Bioc-friendly feature suggestions

[lcolladotor]

Hi,

Based on my recent work for r-lib/actions#84 and at https://github.com/leekgroup/derfinderPlot/blob/master/dev/01_setup.R, I want to make a few small PRs to usethis.

PR idea 1

One of them is basically about mentioning the Bioconductor Support website for .github/SUPPORT.md. Currently I did so at https://github.com/leekgroup/derfinderPlot/blob/master/dev/01_setup.R#L36-L45 but it could be it's own function or editing the tidyverse template (which you might not want to do as it would be a more global change).

## Customize the support message to mention the Bioconductor Support Website
usethis::use_tidy_support()
support <- readLines(".github/SUPPORT.md")
support <-
    gsub(
        "\\[community.rstudio.com\\]\\(https://community.rstudio.com/\\), and/or StackOverflow",
        "the [Bioconductor Support Website](https://support.bioconductor.org/) using the appropriate package tag",
        support
    )
writeLines(support, ".github/SUPPORT.md")

PR idea 2

A second one could be a badge that has a specific message for the GitHub action I'm suggesting at r-lib/actions#84 .

PR idea 3

I also have a more custom issue_template.md https://github.com/leekgroup/derfinderPlot/blob/master/dev/01_setup.R#L47-L51. Since that code uses ::: at some point, maybe a function that allows custom templates would be useful.

Before making any PRs, I wanted to bring these ideas up.

Best,
Leo

[lcolladotor]

Hi,

In the end, I made a new R package called biocthis at https://lcolladotor.github.io/biocthis/ that builds upon usethis to do all the things I had suggested here and a bit more. See https://lcolladotor.github.io/biocthis/articles/biocthis.html#biocthis-functions-overview for the list of functions.

biocthis relies on several un-exported functions from usethis as noted at https://github.com/lcolladotor/biocthis/runs/659819160?check_suite_focus=true#step:10:64. If in the future there's a new package for expanding usethis (image an rlang but for usethis) or these functions become exported, I'll update biocthis accordingly.

I also noticed that usethis::use_bioc_badge() only works for Bioconductor software packages (experiment, annotation and workflow packages are different) on the Bioc-release branch. Anyway, most Bioconductor packages are software ones so there's likely no real need to expand usethis::use_bioc_badge(), specially since usethis::use_badge() is flexible to support new scenarios. However, if you do decide to expand usethis::use_bioc_badge() let me know and I'll help.

Best,
Leo

[jennybc]

Nice work! I think it is best to approach the way you have, i.e. a bioc-flavored extension of usethis.

I see a lot of calls of this form in the function overview:

withr::with_dir(pkgdir, {
    usethis::use_git()
})

In case you haven't found them yet, I think a better fit for your intention might be usethis::with_project() and usethis::local_project(), instead of with::with_dir().

Would it be possible to write that overview assuming that someone is in their source package? It would seem to be a reasonable assumption and would put the focus on the biocthis functions vs. the withr::with_dir() wrapping.

[lcolladotor]

Hi Jenny,

Thank you! And thanks for the feedback! I indeed was not familiar with usethis::with_project() and usethis::local_project() and at lcolladotor/biocthis@e89f16d I am no longer using them, so the vignette looks cleaner like you anticipated.

For styler::style_pkg() I ended up using the path argument since it wanted to use the main directory instead of following what usethis::local_project() had set.

Thanks again! The GHA workflow is currently running, but I ran a test on my computer so it should all go well in a couple of minutes.

Best,
Leo