-
Notifications
You must be signed in to change notification settings - Fork 7
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Conversion to BiocBook #11
base: main
Are you sure you want to change the base?
Conversation
This looks great, thank you very much for this @js2264 and sorry for not getting back to you in time. I will take time by the end of the year and get back to you. |
This is a good point, indeed. But the book is foremost part of the R for Mass Spectrometry initiative, and the repo name book makes most sense here. I suppose we could rename the repo RforMassSpectrometryBook, to fit the Bioconductor package name requirement, event though I can see two issues:
I am also wondering to what extend the naming rule should be applied as is in the context of books. |
IMO these are valid reasons to keep As a remainder:
So the package name is quite important, even though it won't be directly installed by end-users. |
@jorainer - what do you think if converting the book to a BiocBook/package? I think we should go for it, merge, as address the (minor) open points as we go. |
Hi @lgatto and colleagues,
I had the opportunity to discuss with you during the EuroBioc23 conf. I've been working on adapting your great book to the
BiocBook
infrastructure. If you are interested in accepting this PR, let me know and we can discuss in more detail to make sure things run ok.Few points worth bringing up:
qmd
(quarto) format, and located ininst/index.qmd
andinst/pages/*qmd
. You can add any page to the book by creating a new.qmd
file ininst/pages/
and reference this file in theinst/assets/_book.yml
listing.msmbstyle
). This should allow pdf rendering (the rendering was crashing with themsmbstyle
tags).devel
branch on therformassspectrometry/book
repo, not thebase
I currently selected (but I cannot directly create this branch in your repo). This would allow automatic detection of theBioc
version to use: a branch nameddevel
(orRELEASE_3_18
) will usebioc devel
(orbioc 3.18
) to build the book (and deploy it togh-pages:docs/3.18
). Themain
branch is not going to trigger automated book building at all.gh-pages
branch (root
folder). An automated redirection sends togh-pages:docs/devel
, but can be set up to other versions (if anyRELEASE_*
branch exists). The URL that points to an actual book would be https://.github.io//docs/devel/ (or https://.github.io//docs/RELEASE_*/).remotes::install_github("js2264/R4MS")
, which sets up all the dependencies from CRAN/Bioc. Alternatively, a docker image with pre-configured RStudio server is available ("docker pull ghcr.io/js2264/r4ms:devel"). Once the PR pulled, this would becomerformassspectrometry/book
of course.rformassspectrometry/book
is not very informative, and notably is in conflict with the conventions for Bioconductor package submissions (which state that the package repository should have the same name as the package itself). If you intend to submit this book as a BiocBook package to Bioconductor, you'd have to consider renaming the repository or the package.Let me know if there is anything unclear!