Notebooks fail

Question

Notebooks fail

Closed this issue 4 years ago · 4 comments

yannikschaelte commented 4 years ago

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

Answer 1 · 2021-02-05T09:34:04.000Z

which ones fail?

Answer 2 · 2021-02-05T10:14:33.000Z

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%]

Answer 3 · 2021-02-05T15:18:09.000Z

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

Answer 4 · 2021-02-05T15:22:58.000Z

@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.