMAContext.R
@jp-dark jp-dark force-pushed the dark/deprecations branch from c4f714e to 15d3947 Compare April 16, 2026 13:17
@jp-dark jp-dark force-pushed the dark/deprecations branch from 15d3947 to 6c05b4e Compare April 16, 2026 15:45
@jp-dark jp-dark requested a review from mojaveazure April 16, 2026 18:00
mojaveazure
mojaveazure reviewed Apr 16, 2026
View reviewed changes
Comment thread apis/r/R/write_seurat.R Outdated
Comment thread apis/r/R/write_seurat.R Outdated
Comment thread apis/r/R/write_seurat.R Outdated
Comment thread apis/r/R/write_seurat.R Outdated
Comment thread apis/r/R/write_bioc.R Outdated
Comment thread apis/r/R/write_bioc.R Outdated
Comment thread apis/r/R/write_bioc.R Outdated
Comment thread apis/r/R/write_bioc.R Outdated
Comment thread apis/r/R/SOMATileDBContext.R
@jp-dark jp-dark requested a review from mojaveazure April 16, 2026 20:26
mojaveazure
mojaveazure approved these changes Apr 16, 2026
View reviewed changes
Copy link
Copy Markdown
Member

@mojaveazure mojaveazure left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM on the R side, thanks! Please bump the develop version before landing

XanthosXanthopoulos
XanthosXanthopoulos approved these changes Apr 17, 2026
View reviewed changes
Comment thread apis/python/tests/test_tiledbobject.py
@jp-dark jp-dark merged commit 126c237 into main Apr 17, 2026
23 checks passed
@jp-dark jp-dark deleted the dark/deprecations branch April 17, 2026 14:41
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@mojaveazure mojaveazure mojaveazure approved these changes

@XanthosXanthopoulos XanthosXanthopoulos XanthosXanthopoulos approved these changes

@aaronwolen aaronwolen Awaiting requested review from aaronwolen

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@jp-dark @mojaveazure @XanthosXanthopoulos