[Bioc-devel] improving navigation within workflows

Andrzej Oleś andrzej.oles at gmail.com
Fri Aug 4 15:19:22 CEST 2017


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> 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/ (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> website template. Links to the TOC, such as
> > ones in e.g.
> > 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>> 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>
> >     >
> >     > 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>>> 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/>>
> >     >
> >     >     ... 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>>)
> >     would be
> >      >     useful.
> >      >
> >      >     Cheers,
> >      >
> >      >     Aaron
> >      >     _______________________________________________
> >      > Bioc-devel at r-project.org <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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> list
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> >
> >
>

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