[Bioc-devel] improving navigation within workflows
Martin Morgan
martin.morgan at roswellpark.org
Sun Aug 6 17:56:06 CEST 2017
On 08/04/2017 05:00 PM, 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 as figure/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.
I feel like most of the provenance and installation instruction at the
top is relevant and important for successful use of the workflows,
including the package name, installation instructions, and built /
modified date. That leaves the Rscript (not essential but useful) and
tar balls (obscure detail) which in principle could be moved.
Maybe there is scope for making the presentation of this information and
similar information on package landing pages more consistent?
Martin
>
> Cheers,
> Andrzej
>
> On Fri, Aug 4, 2017 at 5:01 PM, Vincent Carey <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> 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.ht
>>> ml
>>>> <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.ht
>>> ml
>>>> <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>>
>>>> > <mailto: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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>>>
>>
>>
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