[Bioc-devel] Package reference manuals in html
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Fri Dec 23 18:52:43 CET 2016
Seems to be a good start.
But I don't understand why NEWS.md is ok and NEWS.Rd is ignored, given than
NEWS.md is not (I think) compatible and NEWS.Rd is.
Best,
Kasper
On Fri, Dec 23, 2016 at 12:24 PM, Robert M. Flight <rflight79 at gmail.com>
wrote:
> Yes, this seems like a time where using a non-standard site directory on
> Github is useful, or as Sean said, using a separate branch to serve the
> html content.
>
> -Robert
>
> On Fri, Dec 23, 2016 at 12:19 PM Sean Davis <seandavi at gmail.com> wrote:
>
> > Github allows you to set the branch for the docs directory if I recall.
> > Perhaps a separate branch with a docs directory (not master) is a viable
> > way to go?
> >
> > Sean
> >
> > > On Dec 23, 2016, at 12:16 PM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
> > >
> > >
> > > There's actually another side-effect for Bioconductor. The package
> > > website is (by default) generated in the package's ./docs
> > > directory. This is very handy, as it can be set directly on Github as a
> > > Github page and becomes available as https://username.github.io/
> pkgname.
> > >
> > > This also means that the docs directory (which is about 5.5M for
> > > MSnbase) ends up on hedgehog. It is easy for it not to be part of the
> > > package build artefact using .Rbuildignore, but I am not sure how to
> > > easily push it to github but not hedgehog when using git-svn.
> > >
> > > Laurent
> > >
> > > On 23 December 2016 16:36, Laurent Gatto wrote:
> > >
> > >> Dear all,
> > >>
> > >> I'm following up re my online references suggestion with my recent
> > >> experience with Hadley's pkgdown package
> > >>
> > >> https://github.com/hadley/pkgdown
> > >>
> > >> It doesn't address the cross-package issue (which is a difficult one
> > >> anyway), but does pretty much everything else (with some caveats
> though,
> > >> see below).
> > >>
> > >> Here are 2 examples
> > >>
> > >> - MSnbase: http://lgatto.github.io/MSnbase/
> > >> - hpar: http://lgatto.github.io/hpar/
> > >>
> > >> It uses the REAMDE file as index page, creates html documents for all
> Rd
> > >> files in man, an article tab for vignettes (but see below) and a News
> > >> tab (but see below)
> > >>
> > >> The biggest caveats is that only Rmd vignettes are taken into account;
> > >> Rnw are completely ignored (they don't show up at all in the Articles
> > >> tab). This is not going to be tackled by the developer [1].
> > >>
> > >> [1] https://github.com/hadley/pkgdown/issues/220
> > >>
> > >> I had a quick look at the code and patching pkgdown (and probably
> > >> rmarkdown) to build Rnw/pdf vignettes would take too much time I could
> > >> devote at the moment. I would be satisfied if the Rnw were not build
> but
> > >> at least there were links in the Articles tab pointing to the
> vignettes
> > >> Bioconductor landing pages. On the other hand, I am migrating to
> > >> BiocStyle's html_document2 with the nice floating table of contents...
> > >>
> > >> Regarding the News tab, only NEWS.md (markdown format) are considered;
> > >> NEWS in Rd are ignored too.
> > >>
> > >> Hope this helps.
> > >>
> > >> Best wishes,
> > >>
> > >> Laurent
> > >>
> > >> On 16 March 2016 23:33, Andrzej Oleś wrote:
> > >>
> > >>> Hi all,
> > >>>
> > >>> I had a discussion earlier today with Martin and Dan on providing
> > >>> online man pages for Bioconductor packages. As we dived into
> > >>> implementation details, it turned out that this idea is a little bit
> > >>> more complex and resource-intensive than originally anticipated.
> > >>>
> > >>> The main problem in generating man pages in a repository-wide fashion
> > >>> seems to be the cross-linking of packages. Briefly, in order to
> > >>> generate the links, apparently one needs to generate the html pages
> in
> > >>> an R installation which is aware of the other packages. For example,
> > >>> the Rd macro \linkS4class{ClassName} takes as argument only the class
> > >>> name, and the corresponding package containing the class definition
> is
> > >>> "automagically" resolved by R. I'm not sure how this could be done
> > >>> manually, on a per-package basis. So by the end of the day, in order
> to
> > >>> generate static man pages, we would need to maintain a complete BioC
> > >>> repo installation, possibly on a system with the
> --enable-prebuilt-html
> > >>> configure option. Unfortunately, it seems unfeasible to exploit the
> > >>> build servers for this, as this would significantly increase the
> > >>> computational burden. This is because currently only around 2/5 of
> all
> > >>> software and data packages are actually being installed by the build
> > >>> system. The rest which does not have any reverse dependencies is
> > >>> skipped. Installing the remaining 3/5 of packages on a regular basis,
> > >>> not to mention the heavy annotation packages, is a little bit of an
> > >>> overkill. So piggy-backing on the existing infrastructure doesn't
> seem
> > >>> realistic.
> > >>>
> > >>> On top of this, even if we would have access to a machine with a
> > >>> complete, up-to-date BioC installation (maybe by just updating the
> > >>> packages after the repo gets rebuild rather than re-installing them
> > >>> each time from scratch), it remains an open question how "external"
> > >>> links to, let's say, CRAN packages, or even base R packages, should
> be
> > >>> handled.
