Document the existence of rworkflows externally

[lcolladotor]

Hi,

You might want to consider getting in touch with Kevin @kevinrue who has been working on some documentation on how to make a Bioconductor package. See https://bioconductor.github.io/bioc_mentorship_docs/bioc-package.html for more details.

We could also mention rworkflows on the biocthis::use_bioc_pkg_templates() files.

Best, Leo

[bschilder]

Thanks for alerting me about this effort @lcolladotor !

@kevinrue is this something you would be interesting in adding to your tutorial? Perhaps somewhere around here. https://bioconductor.github.io/bioc_mentorship_docs/bioc-package.html?q=actions#using-github-actions

For some context, rworkflows has a lot of overlapping functionality with the workflow produced by biocthis::use_bioc_github_action(), but instead uses a centralized action on the GitHub Marketplace that I maintain It means that users don't have to individually troubleshoot when things go awry, and that there's better version control of the action.

Happy to help write up some materials for this!

[kevinrue]

Sounds like a great idea. I'm hugely overcommitted in the near future, so it'll have to wait 2023 though. Let's stay in touch!

[bschilder]

No worries @kevinrue, totally understand! That's great to hear you're interested, let's def revisit post-holidays. The preprint should be up by then as well. Thanks!

[bschilder]

Also advertised rworkflows on relevant Turing-related Slack communities.

• The Turing Way
• RSE (Research Software Engineering)
• UCL Research Programming Hub
• InSilicoUK

As well as UKDRI Slack channels:

• reproducible-research

As well as the bioc-devel email listserve.

[bschilder]

Hey @kevinrue just wanted to check in and see if I might be able to contribute something to this. If you like, I can make a PR directly to your repo to add some docs on rworkflows: https://github.com/Bioconductor/bioc_mentorship_docs

[kevinrue]

Hi. Thanks for nudging me. I haven't forgotten, but you wouldn't believe how busy life has been since January for me. I've just finished teaching, and I only have a few weeks to get anything done before another round of teaching. I would recommend that you work on a PR while I get other stuff done, before I see when I can calmly work on this myself. Do feel free to ask me questions if you have any doubt or need any help, it's the least I can do to help you contribute!

[bschilder]

No worries at all @kevinrue, totally understand the chaos of juggling multiple things at once! I'll get started on this and will be sure to reach out if I have any questions.

Thanks so much!

[bschilder]

PR now made here: https://github.com/Bioconductor/bioc_mentorship_docs/pull/23

@NathanSkene see here for the updated bookdown chapter describing how rworkflows strategy can be used as an alternative to (or in conjunction with) the usethis + biocthis strategy: https://neurogenomics.github.io/bioc_mentorship_docs/bioc-package.html

Differences between these strategies are described throughout, but here are the two most important sections: https://neurogenomics.github.io/bioc_mentorship_docs/bioc-package.html#create-a-package-template https://neurogenomics.github.io/bioc_mentorship_docs/bioc-package.html#github_actions

[bschilder]

Will make a PR here as well for several of my packages https://github.com/IndrajeetPatil/awesome-r-pkgtools#dependency-management-%EF%B8%8F

• rworkflows
• templateR
• echogithub
• echodeps
• devoptera