Regarding the metadata: I think that the installation instructions should always be visible. However, the rest of the details could be stored in a hidden section that can be clicked to expose the full details (e.g., expands upon clicking a link saying "Click here for more details").
Andrzej Oleś wrote: > Hi Vince, > > thanks for your feedback. The floating TOC would be technically > possible, the question is more about the aesthetics of such solution. > As we thought of using the right column for the supplementary stuff > such asfigure/table captions or footnotes, this space cannot harbor a > floating TOC as it would obscure the view of these items. > > Regarding the document metadata section at the top: this is a fair > point and I'm interested to hear the opinion of others. Personally I > would argue that some of these information is quite important and > should be emphasized at the beginning, such as installation > instructions or recent modification and compilation dates. I agree > that links to package tarballs are more obscure and could be maybe > moved somewhere downstream. As workflow pages tend to be relatively > long documents, I'm a bit worried though whether burying it at the > very bottom after the output of `sessionInfo()` won't virtually > prevent people from reaching it at all. I'm looking forward to the > thoughts of other developers on this. > > Cheers, > Andrzej > > On Fri, Aug 4, 2017 at 5:01 PM, Vincent Carey > <st...@channing.harvard.edu <mailto:st...@channing.harvard.edu>> wrote: > > interesting. is the floating toc not an option for this? also, > IMHO the "about this document" should go at the end. one wants > the content to hit the reader right away, not the provenance, i think. > > On Fri, Aug 4, 2017 at 9:33 AM, Aaron Lun <a...@wehi.edu.au > <mailto:a...@wehi.edu.au>> wrote: > > Mind -> blown. Yes, that's exactly what I wanted, thanks. > > -Aaron > > On 04/08/17 14:19, Andrzej Oleś wrote: > > Hi Aaron, > > > > I'm happy to inform that I've implemented your suggestion to add > > navigation links at workflow pages. Feel free to have a look > at the > > working prototype under > > > https://www.bioconductor.org/help/workflows/testproj/testfile/ > <https://www.bioconductor.org/help/workflows/testproj/testfile/> > > > > The new workflow-rendering engine which includes the > navigation links > > will be enabled soon after some additional testing is > finished. The > > transition will be announced in a separate email to the > devel mailing list. > > > > Cheers, > > Andrzej > > > > > > On Mon, Jul 17, 2017 at 10:15 AM, Aaron Lun > <a...@wehi.edu.au <mailto:a...@wehi.edu.au> > > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au>>> wrote: > > > > Hi Andrzej, > > > > Interesting. I also didn't realize that we could get > figure referencing > > via bookdown, that's nice to know. I was thinking that > the floating TOC > > could go onto the right margin, but I guess that doesn't > fit anymore now > > that you have the footnotes and figure captions. > > > > CRAN-style links might be the best compromise, e.g., if > they can be > > placed in the right margin. A simple set of three links > > (<previous><contents><next>) beside each > section/subsection heading > > would probably sufficient for effective navigation, > without using up too > > much space. > > > > Cheers, > > > > Aaron > > > > On 17/07/17 00:35, Andrzej Oleś wrote: > > > Hi Aaron, > > > > > > thanks for your feedback. We are currently looking > into ways of > > > improving the building of workflows for the website in > order to enable > > > cross references, html widgets, and similar. So far > these were not > > > supported because of some technical constraints of the > current > > > implementation which involves rendering the workflows > into an > > > intermediate .md file. The new approach will overcome > these limitations > > > by skipping this intermediate step and rendering > directly to html. For a > > > preview see: > > > > https://www.bioconductor.org/help/workflows/testproj/testfile/ > <https://www.bioconductor.org/help/workflows/testproj/testfile/> > > > <https://www.bioconductor.org/help/workflows/testproj/testfile/ > <https://www.bioconductor.org/help/workflows/testproj/testfile/>> > (it > > also > > > uses a slightly modified layout with some of the > supporting information > > > such as figure and table captions, or footnotes moved > to the right column) > > > > > > Regarding the navigation, a floating TOC would be in > principle possible > > > in the new implementation. It is not entirely clear to > me, however, > > > weather this will visually work with the > bioconductor.org <http://bioconductor.org> > <http://bioconductor.org> > > > <http://bioconductor.org> website template. Links to > the TOC, such as > > > ones in e.g. > > > > https://www.bioconductor.org/help/workflows/highthroughputassays > <https://www.bioconductor.org/help/workflows/highthroughputassays> > > > <https://www.bioconductor.org/help/workflows/highthroughputassays > <https://www.bioconductor.org/help/workflows/highthroughputassays>> > could > > > be relatively easily inserted automatically after each > section. Static > > > CRAN-like solution as you mentioned it would probably > require some more > > > work. > > > > > > Cheers, > > > Andrzej > > > > > > On Sun, Jul 16, 2017 at 9:36 PM, Aaron Lun > <a...