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Fix initial state issues with PEtab #2382

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merged 3 commits into from
Mar 18, 2024

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@dweindl dweindl commented Mar 13, 2024

  • Ensure initial state parameters are always fixed parameters
  • Ensure initial concentration for preequilibration and simulation are both set in both phases to avoid NaN issues
  • Fix initialAssignment handling during PEtab import (missed in SBML import: Evaluate initial assignments #2359)

* Ensure initial state parameters are always fixed parameters
* Ensure initial concentration for preequilibration and simulation are both set in both phases to avoid NaN issues
* Fix initialAssignment handling during PEtab import (missed in AMICI-dev#2359)
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codecov bot commented Mar 13, 2024

Codecov Report

Attention: Patch coverage is 0% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 76.26%. Comparing base (41b4ce4) to head (1bcbf32).

Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2382      +/-   ##
===========================================
- Coverage    77.68%   76.26%   -1.43%     
===========================================
  Files          324      319       -5     
  Lines        20869    20711     -158     
  Branches      1458     1458              
===========================================
- Hits         16213    15796     -417     
- Misses        4653     4911     +258     
- Partials         3        4       +1     
Flag Coverage Δ
cpp 73.45% <0.00%> (-0.02%) ⬇️
cpp_python 34.21% <0.00%> (-0.01%) ⬇️
petab ?
python 72.22% <0.00%> (-0.02%) ⬇️
sbmlsuite ?

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

Files Coverage Δ
python/sdist/amici/petab/sbml_import.py 28.16% <0.00%> (-26.77%) ⬇️
python/sdist/amici/petab/parameter_mapping.py 52.63% <0.00%> (-28.12%) ⬇️

... and 16 files with indirect coverage changes

@dweindl dweindl marked this pull request as ready for review March 18, 2024 10:59
@dweindl dweindl requested a review from a team as a code owner March 18, 2024 10:59
@dweindl dweindl merged commit 790ab44 into AMICI-dev:develop Mar 18, 2024
17 of 20 checks passed
@dweindl dweindl deleted the fix_petab_initials branch March 18, 2024 11:23
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2 participants