[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

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

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[Bioc-devel] BiocStyle and R markdown

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