@wehi.edu.au <mailto:a...@wehi.edu.au> > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au>> > > > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au> > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au>>>> wrote: > > > > > > Indeed, that's exactly what I was thinking of. I > have a floating TOC in > > > my own Rmarkdown files, but I'm not sure if it's > supported by the > > > workflow builder, given that it adds a separate > hyperlinked TOC to the > > > start of the workflow page. > > > > > > On 16/07/17 19:29, Vincent Carey wrote: > > > > like this? > > > > > > > > > > http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html> > > > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html>> > > > > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html> > > > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html > > <http://bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/AuthoringRmdVignettes.html>>> > > > > > > > > On Sun, Jul 16, 2017 at 11:53 AM, Aaron Lun > <a...@wehi.edu.au <mailto:a...@wehi.edu.au> > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au>> > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au> > > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au>>> > > > > <mailto:a...@wehi.edu.au > <mailto:a...@wehi.edu.au> <mailto:a...@wehi.edu.au > <mailto:a...@wehi.edu.au>> > > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au> > <mailto:a...@wehi.edu.au <mailto:a...@wehi.edu.au>>>>> wrote: > > > > > > > > Hello all, > > > > > > > > I was wondering if there's any plans to > improve the > > navigation for the > > > > BioC workflows. I was looking at my > simpleSingleCell > > workflow: > > > > > > > > > > > https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/> > > > <https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/>> > > > > > > <https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/> > > > <https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/>>> > > > > > > > <https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/> > > > <https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/>> > > > > > > <https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/> > > > <https://www.bioconductor.org/help/workflows/simpleSingleCell/ > <https://www.bioconductor.org/help/workflows/simpleSingleCell/>>>> > > > > > > > > ... and I've realized that it's gotten > pretty long. > > It's a pain to keep > > > > on scrolling up and down when I'm stuck in > the middle > > of the document > > > > and I want to jump somewhere else quickly > (or even just > > go to the TOC). > > > > > > > > It would be nice to have some sort of floating > > navigation bar containing > > > > links to every section, rather than a TOC > at the top. > > Failing that, > > > > section numbers and hyperlinks to the top > or end (a la > > > > > > > https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html> > > > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html>> > > > > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html> > > > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html>>> > > > > > > > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html> > > > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html>> > > > > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html> > > > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html > <https://cran.r-project.org/doc/manuals/r-release/R-exts.html>>>>) > > > would be > > > > useful. > > > > > > > > Cheers, > > > > > > > > Aaron > > > > > _______________________________________________ > > > > Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org> > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org>> > > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org> > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org>>> > > > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org> > > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org>> > <mailto:Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> > > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org>>>> > > > mailing list > > > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> > > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>> > > > > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> > > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>>> > > > > > > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org> > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org>> > > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org> > <mailto:Bioc-devel@r-project.org > <mailto:Bioc-devel@r-project.org>>> > > mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> > > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > <https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel>>> > > > > > > > > > > > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel