[Bioc-devel] BiocStyle for styling Sweave (and other?) vignettes

Hi,

this package is a nice idea indeed. For what is worth, I developed a similar
feature within the pkgmaker package (on CRAN), especially to enable easy
CRAN/Bioc package referencing/linking, with the inclusion of an extra bib file
generated on the fly from \cite-like commands (although the parsing is currently
done externally, before running knitr). But this could be tuned using a similar
trick as Carl's knitrcitation package to add citations within each call to a
\cite command.
The package's REFERENCE.bib file is also included and available for citations.

It works pretty much like BioCStyle with the injection of a raw latex preamble
that defines extra link, citation commands.
I use it in all my packages' vignettes (e.g.
https://github.com/renozao/NMF/blob/master/pkg/vignettes/NMF-vignette.Rnw):

% add preamble from pkgmaker
<<pkgmaker_preamble, echo=FALSE, results='asis'>>=
pkgmaker::latex_preamble()

@

% REFERENCES
\usepackage[citestyle=authoryear-icomp
, doi=true
, url=true

, maxnames=1
, maxbibnames=15
, backref=true
, backend=bibtex]{biblatex}
\AtEveryCitekey{\clearfield{url}}

<<bibliofile, echo=FALSE, results='asis'>>=
pkgmaker::latex_bibliography('NMF')
@
\bibliography{Rpackages}


This proved to be very useful to me and I believe the idea can be push quite far
in standardising vignettes.
Other comments:

1) It would be nice if the package was a CRAN package though so that it can
benefit to all R package developers, without depending on having Bioc
repositories enabled, (rename? :)), with an option to enable a fully "branded"
Bioconductor style (e.g. Mention to "This package is par to Bioconductor ...").
Or alternatively, still name it BiocStyle, but with an option to disable the
"branding", but give access to all useful features (refernecs, links, etc...).

2) One should avoid to lock the user into too restrictive coding pattern,
especially the style and commands should be compatible with knitr, which makes a
really good job highlighting, caching, , multiple figures inclusion, etc...

3) Support to non Latex vignettes would be good, Rmd and slideshows.

4) Styling could be made even more transparent if vignette engines were allowed
to some config files that lies in the package vignettes/ subdirectory, which
enables choosing a style without modifying the vignette sources. I believe this
would be easily implementable for knitr vignettes (just need to log an issue to
Yihui, maybe this even already exists...). For example this would allow
Bioconductor building farm to build packages with a special styling on the fly:
the developers would not even have to change their code!!

This is all exciting :D

Bests,
Renaud