[Bioc-devel] BiocStyle and R markdown

[Kasper Daniel Hansen]

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.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
>> >>>>>>
>> >>>>>
>> >>
>>
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>>
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