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CI: Ignore petab1to2 warning about a renamed experimentId column - #3494

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dweindl merged 1 commit into
AMICI-dev:mainfrom
dweindl:ci-ignore-experimentid-warning
Oct 26, 2026
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dweindl merged 1 commit into
AMICI-dev:mainfrom
dweindl:ci-ignore-experimentid-warning

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@dweindl dweindl commented Oct 26, 2026

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Since PEtab-dev/libpetab-python#572, petab1to2 warns when it renames a v1 measurement table column experimentId, which is reserved in PEtab v2. With warnings as errors, the v1→v2 auto-upgrade fails, and so do the JAX benchmark tests for Brannmark_JBC2010 and Isensee_JCB2018 (e.g., https://github.com/AMICI-dev/AMICI/actions/runs/40377463587/job/121764332167). The renamed column is not used for simulation, so the warning is ignored.

🤖 Generated with Claude Code

Since PEtab-dev/libpetab-python#572, `petab1to2` warns when it renames
a v1 measurement table column `experimentId`, which is reserved in PEtab
v2. With warnings as errors, this made the v1->v2 auto-upgrade, and
thus the JAX benchmark tests for Brannmark_JBC2010 and Isensee_JCB2018,
fail. The renamed column is not used for simulation.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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dweindl marked this pull request as ready for review October 26, 2026 19:09
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dweindl requested a review from a team as a code owner October 26, 2026 19:09
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dweindl enabled auto-merge October 26, 2026 19:09
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codecov Bot commented Oct 26, 2026 •

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.97%. Comparing base (2ace80e) to head (c521b1e).
⚠️ Report is 1 commits behind head on main.

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@@            Coverage Diff             @@
##             main    #3494      +/-   ##
==========================================
+ Coverage   79.93%   79.97%   +0.03%     
==========================================
  Files         331      331              
  Lines       23284    23284              
  Branches     1614     1614              
==========================================
+ Hits        18613    18621       +8     
+ Misses       4665     4657       -8     
  Partials        6        6              
Flag Coverage Δ
cpp 74.38% <ø> (+0.03%) ⬆️
cpp_python 34.70% <ø> (ø)
petab 47.80% <ø> (ø)
petab_sciml 16.71% <ø> (ø)
petab_sciml_benchmarks 15.29% <ø> (ø)
python 72.28% <ø> (+0.03%) ⬆️

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see 1 file with indirect coverage changes

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dweindl disabled auto-merge October 26, 2026 19:56
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dweindl merged commit f91e510 into AMICI-dev:main Oct 26, 2026
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dweindl deleted the ci-ignore-experimentid-warning branch October 26, 2026 19:57
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