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Bump petab_sciml pin and fix nn.Layer import - #3502

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BSnelling merged 4 commits into
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bes/sciml_import
Nov 2, 2026
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BSnelling merged 4 commits into
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bes/sciml_import

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What does this pull request do, and why?

Bump petab_sciml pin and fix nn.Layer import, to make use of the latest petab_sciml version.

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Use of AI tools

Claude Code diagnosed and wrote the changelog entry.

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  • I have run the relevant tests locally
  • I have added a changelog entry in changelog.d/ (or it is not needed)

@BSnelling
BSnelling requested a review from a team as a code owner October 30, 2026 15:42
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codecov Bot commented Oct 30, 2026 •

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 80.26%. Comparing base (b15fed8) to head (ad5c4a5).

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #3502      +/-   ##
==========================================
+ Coverage   80.23%   80.26%   +0.02%     
==========================================
  Files         331      331              
  Lines       23420    23420              
  Branches     1631     1631              
==========================================
+ Hits        18792    18797       +5     
+ Misses       4622     4617       -5     
  Partials        6        6              
Flag Coverage Δ
cpp 74.85% <ø> (+0.02%) ⬆️
cpp_python 34.65% <ø> (ø)
petab 46.64% <ø> (ø)
petab_sciml 16.61% <ø> (ø)
petab_sciml_benchmarks 15.20% <ø> (ø)
python 72.58% <ø> (+0.01%) ⬆️
sbmlsuite-jax 38.29% <ø> (ø)

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

Files with missing lines Coverage Δ
python/sdist/amici/exporters/jax/nn.py 93.92% <ø> (ø)

... and 3 files with indirect coverage changes

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

petab_sciml 9d076fe dropped `from __future__ import annotations` from
nn_model.py, so importing petab.v2 failed with NameError wherever torch
was not installed. Pin to 76a2006 (PEtab-dev/petab_sciml#97), which
restores it, and bring the docs requirements in line.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
@BSnelling
BSnelling added this pull request to the merge queue Nov 2, 2026
Merged via the queue into main with commit adfd4b2 Nov 2, 2026
45 checks passed
@BSnelling
BSnelling deleted the bes/sciml_import branch November 2, 2026 15:32
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2 participants