[Bioc-devel] Bioconductor Workflows: TOC and displaying document details
Hi Andrzej, ----- Original Message -----
From: "Andrzej Ole?" <andrzej.oles at gmail.com> To: "bioc-devel" <bioc-devel at r-project.org> Sent: Tuesday, October 13, 2015 5:39:25 AM Subject: [Bioc-devel] Bioconductor Workflows: TOC and displaying document details
Hi everyone, while browsing through http://www.bioconductor.org/help/workflows/ I've noticed some inconsistency in using TOC in workflow vignettes. As the TOC is currently not automatically generated, some authors create it manually, while others do not have it at all. I suggest to address this shortcoming by leveraging the rmarkdown build in mechanism to automatically generate a TOC for all workflows freeing up the authors from the burden of curating it manually. For this to work, it would be probably enough to use during document conversion library(rmarkdown) render("document.Rmd", md_document(toc = TRUE))
I have implemented this. The next time workflow authors trigger a build by committing their source document(s), the automatic TOC will be generated, so I suggest that workflow authors remove any manually-generated TOC before committing. Incidentally, rebuilding will also cause the workflow to be rebuilt under the newly released Bioconductor 3.2.
possibly with the depth limited with 'toc_depth = 2'.
I decided not to limit the TOC depth.
Also, I think that it would be more readable and visually appealing to present the document title, author and date in form of a proper document header (similarly as for regular BioC vignettes) above the "About This Document" table. Regarding the table itself, it contains a lot of technical details (actually, even more than on package landing pages, like "First Committed" or "SVN Revision"), which I'm not sure if they are informative to the end user and relevant to the content. Maybe these could be either moved to the document footer or dropped completely?
I will think about this one. Thanks, Dan
Cheers, Andrzej [[alternative HTML version deleted]]
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