Update PEtab tutorial #1119
Update PEtab tutorial #1119
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Thanks! Yeah, tests and docs are all broken in different ways (docs are I think from changes in MTK). Once that stuff gets fixed I'll rebase this so that hopefully docs can build. |
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Great, thanks! |
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@sebapersson seems there is an error in the tutorial? |
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I have updated the tutorial to address the minor bugs. The current failure seems unrelated to PEtab, but I do not know why the doc build fails. |
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xvfb just randomly fails on GitHub Actions for some reason, but we need it for GLMakie. |
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This looks like a real failure in the tutorial. |
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The docs should work now :) |
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| ## [Additional features: Initial conditions](@id petab_simulation_initial_conditions) | ||
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| ### [Fitting initial conditions](@id petab_simulation_initial_conditions_fitted) | ||
| Sometimes, initial conditions are uncertain quantities which we wish to fit to the data. This is possible by [defining an initial condition as a parameter](@ref dsl_description_parametric_initial_conditions): |
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any reason to remove this? Seems like a relevant reference?
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It failed the link check when building before (thought it had been removed), but that might actually been due to something else (as I can actually find the @id block in the code). I agree, I will add it back.
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Seems like an excellent reason to remove it. Yes, the link should be dsl_advanced_options_parametric_initial_conditions. Probably got changed while PEtab doc was disabled so this wasn't caught somehow.
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Ok, seems you found the new link as well
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@sebapersson thanks for the updates! |
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Additional context
I have updated the code in the PEtab tutorial and added it again to the documentation. The tutorial runs locally for me, but I have problem to precompile the doc environment due to BifurcationKit (which is why the doc runs might fail).