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Bioconductor / AnVILPublish

https://bioconductor.org/packages/AnVILPublish
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Peculiar ipynb link after requesting rmd transfer #12

Closed vjcitn closed 12 months ago

vjcitn commented 1 year ago

Notice the hyperlink towards the bottom, to an ipynb file ... intended?

request was

as_workspace("BiocHail", "landmarkanvil2", update=TRUE, use_readme=TRUE, type="rmd")

AnVILPublish 1.9.0

apub

mtmorgan commented 1 year ago

Yes, I see why this occurs; it seems like it has always been like this (and wrong). I guess that the Rmd notebooks show up under the ANALYSES tab and in RStudio...?

vjcitn commented 1 year ago

hmph ... i went to check and it logged me out. yes they show up in the analyses tab, but i wonder if they are pushed (or received) with suffix .ipynb and then are renamed? because i am pretty sure i saw them first as ipynb.

mtmorgan commented 1 year ago

AnVILPublish doesn't change the extension under ANALYSES; it copies the Rmd file. Things might go awry if there are also .ipynb versions of the notebooks in the vignettes/ directory of the source package?

mtmorgan commented 1 year ago

https://github.com/Bioconductor/AnVILPublish/tree/R-3-16-link-Rmd-from-dashboard (BiocManager::install("Bioconductor/AnVILPublish", ref = "R-3-16-link-Rmd-from-dashboard")) starts to address this.

The Rmd and / or ipynb are now linked correctly to the dashboard.

It seems that clicking on these links mostly fails (I believe the 'Preview' feature of Terra relies on an out-of-date R installation without packages such as BiocStyle that might be mentioned in the YAML, and also for other less transparent reasons -- I'll work on getting these to the attention of the Terra team -- quarto render <file.Rmd> --to gfm --no-execute should be good enough for a preview and does not require a complicated R installation).

vjcitn commented 1 year ago

type = "rmd" still produces .ipynb link on the dashboard (but I did not try the branch mentioned above). Should the branch be merged?

mtmorgan commented 1 year ago

Please try the branch. Any comments on the restrictions? Does preview still fail?