[Bioc-devel] improving navigation within workflows
Aaron Lun
alun at wehi.edu.au
Fri Aug 4 15:33:33 CEST 2017
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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