8000 Support for PEtab SciML in jax by FFroehlich · Pull Request #2614 · AMICI-dev/AMICI · GitHub
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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 FFroehlich commented Dec 2, 2024 •
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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 •
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Codecov Report

Attention: Patch coverage is 3.19149% with 182 lines in your changes missing coverage. Please review.

Project coverage is 34.75%. Comparing base (71da562) to head (0348ee4).

Files with missing lines Patch % Lines
python/sdist/amici/jax/nn.py 0.00% 73 Missing ⚠️
python/sdist/amici/jax/petab.py 0.00% 65 Missing ⚠️
python/sdist/amici/de_model.py 7.89% 35 Missing ⚠️
python/sdist/amici/jax/ode_export.py 0.00% 5 Missing ⚠️
python/sdist/amici/jax/jaxcodeprinter.py 0.00% 2 Missing ⚠️
python/sdist/amici/jax/model.py 0.00% 1 Missing ⚠️
python/sdist/amici/sbml_import.py 50.00% 1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (71da562) and HEAD (0348ee4). Click for more details.

HEAD has 19 uploads less than BASE
Flag BASE (71da562) HEAD (0348ee4)
petab 2 0
python 14 4
cpp_python 3 2
cpp 3 0
sbmlsuite-jax 3 0
Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff              @@
##           develop    #2614       +/-   ##
============================================
- Coverage    80.32%   34.75%   -45.57%     
============================================
  Files          328      324        -4     
  Lines        22344    22332       -12     
  Branches      1512     1511        -1     
============================================
- Hits         17948     7762    -10186     
- Misses        4385    14546    +10161     
- Partials        11       24       +13
Flag Coverage Δ
cpp ?
cpp_python 33.56% <3.19%> (-0.30%) ⬇️
petab ?
python 32.02% <3.19%> (-42.46%) ⬇️
sbmlsuite-jax ?

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 94.55% <100.00%> (-2.86%) ⬇️
python/sdist/amici/jax/__init__.py 0.00% <ø> (-100.00%) ⬇️
python/sdist/amici/petab/parameter_mapping.py 64.03% <100.00%> (-20.69%) ⬇️
python/sdist/amici/petab/petab_import.py 100.00% <ø> (ø)
python/sdist/amici/petab/sbml_import.py 61.60% <ø> (-12.81%) ⬇️
python/sdist/amici/petab/util.py 46.66% <ø> (-40.00%) ⬇️
python/sdist/amici/jax/model.py 0.00% <0.00%> (-86.93%) ⬇️
python/sdist/amici/sbml_import.py 71.60% <50.00%> (-22.60%) ⬇️
python/sdist/amici/jax/jaxcodeprinter.py 0.00% <0.00%> (-88.89%) ⬇️
python/sdist/amici/jax/ode_export.py 0.00% <0.00%> (-97.92%) ⬇️
... and 3 more

... and 252 files with indirect coverage changes

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Quality Gate Passed Quality Gate passed

Issues
7 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@sonarqubecloud SonarQubeCloud
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Quality Gate Passed Quality Gate passed

Issues
7 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@sonarqubecloud SonarQubeCloud
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Quality Gate Passed Quality Gate passed

Issues
7 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@sonarqubecloud SonarQubeCloud
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Quality Gate Passed Quality Gate passed

Issues
7 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

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