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Support for PEtab SciML in jax #2614

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Support for PEtab SciML in jax #2614

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FFroehlich
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@FFroehlich FFroehlich commented Dec 2, 2024

CI

  • turn testcase runner into proper pytest
  • add github workflow

neural nets

  • fix non-passing networks tests involving convolutional layers (004-008, 021, 022, 046 - 048, 050)

amici core

tests

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codecov bot commented Dec 3, 2024

Codecov Report

Attention: Patch coverage is 26.11111% with 133 lines in your changes missing coverage. Please review.

Project coverage is 76.12%. Comparing base (57f5ed5) to head (6089a95).

Files with missing lines Patch % Lines
python/sdist/amici/jax/nn.py 13.69% 63 Missing ⚠️
python/sdist/amici/de_model.py 7.89% 35 Missing ⚠️
python/sdist/amici/jax/petab.py 44.64% 31 Missing ⚠️
python/sdist/amici/jax/ode_export.py 66.66% 2 Missing ⚠️
python/sdist/amici/jax/jaxcodeprinter.py 50.00% 1 Missing ⚠️
python/sdist/amici/sbml_import.py 50.00% 1 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2614      +/-   ##
===========================================
- Coverage    77.03%   76.12%   -0.91%     
===========================================
  Files          332      326       -6     
  Lines        22970    21963    -1007     
  Branches      1478     1476       -2     
===========================================
- Hits         17695    16720     -975     
+ Misses        5264     5234      -30     
+ Partials        11        9       -2     
Flag Coverage Δ
cpp 73.76% <26.11%> (-0.39%) ⬇️
cpp_python 33.19% <3.33%> (-0.29%) ⬇️
petab ?
python 72.17% <26.11%> (+0.05%) ⬆️

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

Files with missing lines Coverage Δ
python/sdist/amici/de_export.py 97.04% <100.00%> (+1.69%) ⬆️
python/sdist/amici/jax/__init__.py 100.00% <ø> (ø)
python/sdist/amici/jax/model.py 82.60% <100.00%> (-4.56%) ⬇️
python/sdist/amici/petab/parameter_mapping.py 54.95% <100.00%> (-26.99%) ⬇️
python/sdist/amici/petab/petab_import.py 66.66% <ø> (-9.61%) ⬇️
python/sdist/amici/petab/sbml_import.py 45.45% <ø> (-30.57%) ⬇️
python/sdist/amici/petab/util.py 43.33% <ø> (-37.62%) ⬇️
python/sdist/amici/jax/jaxcodeprinter.py 81.81% <50.00%> (-2.80%) ⬇️
python/sdist/amici/sbml_import.py 78.38% <50.00%> (-1.09%) ⬇️
python/sdist/amici/jax/ode_export.py 94.54% <66.66%> (-2.33%) ⬇️
... and 3 more

... and 50 files with indirect coverage changes

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