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Refactor DEModel, remove SbmlImporter dependency #2312

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merged 7 commits into from
Feb 27, 2024

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@dweindl dweindl commented Feb 23, 2024

SbmlImporter should construct a DEModel, instead of DEModel importing an SbmlImporter.

Will allow moving DEModel to a separate module. Closes #2308.

No changes in functionality.

Related to AMICI-dev#2306.
`SbmlImporter` should construct a `DEModel`, instead of `DEModel` importing an `SbmlImporter`.

Closes AMICI-dev#2308.
@dweindl dweindl self-assigned this Feb 23, 2024
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codecov bot commented Feb 23, 2024

Codecov Report

Attention: Patch coverage is 84.21053% with 12 lines in your changes are missing coverage. Please review.

Project coverage is 77.76%. Comparing base (5e386ee) to head (e151b4b).

Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2312      +/-   ##
===========================================
- Coverage    77.76%   77.76%   -0.01%     
===========================================
  Files          321      321              
  Lines        20538    20601      +63     
  Branches      1436     1436              
===========================================
+ Hits         15972    16020      +48     
- Misses        4563     4578      +15     
  Partials         3        3              
Flag Coverage Δ
cpp 73.53% <76.31%> (-0.03%) ⬇️
cpp_python 34.12% <71.05%> (+0.09%) ⬆️
petab 36.56% <76.31%> (+0.15%) ⬆️
python 72.34% <82.89%> (+0.01%) ⬆️
sbmlsuite ∅ <ø> (∅)

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

Files Coverage Δ
python/sdist/amici/de_export.py 93.71% <100.00%> (+0.01%) ⬆️
python/sdist/amici/de_model.py 93.33% <100.00%> (+0.04%) ⬆️
python/sdist/amici/splines.py 79.49% <ø> (ø)
python/sdist/amici/sbml_import.py 78.58% <80.64%> (+0.10%) ⬆️

... and 3 files with indirect coverage changes

@dweindl dweindl marked this pull request as ready for review February 26, 2024 17:10
@dweindl dweindl requested a review from a team as a code owner February 26, 2024 17:10
@dweindl dweindl merged commit 6a1cc3c into AMICI-dev:develop Feb 27, 2024
24 of 26 checks passed
@dweindl dweindl deleted the fix_2308_demodel_nosbml branch February 27, 2024 11:37
@dweindl dweindl restored the fix_2308_demodel_nosbml branch February 27, 2024 11:37
@dweindl dweindl deleted the fix_2308_demodel_nosbml branch February 27, 2024 11:37
@dweindl dweindl linked an issue Feb 27, 2024 that may be closed by this pull request
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Refactor DEModel, remove SbmlImporter dependency
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