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Simplify / document antimony import #2142

Merged
merged 4 commits into from
Jul 10, 2023
Merged

Simplify / document antimony import #2142

merged 4 commits into from
Jul 10, 2023

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dweindl
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@dweindl dweindl commented Jul 8, 2023

  • Wrapper for importing antimony models, this will allow for more concise test cases in the future
  • Remove tellurium dependency, use libantimony directly (so we don't need ncurses and other deps)
  • Add antimony example

* Wrapper for importing antimony models, this will allow for more concise test cases in the future
* Remove tellurium dependency, use libantimony directly (so we don't need ncurses and other deps)
* Add antimony example
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codecov bot commented Jul 8, 2023

Codecov Report

Merging #2142 (17d7481) into develop (3d7bbc4) will increase coverage by 0.06%.
The diff coverage is 94.11%.

Additional details and impacted files

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #2142      +/-   ##
===========================================
+ Coverage    76.61%   76.67%   +0.06%     
===========================================
  Files           81       82       +1     
  Lines        14926    14943      +17     
===========================================
+ Hits         11435    11458      +23     
+ Misses        3491     3485       -6     
Flag Coverage Δ
cpp 73.57% <ø> (+0.07%) ⬆️
petab 54.26% <0.00%> (-0.17%) ⬇️
python 77.29% <94.11%> (+0.05%) ⬆️
sbmlsuite ?

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

Impacted Files Coverage Δ
python/sdist/amici/antimony_import.py 94.11% <94.11%> (ø)

... and 4 files with indirect coverage changes

@dweindl dweindl marked this pull request as ready for review July 8, 2023 13:55
@dweindl dweindl requested a review from a team as a code owner July 8, 2023 13:55
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nice! does it make sense to also enable petab import for antimony?

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dweindl commented Jul 10, 2023

does it make sense to also enable petab import for antimony?

At least for now, I would not do that. Antimony<->SBML interconversion is rather lossless and fast, so I don't think there is much of an advantage to support antimony directly with PEtab. I would still default to SBML in PEtab unless there is compelling reason to use something else. If there is a request backed by sufficiently many users, we could add it at some point, though.

@dweindl dweindl merged commit 7e0832a into develop Jul 10, 2023
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@dweindl dweindl deleted the antimony branch July 10, 2023 10:21
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2 participants