[Bioc-devel] BiocStyle and R markdown

Dan Tenenbaum dtenenba at fredhutch.org
Thu Jul 30 20:36:04 CEST 2015



----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, July 30, 2015 10:05:05 AM
> Subject: Re: [Bioc-devel] BiocStyle and R markdown
> 
> 
> 
> ----- Original Message -----
> > From: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> > To: "Jim Hester" <james.f.hester at gmail.com>
> > Cc: bioc-devel at r-project.org
> > Sent: Thursday, July 30, 2015 7:01:46 AM
> > Subject: Re: [Bioc-devel] BiocStyle and R markdown
> > 
> > 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.
> > 
> 
> 
> There is a read-only github mirror for every software package in
> Bioconductor. So it does not make sense to allow pull requests and
> issues on those mirrors because the package maintainer may not even
> be aware of the repository and in any case does not have the
> permissions to accept pull requests on it or to mark issues as
> resolved.
> 
> Therefore these repos do not have issues enabled, and pull requests
> will be automatically rejected by a bot.
> 
> Users can find your canonical git repos if you follow the
> instructions at
> http://bioconductor.org/developers/how-to/git-mirrors/#how-do-i-let-users-know-i-am-using-github-for-development-and-contributions
> 

After some discussion, I've forked the read-only mirror to

https://github.com/Bioconductor/BiocStyle

This can be considered the canonical github repos for BiocStyle, where issues and pull requests should be submitted.

The URL and BugReports fields in the DESCRIPTION file have been updated accordingly.

Thanks,
Dan



> Dan
> 
> 
> > Best,
> > Kasper
> > 
> > On Thu, Jul 30, 2015 at 9:45 AM, Jim Hester
> > <james.f.hester at 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 <
> > > 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
> > >> >>>>>>
> > >> >>>>>
> > >> >>
> > >>
> > >>         [[alternative HTML version deleted]]
> > >>
> > >> _______________________________________________
> > >> Bioc-devel at r-project.org mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >
> > >
> > 
> > 	[[alternative HTML version deleted]]
> > 
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