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@IAlibay IAlibay commented Apr 5, 2022

~ don't merge yet ~

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github-actions bot commented Apr 5, 2022

Binder 👈 Launch a binder notebook on branch OpenFreeEnergy/ExampleNotebooks/april2022

@IAlibay IAlibay changed the title [WIP] updating notebook for april 2022 release Updating notebook for april 2022 release Apr 5, 2022
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IAlibay commented Apr 5, 2022

Workflow diagram needs updating but let's get the notebook out first, can update diagram tomorrow.

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You've got a typo, in 'HBonds' you're spelling it 'Hbonds'. Tbh we should normalize this internally to avoid this sort of finger trouble, but it'll need to get fixed here for now.

I wonder if this would be better if we split out the JNK ligand set into a separate notebook (to showcase the network creation system) and mostly skip over it here.

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@mikemhenry I think I'm gonna have to cut a 0.2.1 since we found a couple little issues, then I'll pin this repo to that ( so we can develop freely)

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@mikemhenry I think I'm gonna have to cut a 0.2.1 since we found a couple little issues, then I'll pin this repo to that ( so we can develop freely)

Sounds good! I asked Irfan this but I might as well make this public:

I need to make the simulations shorter so the CI can do them, do you have any objects to me adding some sort of comment that says "you will want to run these longer for production but for demonstration purposes we are going to do only a few steps" or something like that?

The alternative is to use tags to skip the cells (users won't see them) but if we skip them 1) they won't be tested and 2) the analysis cells will also have to be skipped.

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IAlibay commented Apr 7, 2022

The comment re: longer simulations should be in the notebook for this month.

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IAlibay commented Apr 7, 2022

I would prefer we just skip the cells from CI though, it's not necessary, at that point we should know the things work.

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Fixes #3

@richardjgowers richardjgowers merged commit a0b0633 into master Apr 7, 2022
@richardjgowers richardjgowers deleted the april2022 branch April 7, 2022 17:04
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4 participants