[Bioc-devel] improving navigation within workflows
Vincent Carey
stvjc at channing.harvard.edu
Fri Aug 4 17:01:40 CEST 2017
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 <alun at 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/
> >
> > 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 <alun at wehi.edu.au
> > <mailto:alun at 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/> (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> 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>
> 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 <alun at wehi.edu.au
> <mailto:alun at wehi.edu.au>
> > > <mailto:alun at wehi.edu.au <mailto:alun at 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>>
> > > >
> > > > On Sun, Jul 16, 2017 at 11:53 AM, Aaron Lun <
> alun at wehi.edu.au <mailto:alun at wehi.edu.au> <mailto:alun at wehi.edu.au
> > <mailto:alun at wehi.edu.au>>
> > > > <mailto:alun at wehi.edu.au <mailto:alun at wehi.edu.au>
> > <mailto:alun at wehi.edu.au <mailto:alun at 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/>>>
> > > >
> > > > ... 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>>>)
> > > would be
> > > > useful.
> > > >
> > > > Cheers,
> > > >
> > > > Aaron
> > > > _______________________________________________
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> > <mailto:Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>>
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> > <mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org
> > <mailto:Bioc-devel at r-project.org>>>
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> > > >
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