[Bioc-devel] improving navigation within workflows
Aaron Lun
alun at wehi.edu.au
Fri Aug 4 23:21:14 CEST 2017
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
> <stvjc at channing.harvard.edu <mailto:stvjc at 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 <alun at wehi.edu.au
> <mailto: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/
> <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>
> > <mailto: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/>
> >
> <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
> <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:
> > >
> > > 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
> <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>>>
> > > > <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 <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/>>>
> > > >
> >
> <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 at r-project.org
> <mailto:Bioc-devel at r-project.org>
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> <mailto:Bioc-devel at r-project.org>>
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