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 < kasperdanielhan...@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.gi...@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 < > > kasperdanielhan...@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.gi...@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 < > >>> kasperdanielhan...@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 < > >>>> kasperdanielhan...@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.gi...@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@r-project.org mailing list > >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >>>>>> > >>>>> > >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
