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account for plist in edata when slicing amici results #621

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merged 9 commits into from
Apr 13, 2021

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FFroehlich
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codecov-io commented Apr 9, 2021

Codecov Report

Merging #621 (c2a66e9) into develop (160c2a8) will decrease coverage by 0.66%.
The diff coverage is 86.75%.

❗ Current head c2a66e9 differs from pull request most recent head dff1d13. Consider uploading reports for the commit dff1d13 to get more accurate results
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@@             Coverage Diff             @@
##           develop     #621      +/-   ##
===========================================
- Coverage    88.16%   87.50%   -0.67%     
===========================================
  Files           79       93      +14     
  Lines         5257     5890     +633     
===========================================
+ Hits          4635     5154     +519     
- Misses         622      736     +114     
Impacted Files Coverage Δ
pypesto/ensemble/covariance_analysis.py 18.36% <0.00%> (-0.39%) ⬇️
pypesto/objective/amici_calculator.py 90.00% <ø> (-1.67%) ⬇️
pypesto/objective/amici.py 85.02% <20.00%> (-4.81%) ⬇️
pypesto/predict/task.py 43.75% <43.75%> (ø)
pypesto/petab/__init__.py 63.63% <50.00%> (ø)
pypesto/engine/mpi_pool.py 66.66% <66.66%> (ø)
pypesto/objective/amici_util.py 75.43% <66.66%> (-0.46%) ⬇️
pypesto/ensemble/constants.py 91.30% <71.42%> (-8.70%) ⬇️
pypesto/visualize/misc.py 82.41% <72.22%> (-2.52%) ⬇️
pypesto/predict/result.py 33.33% <75.00%> (ø)
... and 58 more

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looks good. maybe just wait for next amici release?

pypesto/objective/amici_util.py Outdated Show resolved Hide resolved
test/petab/test_petab_import.py Outdated Show resolved Hide resolved
"""Test that the AMICI objective created via PEtab correctly maps
gradients entries when some parameters are not estimated (realized via
edata.plist)."""
model_name = "Boehm_JProteomeRes2014"
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boehm has 2 fixed parameters at -1, -5, therefore this should be a good example 👍

Fabian Fröhlich and others added 2 commits April 11, 2021 11:28
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
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4 participants