Hi Andrzej, ----- Original Message ----- > From: "Andrzej Oleś" <andrzej.o...@gmail.com> > To: "bioc-devel" <bioc-devel@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]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
