Add manuscript to existing code repo

[kescobo]

At the moment, it seems like the setup workflow is only suitable for starting a manuscript in a brand new repository, where the only thing in the repository is the manuscript. It would be nice if the manuscript could live alongside code and other content in a single repository.

From what I can tell, this may require:

• [ ] decoupling folder structure to avoid clashes (perhaps things that are critical could go in a manuscript/ or ./manuscript subfolder)
• [ ] tools for running manuscript CI along with CI for code tests etc

Alternatively, perhaps git submodules could be effective here, and all that would be required is some documentation.

[agitter]

@kescobo you're correct that the current setup assumes your repository will only contain the manuscript. We agree that having the manuscript be more self-contained is desirable. https://github.com/manubot/template/issues/1 discusses some of that roadmap and how a refactored Manubot could greatly simplify the manuscript repository.

Currently, many projects have a code/analysis repository and a separate manuscript repository. A recent example:

• iscb-diversity-manuscript
• iscb-diversity code

We have also used submodules in the past as you suggested:

• meta-review manuscript repo
• submodule with deep-review repo for updated statistics

[kescobo]

Thanks for the links - I'll take a look. The new template does look like a good approach. I'll dig some more and chime in if anything occurs to me 👍

[dhimmel]

Yeah. I think the @kescobo touches on an important limitation. Currently, SETUP does not allow adding a manuscript to a pre-existing code repo.

Our plan in the future with manubot/template is to reduce Manubot setup to just having the .github/workflows/manubot.yaml file in the repo. This would run the GitHub action, which would detect the manuscript location or perhaps read a manubot config file that would tell it where to look and what to do.

This would allow @kescobo to create a manuscript alongside project code. There would be a few restriction like reserving the gh-pages branch for Manubot.

For now, I think the best solution would be to create separate repos, since manubot/template could still be some ways off.

[kescobo]

Thanks @dhimmel. For now, that's what I'm doing, and I'll probably end up going the submodule route. Not done, but https://github.com/Klepac-Ceraj-Lab/resonance1_manuscript

I didn't quite get this set up in time for preprint and submission, but here's the preprint

[dhimmel]

Not done, but https://github.com/Klepac-Ceraj-Lab/resonance1_manuscript

Ah cool! Feel free to add your manuscript to the catalog source at any point if you'd like it to show up at https://manubot.org/catalog/.

[agitter]

I'm cross-referencing https://github.com/manubot/manubot/issues/229#issuecomment-632756812 where there are links to a custom manuscript build process for a repository configured as @kescobo described. That could be a short term workaround until manubot/template is ready.