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[python] Additional deprecation removals schedules for the 3.0.0 release#4448

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jp-dark merged 7 commits into
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dark/additional-deprecations
Apr 20, 2026
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[python] Additional deprecation removals schedules for the 3.0.0 release#4448
jp-dark merged 7 commits into
mainfrom
dark/additional-deprecations

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@jp-dark

@jp-dark jp-dark commented Apr 20, 2026

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Changes:

  • Add a defunct section to R NEWS. We have a deprecate, defunct, and remove stage in our deprecation policy. Adding an explicit defunct header to the news helps make it more clear what the current state is.
  • Remove resume ingest mode (deprecated in 1.18.0).
  • Remove straggling delete-in-write-mode warning.

jp-dark and others added 4 commits April 20, 2026 09:50
Distinguishes items that raise a defunct error but are still present in
the namespace from items that have been genuinely removed, so users can
tell the two lifecycle stages apart.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
The "resume" ingest_mode has been deprecated since 1.18.0. The current
implementation has a known issue that can cause multi-dataset appends
to not resume correctly. The recommended recovery path is to delete
the partially-written SOMA Experiment and restart ingestion from the
original input files or a known-good backup.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@jp-dark jp-dark requested review from aaronwolen and removed request for aaronwolen April 20, 2026 14:41
@jp-dark jp-dark marked this pull request as draft April 20, 2026 14:56
@jp-dark jp-dark requested a review from aaronwolen April 20, 2026 14:57
Comment thread apis/python/src/tiledbsoma/io/ingest.py Outdated

@aaronwolen aaronwolen left a comment

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Thanks! I had one question about a private method still accepting the ingest_params arg but otherwise looks ready to ship.

@jp-dark jp-dark marked this pull request as ready for review April 20, 2026 16:48
jp-dark and others added 2 commits April 20, 2026 12:54
Co-Authored-By: Claude Sonnet 4.6 (1M context) <noreply@anthropic.com>
@codecov

codecov Bot commented Apr 20, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 85.26%. Comparing base (e737059) to head (04edb98).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #4448      +/-   ##
==========================================
+ Coverage   85.23%   85.26%   +0.02%     
==========================================
  Files         136      136              
  Lines       21365    21263     -102     
==========================================
- Hits        18211    18130      -81     
+ Misses       3154     3133      -21     
Flag Coverage Δ
python 88.42% <100.00%> (+0.12%) ⬆️

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

Components Coverage Δ
python_api 88.42% <100.00%> (+0.12%) ⬆️
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 merged commit 1ba587f into main Apr 20, 2026
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@jp-dark jp-dark deleted the dark/additional-deprecations branch April 20, 2026 19:39
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2 participants