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ICB-DCM / pyPESTO

python Parameter EStimation TOolbox
https://pypesto.readthedocs.io
BSD 3-Clause "New" or "Revised" License
207 stars 45 forks source link

Roadrunner as simulator #1336

Closed PaulJonasJost closed 3 months ago

PaulJonasJost commented 3 months ago

Added functionality for RoadRunner simulations. Currently still dependent on PEtab (which might be removed at a later stage). Unifying PEtabImporter for amici, roadrunner and general scenarios will be put into another PR to have this one standalone.

Tests for roadrunner are petab_testsuite except for 3 tests that expectedly fail. One is just not supported in pyPESTO (Timepoint-specific parameter overrides), one is still not supported in functionality (more complex noise formulas) and one is not clear whether this is an intended test (proclaiming a species as parameter in .xml).

codecov-commenter commented 3 months ago

Codecov Report

Attention: Patch coverage is 82.51748% with 75 lines in your changes are missing coverage. Please review.

Project coverage is 84.21%. Comparing base (f418577) to head (af4938c).

Files Patch % Lines
.../objective/roadrunner/petab_importer_roadrunner.py 72.22% 35 Missing :warning:
...esto/objective/roadrunner/roadrunner_calculator.py 85.71% 17 Missing :warning:
pypesto/objective/roadrunner/utils.py 88.28% 15 Missing :warning:
pypesto/objective/roadrunner/road_runner.py 83.67% 8 Missing :warning:

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #1336 +/- ## =========================================== - Coverage 84.27% 84.21% -0.07% =========================================== Files 152 157 +5 Lines 12441 12870 +429 =========================================== + Hits 10485 10838 +353 - Misses 1956 2032 +76 ```

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PaulJonasJost commented 3 months ago

Please add the new files/dir to .github/CODEOWNERS.

Not really needed imo as I am sole code owner of objective? 🤔

dweindl commented 3 months ago 
  /home/runner/work/pyPESTO/pyPESTO/pypesto/objective/roadrunner/utils.py:304: SettingWithCopyWarning: 
  A value is trying to be set on a copy of a slice from a DataFrame.
  Try using .loc[row_indexer,col_indexer] = value instead
PaulJonasJost commented 3 months ago 
  /home/runner/work/pyPESTO/pyPESTO/pypesto/objective/roadrunner/utils.py:304: SettingWithCopyWarning: 
  A value is trying to be set on a copy of a slice from a DataFrame.
  Try using .loc[row_indexer,col_indexer] = value instead

from what in understand on pandas website this will go away anyways at pandas 3.0

dweindl commented 3 months ago

this will go away anyways at pandas 3.0

Well, the warning will go away, yes. It will be an error by then.