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More informative exceptions#3037

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dweindl merged 2 commits intoAMICI-dev:mainfrom
dweindl:dbg_info
Nov 15, 2025
Merged

More informative exceptions#3037
dweindl merged 2 commits intoAMICI-dev:mainfrom
dweindl:dbg_info

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@dweindl dweindl commented Nov 15, 2025

  • Add more context to exceptions
  • Convert NotImplementedErrors during SBML import to SBMLException as done in other places

@dweindl dweindl requested a review from a team as a code owner November 15, 2025 08:35
@dweindl dweindl self-assigned this Nov 15, 2025
@dweindl dweindl enabled auto-merge November 15, 2025 08:35
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codecov bot commented Nov 15, 2025

Codecov Report

❌ Patch coverage is 53.84615% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.37%. Comparing base (7bf3b76) to head (327a8a6).
⚠️ Report is 61 commits behind head on main.

Files with missing lines Patch % Lines
python/sdist/amici/gradient_check.py 40.00% 3 Missing ⚠️
python/sdist/amici/exporters/sundials/de_export.py 50.00% 2 Missing ⚠️
python/sdist/amici/importers/sbml/__init__.py 75.00% 1 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #3037      +/-   ##
==========================================
- Coverage   77.41%   77.37%   -0.04%     
==========================================
  Files         311      311              
  Lines       20594    20603       +9     
  Branches     1500     1499       -1     
==========================================
- Hits        15942    15941       -1     
- Misses       4642     4652      +10     
  Partials       10       10              
Flag Coverage Δ
cpp 70.30% <53.84%> (-0.04%) ⬇️
cpp_python 36.74% <53.84%> (-0.01%) ⬇️
petab 45.72% <53.84%> (-0.01%) ⬇️
petab_sciml 13.65% <0.00%> (-0.01%) ⬇️
python 69.32% <53.84%> (-0.03%) ⬇️

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

Files with missing lines Coverage Δ
python/sdist/amici/importers/pysb/__init__.py 94.54% <ø> (ø)
python/sdist/amici/importers/sbml/__init__.py 82.13% <75.00%> (-0.07%) ⬇️
python/sdist/amici/exporters/sundials/de_export.py 96.38% <50.00%> (-0.53%) ⬇️
python/sdist/amici/gradient_check.py 93.33% <40.00%> (-2.36%) ⬇️

... and 3 files with indirect coverage changes

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GitHub Action runners run out of disk space when installing petab-sciml with all its huge dependencies.
Don't install that for now. So far, it's not used anywhere for the documentation build as far as I can see.
This won't prevent enabling intersphinx later on.
* Add more context to exceptions
* Convert `NotImplementedError`s during SBML import to `SBMLException` as done in other places
* Catch simulation errors early
@dweindl dweindl added this pull request to the merge queue Nov 15, 2025
Merged via the queue into AMICI-dev:main with commit f28efae Nov 15, 2025
30 of 33 checks passed
@dweindl dweindl deleted the dbg_info branch November 15, 2025 14:09
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2 participants