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cytomining / profiling-handbook

Image-based Profiling Handbook
https://cytomining.github.io/profiling-handbook/
Creative Commons Zero v1.0 Universal
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Move builds to JupyterBook and GH Actions #65

Closed bethac07 closed 2 years ago

bethac07 commented 2 years ago

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

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.

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.

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)

Originally posted by @shntnu in https://github.com/cytomining/profiling-handbook/issues/64#issuecomment-1061717534

bethac07 commented 2 years ago

@callum-jpg

bethac07 commented 2 years ago

Done!