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PEtab-dev / libpetab-python

Python package for working with PEtab files
https://libpetab-python.readthedocs.io
MIT License
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Add abstraction for (SBML) models #133

Closed dweindl closed 2 years ago

dweindl commented 2 years ago

Add abstraction for models. This helps to keep libsbml code closely together and to potentially accommodate non-SBML models in the future(https://github.com/PEtab-dev/PEtab/pull/538).

Wraps libsbml.Model using petab.models.Model and replaces the respective function arguments. In the (what I consider) most relevant function for downstream use, the sbml_model argument is kept, but deprecated.

codecov-commenter commented 2 years ago

Codecov Report

Merging #133 (d540c47) into develop (7a0b77e) will increase coverage by 0.11%. The diff coverage is 74.04%.

@@             Coverage Diff             @@
##           develop     #133      +/-   ##
===========================================
+ Coverage    77.14%   77.25%   +0.11%     
===========================================
  Files           26       29       +3     
  Lines         2437     2572     +135     
  Branches       579      593      +14     
===========================================
+ Hits          1880     1987     +107     
- Misses         404      428      +24     
- Partials       153      157       +4
Impacted Files Coverage Δ
petab/lint.py 67.55% <51.85%> (-0.30%) :arrow_down:
petab/problem.py 67.19% <64.91%> (-0.58%) :arrow_down:
petab/parameters.py 88.19% <71.42%> (+0.30%) :arrow_up:
petab/models/model.py 72.00% <72.00%> (ø)
petab/parameter_mapping.py 70.15% <78.26%> (-0.18%) :arrow_down:
petab/models/sbml_model.py 91.37% <91.37%> (ø)
petab/models/__init__.py 100.00% <100.00%> (ø)
petab/observables.py 100.00% <100.00%> (ø)

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