lfs => dvc

[ErinWeisbart]

Updates the handbook to reflect recent changes to the profiling-recipe wherein we switch from the use of Git LFS to DVC for large file management.

[shntnu]

I can fix this build error, but I wonder if this is the right time to do the thing @bethac07 suggested below.

Over to you two to decide @ErinWeisbart @bethac07

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From: Beth Cimini bcimini@broadinstitute.org
Date: Tue, Nov 30, 2021 at 6:49 AM
To: Shantanu Singh shsingh@broadinstitute.org

FWIW, I don't think the "lift" is currently probably worth it, but if we did want to switch to JupyterBook somewhere down the road, it looks like it takes Rmd pages so it would be a fast start-up.

https://jupyterbook.org/file-types/jupytext.html?highlight=rmd

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From: Shantanu Singh shsingh@broadinstitute.org
Date: Tue, Nov 30, 2021 at 6:56 AM
To: Beth Cimini bcimini@broadinstitute.org

Neat! The conversion would be a nice project (~2-3 days?) for someone who is interested in creating training material and learning about GitHub Actions.

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From: Beth Cimini bcimini@broadinstitute.org
Date: Tue, Nov 30, 2021 at 7:11 AM
To: Shantanu Singh shsingh@broadinstitute.org

Since it can read Rmd files directly, and GH actions is already documented, assuming we stuck with the Rmd files we have in theory it's a 30 minute project; someone with not a ton of experience still could probably get it up and running in a day.

It doesn't look like there are any good tools (ala pandoc) for a straight Rmd-to-MyST conversion, but with the VSCode extensions for Rmd and for MyST both installed and a MyST cheat sheet, I still can't see it taking much more than a few hours.

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From: Shantanu Singh shsingh@broadinstitute.org
Date: Tue, Nov 30, 2021 at 7:15 AM
To: Beth Cimini bcimini@broadinstitute.org

Good point – just 6 Rmd files, and it's mostly just the code blocks that will need conversion (if done by hand)

[bethac07]

@ErinWeisbart your call; we can discuss at checkin today if you need more info

[bethac07]

Otherwise, I would say might be a good project for Callum since a) he's working on CellProfiler so he's going to need to know a bit about GHActions for build stuff and b) he's planning on putting together the documentation for Piximi in Jupyter book and so having an easy starter project for that might be good practice.

[bethac07]

Callum has said he's happy to work on this next week, so let's maybe just pull this and make a separate GH issue for the migration?

[bethac07]

@ErinWeisbart you're also welcome to work on this too, or we can all work on it together, not trying to take it if you're interested :)

[ErinWeisbart]

I've got plenty on my plate at the moment and I'm happy to have Callum handle the integration.

[bethac07]

I'm going to go ahead and merge then, and move the changing the build to a new issue.