Fix differential equation tutorial

TuringLang / docs

Documentation and tutorials for the Turing language

https://turinglang.org/docs/

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Fix differential equation tutorial #296

Closed devmotion closed 2 years ago

devmotion commented 2 years ago

I've wanted to do this for quite some time but unfortunately my computer broke while working on an update...

So here are some fixes for the differential equation tutorial.

Most notably,

it fixes the MvNormal deprecations
fixes the trajectories of posterior samples (the used the wrong parameters)
it uses more "modern" and simpler SciML syntax
specifies the solver for the DDE example correctly.

Preview: https://julialang-buildkite-artifacts.s3.amazonaws.com/turingtutorials/e3c8bc002f5223b50eb6e9c7902473c040159c0aa4d5942d979166fa05bcb422/html/10-bayesian-differential-equations/10_bayesian-differential-equations.html

devmotion commented 2 years ago

@staticfloat I think there might be an issue with coppermind? https://buildkite.com/julialang/turingtutorials/builds/76#9b6b2925-254f-43b2-8401-9a7224be6376/205-207

devmotion commented 2 years ago

@staticfloat It seems it's a problem specifically with aarch64 (or the workers) as it still works with x86_64: https://buildkite.com/julialang/turingtutorials/builds/78#b12d7990-0ba6-422b-9a30-df85278cc46d Probably bash does not support all features in the failing builds? The offending line seems to be https://github.com/staticfloat/coppermind-buildkite-plugin/blob/bc1c8b1f473651490bcaed15dfe16488d447a0e4/hooks/pre-command#L8.

devmotion commented 2 years ago

Ah no, it's just the exit code. So I assume bash might not be available and/or installed properly?

devmotion commented 2 years ago

Will be fixed by https://github.com/TuringLang/TuringTutorials/pull/298.

devmotion commented 2 years ago

There's one remaining issue, namely that pool_chain is not exported by MCMCChains. It's a hack anyway, so I think I'll just go and fix https://github.com/TuringLang/MCMCChains.jl/issues/223. Then pool_chain is not needed anymore and the code becomes simpler.