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yaml2sbml-dev / yaml2sbml

Tool to convert an ODE model specified in the YAML format to SBML.
https://yaml2sbml.readthedocs.io/en/latest/
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Notebooks fail #90

Closed yannikschaelte closed 3 years ago

yannikschaelte commented 3 years ago

Some (3-4) of the notebooks fail when run with pytest --nbmake doc/examples.

jvanhoefer commented 3 years ago

which ones fail?

yannikschaelte commented 3 years ago

The 3 "F"s:

doc/examples/Finite_State_Projection/Finite_State_Projection.ipynb .                           [ 16%]
doc/examples/Format_Features/Format_Features.ipynb F                                              [ 33%]
doc/examples/Lotka_Volterra/Lotka_Volterra_CLI/Lotka_Volterra_CLI.ipy.                      [ 50%]
doc/examples/Lotka_Volterra/Lotka_Volterra_Model_Editor/Lotka_Volterra_Model_Editor.ipynb F    [ 66%]
doc/examples/Lotka_Volterra/Lotka_Volterra_python/Lotka_Volterra.ipynb .                       [ 83%]
doc/examples/Sorensen/yaml2sbml_Sorensen.ipynb F                                               [100%]
jvanhoefer commented 3 years ago

@dilpath : You just fixed two, the Format_Features.ipynb is still open, right?

dilpath commented 3 years ago

@dilpath : You just fixed two, the Format_Features.ipynb is still open, right?

Correct, there is a partial fix in an AMICI PR but that currently leads to additional errors, and may take time to resolve. It is related to the use of a piecewise function in the notebook.