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Bioconductor / sweave2rmd

A project for converting Bioconductor Sweave documents to Rmd
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Script to categorize vignettes in Trello #49

Closed jwokaty closed 1 year ago

jwokaty commented 1 year ago

I think it's possible to write a script to read our list of .Rnw files determine if a package is in Bioconductor 3.17 and how to categorize it on our Sweave2Rmd project board using BiocPkgTools.

You can get the name of the package from that list. You can use the BiocPkgTools::biocPkgList function to check if the package is in 3.17. If a package is in 3.17, you can check if it's maintained by Bioconductor Core with BiocPkgTools::biocMaintained. These are the packages that we'll set to Todo on the project board since we don't need to initiate any communication.

(Note: if a package isn't in 3.17, we still want to note somewhere, likely in the Trello, that no more action is needed.)

If a package is in 3.17 but not maintained by Bioconductor Core, we'll want to determine if it's high priority or low priority. We'll probably want a variable for threshold that we can adjust as needed. If BiocPkgTools::pkgDownloadRank is lower than the threshold, it's high priority; otherwise it's lower.

It might be good to write this to a spreadsheet and attach it to the Trello where the row is a package, with a column for 3.17 package (TRUE/FALSE) Bioc Maintained (TRUE/FALSE), and Priority (high/low).

jwokaty commented 1 year ago

@BerylKanali If you need more help to get started on this, please let me know. This is a good programming task to help me understand where your skills are. I don't expect you to know everything and you should as much as possible use me as a resource to learn as much as you can. I will make time for you. If it's helpful, we can spend time pair programming on it Friday after the meeting or you can also share your script so I can comment on it. You could possibly put it in this repository under an inst\script\ directory.