Jax export

[FFroehlich]

No description provided.

[codecov]

Codecov Report

Attention: Patch coverage is 60.66351% with 83 lines in your changes missing coverage. Please review.

Project coverage is 77.65%. Comparing base (022de60) to head (c242b15).
Report is 1 commits behind head on develop.

Files with missing lines	Patch %	Lines
python/sdist/amici/jax/petab.py	28.57%	50 Missing ⚠️
python/sdist/amici/jax/model.py	74.41%	22 Missing ⚠️
python/sdist/amici/petab/parameter_mapping.py	46.66%	8 Missing ⚠️
python/sdist/amici/de_export.py	92.00%	2 Missing ⚠️
python/sdist/amici/jaxcodeprinter.py	92.30%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1861      +/-   ##
===========================================
- Coverage    77.83%   77.65%   -0.19%     
===========================================
  Files          325      329       +4     
  Lines        21853    22054     +201     
  Branches      1456     1456              
===========================================
+ Hits         17009    17125     +116     
- Misses        4833     4918      +85     
  Partials        11       11              

Flag	Coverage Δ
cpp	73.58% <56.39%> (-0.16%)	⬇️
cpp_python	34.31% <48.81%> (+0.10%)	⬆️
petab	37.25% <47.86%> (+0.09%)	⬆️
python	72.40% <60.66%> (-0.14%)	⬇️

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

Files with missing lines	Coverage Δ
python/sdist/amici/__init__.py	94.44% <ø> (ø)
python/sdist/amici/jax/__init__.py	100.00% <100.00%> (ø)
python/sdist/amici/petab/petab_import.py	66.66% <ø> (ø)
python/sdist/amici/pysb_import.py	94.30% <100.00%> (ø)
python/sdist/amici/jaxcodeprinter.py	92.30% <92.30%> (ø)
python/sdist/amici/de_export.py	95.77% <92.00%> (-0.37%)	⬇️
python/sdist/amici/petab/parameter_mapping.py	78.00% <46.66%> (-3.16%)	⬇️
python/sdist/amici/jax/model.py	74.41% <74.41%> (ø)
python/sdist/amici/jax/petab.py	28.57% <28.57%> (ø)

... and 4 files with indirect coverage changes

---- 🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[sonarqubecloud]

SonarCloud Quality Gate failed.   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
9 Code Smells

59.8% Coverage
0.0% Duplication

[socket-security]

New and removed dependencies detected. Learn more about Socket for GitHub ↗︎

Package	New capabilities	Transitives	Size	Publisher
pypi/beartype@0.19.0	environment, eval, filesystem, shell, unsafe Transitive: network	+23	278 MB	leycec
pypi/diffrax@0.6.0	eval Transitive: environment, filesystem, network, shell, unsafe	+6	1.98 MB	patrick-kidger
pypi/equinox@0.11.8	environment, eval, filesystem Transitive: shell, unsafe	+2	1.17 MB	patrick-kidger
pypi/interpax@0.3.3	environment, eval, filesystem, shell	0	258 kB	f0uriest
pypi/jax@0.4.35	environment, eval, filesystem, network, shell, unsafe	0	8 MB	Jake.Vanderplas, gnecula, google_opensource, ...6 more
pypi/jaxlib@0.4.35	environment, eval, network, shell, unsafe	0	364 MB	Jake.Vanderplas, gnecula, google_opensource, ...6 more
pypi/jaxtyping@0.2.36	None	0	0 B
pypi/optimistix@0.0.9	eval Transitive: environment, filesystem, shell, unsafe	+2	827 kB	patrick-kidger

View full report↗︎

[FFroehlich]

Would be great to get some initial feedback. Quite some room for later optimization, but seems functional now. If API and overall code looks good I would also add a short tutorial notebook to the documentation.

[dweindl]

Thanks, looks good to me. I am not familiar with the jax ecosystem, though.

Having a tutorial/example soon would be great, yes.

[dweindl]

The new dependencies bring in a couple of valgrind issues that need to be added to the suppression list: https://github.com/AMICI-dev/AMICI/actions/runs/11888412281/job/33122901845

[sonarqubecloud]

Quality Gate passed

Issues
2 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