[Bioc-devel] BiocStyle and R markdown

[Jim Hester]

Kasper,

Easiest way to get a GitHub version of BiocStyle is to just fork
https://github.com/Bioconductor-mirror/BiocStyle/

Jim

On Thu, Jul 30, 2015 at 9:28 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> Well, without really knowing details it could just be that more work has
> been done on BiocStyle in devel.
>
> One could backport the change to release, but that would mean that all
> packages (which use BiocStyle) need to be version bumped and re-build,
> purely for cosmetic issues in the vignette.  While I care about aesthetics,
> it is not worth doing a massive update to our stable release branch for
> this.
>
> So lets try to hammer BiocStyle before the next release so we can iron out
> any issues.
>
> Biocore: could we get a Github version of BiocStyle so we could start
> issues etc.  Easy way to keep a todo.
>
> Best,
> Kasper
>
> On Thu, Jul 30, 2015 at 12:13 AM, Thomas Girke <thomas.girke at ucr.edu>
> wrote:
>
> > Yes, they show under Bioc-devel, but not under Bioc-release. Building the
> > exact same *Rmd source from here
> >
> >
> https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
> > under Bioc-release looks quite different:
> > http://biocluster.ucr.edu/~tgirke/HtmlStyle.html
> >
> > Thomas
> >
> > On Wed, Jul 29, 2015 at 7:58 PM Kasper Daniel Hansen <
> > kasperdanielhansen at gmail.com> wrote:
> >
> >>  What exactly do you mean by numbering.  As far as I understand,
> >> numbering is already there in devel:
> >>
> >>
> >>
> https://bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
> >>
> >>  Kasper
> >>
> >> On Wed, Jul 29, 2015 at 10:39 PM, Thomas Girke <thomas.girke at ucr.edu>
> >> wrote:
> >>
> >>> Perfect, if your update in Bioc-devel eliminates the awkward bullets in
> >>> front of the numbers. The lack of numbered content tables in
> Bioc-release
> >>> may be something we have to live with until the next Bioc release? I
> don't
> >>> want to overstretch Dan's or the Bioc team's patience with overly picky
> >>> style requests.
> >>> Thomas
> >>>
> >>>  On Wed, Jul 29, 2015 at 6:49 PM Kasper Daniel Hansen <
> >>> kasperdanielhansen at gmail.com> wrote:
> >>>
> >>>>  When I roll that styles.css into the bioconductor.css file shipping
> >>>> with BiocStyle, it gets rid of the bullets.
> >>>>
> >>>>  Its added to BiocStyle 1.7.5
> >>>>
> >>>> Kasper
> >>>>    On Wed, Jul 29, 2015 at 9:37 PM, Kasper Daniel Hansen <
> >>>> kasperdanielhansen at gmail.com> wrote:
> >>>>
> >>>>> This is just reporting what I see using Bioc-devel:
> >>>>>
> >>>>>  I get a TOC where each line looks like
> >>>>>
> >>>>>    <BULLET> <SECTION_NUMBER_AS_LINK> <SECTION_TITLE_AS_LINK>
> >>>>>
> >>>>>  While I agree that the bullet is kind of ugly (and would be great to
> >>>>> get rid of), I do get the section numbering functionality you want.
> >>>>>
> >>>>>  Note: for this report I am rendering the Rmd file myself, I haven't
> >>>>> tested how it looks when I do it as a vignette.
> >>>>>
> >>>>>  It would be great to expand on the BiocStyle vignette and discuss
> >>>>> citations and other issues and also include a clear template file.
> I am
> >>>>> planning on doing some pull request along those lines soon; I have
> been
> >>>>> testing Rmd -> HTML extensively for a course I am developing, but I
> am also
> >>>>> new to the knitr+markdown thing so I am still experimenting.
> >>>>>
> >>>>>  Kasper
> >>>>>
> >>>>>
> >>>>     On Wed, Jul 29, 2015 at 4:44 PM, Thomas Girke <
> thomas.girke at ucr.edu
> >>>>> > wrote:
> >>>>>
> >>>>      A simple formatting issue:
> >>>>>>
> >>>>>> Since support for table of contents in R markdown vignettes has
> become
> >>>>>> available, it seems like an amazing solution for many online
> >>>>>> documentation needs in the future.
> >>>>>>
> >>>>>> What would help me to fully to adopt to it, is a solution to get rid
> >>>>>> of
> >>>>>> the bullets in a numbered table of content which looks a bit unusual
> >>>>>> to
> >>>>>> me:
> >>>>>>
> >>>>>>
> http://www.bioconductor.org/packages/release/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
> >>>>>> For navigating longer documents numbered tables of contents are an
> >>>>>> essential feature to me, which I believe wasn't available in
> earlier R
> >>>>>> markdown versions or sometimes they showed up in unacceptable places
> >>>>>> like before the title of a document.
> >>>>>>
> >>>>>> A prescribed solution to get rid of these bullets from here
> >>>>>>
> >>>>>>
> http://stackoverflow.com/questions/28138456/rmarkdown-with-knitr-to-html-how-to-hide-bullets-in-toc-table-of-contents
> >>>>>> didn't work for me.
> >>>>>>
> >>>>>> Also, it would be nice to be able to generate the exact same
> vignette
> >>>>>> style in Bioc release and development, but it seems others have
> >>>>>> difficulties with this too, probably due to version differences of R
> >>>>>> markdown as seen here:
> >>>>>>
> >>>>>>
> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocStyle/inst/doc/HtmlStyle.html
> >>>>>
> >>>>>
> >>>>>>
> >>>>>> Thanks for making BiocStyle and R markdown available. I really enjoy
> >>>>>> using them. The resulting HTML pages look professionally designed
> and
> >>>>>> are highly functional while allowing us to focus on generating
> content
> >>>>>> in a consistent format rather than getting lost in formatting
> issues.
> >>>>>>
> >>>>>> Thomas
> >>>>>>
> >>>>>>        _______________________________________________
> >>>>>>
> >>>>>        Bioc-devel at r-project.org mailing list
> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>>
> >>>>>
> >>
>
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