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Combine observables, sigmas and noise distributions parameters for model import#2959

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dweindl merged 1 commit intoAMICI-dev:mainfrom
dweindl:gh-2923-obs-model
Oct 6, 2025
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Combine observables, sigmas and noise distributions parameters for model import#2959
dweindl merged 1 commit intoAMICI-dev:mainfrom
dweindl:gh-2923-obs-model

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@dweindl dweindl commented Oct 3, 2025

Combine observables, sigmas and noise distributions parameters for model import

Closes #2923.

@dweindl dweindl self-assigned this Oct 3, 2025
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codecov bot commented Oct 3, 2025

Codecov Report

❌ Patch coverage is 92.94118% with 6 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.62%. Comparing base (5e0acb2) to head (d4d4a80).
⚠️ Report is 122 commits behind head on main.

Files with missing lines Patch % Lines
python/sdist/amici/de_model.py 83.33% 2 Missing ⚠️
python/sdist/amici/sbml_import.py 94.11% 2 Missing ⚠️
python/sdist/amici/import_utils.py 93.75% 1 Missing ⚠️
python/sdist/amici/petab/import_helpers.py 91.66% 1 Missing ⚠️
Additional details and impacted files

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@@            Coverage Diff             @@
##             main    #2959      +/-   ##
==========================================
- Coverage   77.29%   76.62%   -0.67%     
==========================================
  Files         307      307              
  Lines       19912    19901      -11     
  Branches     1502     1501       -1     
==========================================
- Hits        15391    15250     -141     
- Misses       4508     4638     +130     
  Partials       13       13              
Flag Coverage Δ
cpp 72.78% <90.58%> (+0.01%) ⬆️
cpp_python 38.33% <76.47%> (+0.02%) ⬆️
petab 39.39% <69.41%> (+0.03%) ⬆️
python 70.34% <92.94%> (+0.01%) ⬆️
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/__init__.py 96.07% <ø> (ø)
python/sdist/amici/petab/pysb_import.py 61.76% <ø> (ø)
python/sdist/amici/petab/sbml_import.py 74.60% <100.00%> (+0.20%) ⬆️
python/sdist/amici/pysb_import.py 94.76% <100.00%> (+0.19%) ⬆️
python/sdist/amici/testing/models.py 98.36% <ø> (ø)
python/tests/conftest.py 39.28% <ø> (ø)
python/sdist/amici/import_utils.py 81.64% <93.75%> (-2.13%) ⬇️
python/sdist/amici/petab/import_helpers.py 85.71% <91.66%> (-1.25%) ⬇️
python/sdist/amici/de_model.py 92.33% <83.33%> (-0.60%) ⬇️
python/sdist/amici/sbml_import.py 81.40% <94.11%> (-10.97%) ⬇️

... and 4 files with indirect coverage changes

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@dweindl dweindl force-pushed the gh-2923-obs-model branch 2 times, most recently from 9076be5 to db1c444 Compare October 4, 2025 07:02
@dweindl dweindl marked this pull request as ready for review October 6, 2025 06:01
@dweindl dweindl requested a review from a team as a code owner October 6, 2025 06:01
@dweindl dweindl added the breaking change Issue changes API in backwards-incompatible way label Oct 6, 2025
…del import

Combine observables, sigmas and noise distributions parameters for model import.

Closes AMICI-dev#2923.
@dweindl dweindl force-pushed the gh-2923-obs-model branch from 16df5e4 to d4d4a80 Compare October 6, 2025 13:31
@dweindl dweindl merged commit 712f671 into AMICI-dev:main Oct 6, 2025
23 of 24 checks passed
@dweindl dweindl deleted the gh-2923-obs-model branch October 6, 2025 19:14
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Combine observables, sigmas and noise distributions parameters for model import

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