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Fixes #3303

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codecov bot commented Nov 3, 2025

Codecov Report

❌ Patch coverage is 82.35294% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 89.80%. Comparing base (1acc108) to head (5e809c0).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
c/tskit/tables.c 82.35% 2 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #3309      +/-   ##
==========================================
- Coverage   89.80%   89.80%   -0.01%     
==========================================
  Files          29       29              
  Lines       31026    31043      +17     
  Branches     5679     5682       +3     
==========================================
+ Hits        27863    27877      +14     
- Misses       1777     1779       +2     
- Partials     1386     1387       +1     
Flag Coverage Δ
c-tests 86.85% <82.35%> (-0.01%) ⬇️
lwt-tests 80.38% <ø> (ø)
python-c-tests 87.05% <ø> (ø)
python-tests 98.84% <ø> (ø)
python-tests-no-jit 33.60% <ø> (ø)
python-tests-numpy1 50.18% <ø> (ø)

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Files with missing lines Coverage Δ
c/tskit/tables.c 83.08% <82.35%> (-0.01%) ⬇️
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@benjeffery benjeffery force-pushed the wipe-mutations-before-calculate branch from 91a851b to ccc7d08 Compare November 3, 2025 10:34
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@jeromekelleher jeromekelleher left a comment

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I like it. Just needs a few more tests.

tables.mutations.parent[:] = 42
tables.compute_mutation_parents()
assert tables.mutations.parent[0] == tskit.NULL

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Another test checking the parent data is preserved on error

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if possible we should check the data is preserved on error even if TSK_NO_CHECK_INTEGRITY is on

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@benjeffery benjeffery added this to the Python 1.0 milestone Nov 3, 2025
@benjeffery benjeffery force-pushed the wipe-mutations-before-calculate branch 2 times, most recently from 11aa116 to 17f8200 Compare November 4, 2025 15:09
@benjeffery benjeffery enabled auto-merge November 4, 2025 15:09
@benjeffery benjeffery force-pushed the wipe-mutations-before-calculate branch from 17f8200 to 5e809c0 Compare November 4, 2025 16:18
@benjeffery benjeffery added this pull request to the merge queue Nov 4, 2025
Merged via the queue into tskit-dev:main with commit dacbf38 Nov 4, 2025
17 of 18 checks passed
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compute_mutation_parents errors when existing mutation parents don't make sense

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