Thanks Jim, this prompted me to read the documentation one more time and I understand it better now. Since I have svn write permissions to BiocStyle I can do what you're suggesting.
However, it makes sense to have one location on Github with which to track issues and accept incoming pull requests - at least in my thinking. Of course, I could have a fork where I have the issues I am interested in and will accept the pull requests that I am ready to support and someone else can have a different fork. But it seems to me that we may be loosing track of a central list of issues etc. out by doing so. Or is the thinking that the read-only mirrors should contain issues and then fixes go through individual people. Here I am especially thinking about the packages maintained by core. What is your thinking on this situation? I could see myself making pull request to SummarizedExperiment in the next 6 months for example, or documentation clarifications to all packages? For my own packages, like minfi, it is pretty clear (I hope, from Description and the fact that I maintain) which Github repos is the one true hub for minfi development. Best, Kasper On Thu, Jul 30, 2015 at 9:45 AM, Jim Hester <james.f.hes...@gmail.com> wrote: > 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
