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At ODESystem/CellModel construction time, use list_states and list_params as defaults in constructor #56

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anandijain opened this issue Jul 4, 2021 · 1 comment · Fixed by #100
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At ODESystem/CellModel construction time, use list_states and list_params as defaults in constructor #56

anandijain opened this issue Jul 4, 2021 · 1 comment · Fixed by #100

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@anandijain
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https://mtk.sciml.ai/stable/tutorials/ode_modeling/#Defaults

We should automatically set the defaults. This is in line with how SBMLToolkit is doing it, and it makes usage much nicer.
@anandijain
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anandijain commented Jul 4, 2021 •
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I have to do this big workaround. Since more often than not, users will be working with Systems, not Problems.

I don't know exactly how to do it, but the defaults kwarg just needs to be passed in to the ODESystem constructor in process_component

sys1 = getsys(CellModel(fn))
u0 = Dict(convert(Vector{Pair}, list_states(ml)))
ps = Dict(convert(Vector{Pair}, list_params(ml)))
defaults = merge(u0, ps)
sys1 = ODESystem(equations(sys1), independent_variable(sys1), states(sys1), parameters(sys1); defaults=defaults)

bauglir added a commit to bauglir/CellMLToolkit.jl that referenced this issue Dec 16, 2022
@bauglir
Set known defaults for a CellModels ODESystem
8e79294 
CellML files contain `initial_value` fields specifying initial values
for parameters and states in the system. Retrieving these for the
`ODESystem` was already possible, but had to be done separately or as
part of the `ODEProblem` constructor defined for `CellModel`s.

Defaults are only set for simplified `ODESystem`s. Unsimplified
`ODESystem`s may contain parameters and states for which no defaults are
available resulting in errors trying to construct the `ODESystem`. These
errors will still occur when using the result of calling
`process_components` with `simplify = false`, but as noted in the code
that should only be done for debugging purposes and this functionality
is not exposed at the higher API levels.

Fixes SciML#56.
@bauglir bauglir mentioned this issue Dec 16, 2022
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Set known defaults for a CellModels ODESystem bauglir/CellMLToolkit.jl
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@anandijain