> > >>>
> > >>> A lightweight and easy to implement alternative for those willing to
> > >>> share self-hosted documentation of their packages, could be to
> provide
> > >>> in the package DESCRIPTION file a "Documentation" field containing a
> > >>> link to external resource, which would then appear on the package
> > >>> landing page next to the vignettes and pdf manual. The obvious
> > >>> downsides of this solution are: 1. no package cross-links, and 2. the
> > >>> burden of keeping the documentation in sync with the package version
> on
> > >>> BioC would be in maintainer's hands...
> > >>>
> > >>> I will try to contact the authors of rdocumentation.org - maybe they
> > >>> have some useful comments or even code which they would be willing to
> > >>> share. In any case, it would be good to know what their experience is
> > >>> and why did they stop maintaining their service. Maybe the BioC
> > >>> community could jump in and help them to resolve the bottlenecks and
> > >>> keep the website up to date.
> > >>>
> > >>> Cheers,
> > >>> Andrzej
> > >>>
> > >>>
> > >>> On Tue, Mar 8, 2016 at 4:36 PM, Andrzej Oleś <andrzej.oles at gmail.com
> >
> > >>> wrote:
> > >>>
> > >>> Hi Martin,
> > >>>
> > >>> thank you for your suggestions - I would be happy to contribute to
> > >>> this! I could help with developing the scripts for generating man
> > >>> pages, and integrating them with the website layout.
> > >>>
> > >>> As for rendering the man pages, I suggest that we try a similar
> > >>> approach to the one used by knitr::knit_rd() rather than plain
> > >>> tools::Rd2HTML(). It has the advantage that the examples are
> > >>> actually run, and the results, e.g. plots, are included in the
> > >>> output documents. I hope you can appreciate the added value by
> > >>> comparing the following man page rendered using tools::Rd2HTML()
> > >>> and knitr::knit_rd(), respectively.
> > >>> http://www.huber.embl.de/users/aoles/man/Image.html
> > >>> http://www.huber.embl.de/users/aoles/man/Image-knitr.html
> > >>> Regarding the additional dependencies: we kind of already rely on
> > >>> knitr when compiling vignettes, so this this shouldn't add much to
> > >>> the maintenance burden.
> > >>>
> > >>> Cheers,
> > >>> Andrzej
> > >>>
> > >>> On Fri, Mar 4, 2016 at 2:20 PM, Morgan, Martin <
> > >>> Martin.Morgan at roswellpark.org> wrote:
> > >>>
> > >>> One thing about accessing the html versions locally (e.g., via
> > >>> ? with options(help_type="html")] or help.start() or Rstudio)
> > >>> is that you get the version relevant to your R / Bioconductor,
> > >>> rather than whatever is at the top of google; I guess the same
> > >>> applies to the pdf versions, and the reason that there isn't
> > >>> more current confusion is because the online pdf versions are
> > >>> not as useful as the off-line help system.
> > >>>
> > >>> I think Laurent was interested in an integration of help pages
> > >>> across packages (which is the appeal of rdocumentation.org?),
> > >>> not just rendering the help pages in html rather than pdf? An
> > >>> integration of help pages would definitely be a big job with
> > >>> substantial development and maintenance; we will not be
> > >>> undertaking this ourselves.
> > >>>
> > >>> For the more limited case of adding a (directory of) html
> files
> > >>> for the the manual, it's not impossible that we could find the
> > >>> resources to do this in the next 6 months.
> > >>>
> > >>> One intermediate and helpful step for those willing to help
> > >>> would be to develop the code to process help pages into a
> style
> > >>> consistent with the bioconductor web site. One place where
> this
> > >>> could be implemented would be the BiocStyle package (https://
> > >>> github.com/Bioconductor-mirror/BiocStyle but hmm, seems like
> > >>> there's a slightly out of sync version at https://github.com/
> > >>> Bioconductor/BiocStyle that would be more convenient...).
> > >>> Perhaps this really means only developing a css style sheet
> and
> > >>> R's tools::Rd2HTML() (I'm very reluctant to introduce
> > >>> dependencies into the build system, and am very conservative
> > >>> about inclusion of fancy features in the html -- these become
> > >>> significant maintenance burdens moving forward).
> > >>>
> > >>> The web site is generated by https://github.com/Bioconductor/
> > >>> bioconductor.org, with the style sheet at https://github.com/
> > >>> Bioconductor/bioconductor.org/blob/master/assets/style/
> > >>> bioconductor.css. The package landing pages are templated
> using
> > >>> layouts/_bioc_views_package_detail.html. The idea would be to
> > >>> end up with layouts/_bioc_man_index.html and
> > >>> _bioc_man_body.html that wrapped output from BiocStyle in the
> > >>> overall bioc page.
> > >>>
> > >>> The implementation suggestions above are just a sketch and
> > >>> could be quite misguided. If there's interest then probably we
> > >>> should set up a hangout to discuss in a little more detail.
> > >>>
> > >>> Martin
> > >>>
> > >>> ________________________________________
> > >>> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf
> > >>> of Hartley, Stephen (NIH/NHGRI) [F] <stephen.hartley at nih.gov>
> > >>> Sent: Wednesday, March 2, 2016 11:46 AM
> > >>> To: Laurent Gatto; bioc-devel
> > >>> Subject: Re: [Bioc-devel] Package reference manuals in html
> > >>>
> > >>> I'd like to second this. Currently Bioconductor hosts the pdf
> > >>> reference manuals, but those are often sub-ideal. The page
> > >>> breaks make it harder to read, the fixed width basically makes
> > >>> it either too small or too big depending on your display, you
> > >>> can't navigate cross-package links, and in general using
> > >>> paper-formatted software documentation is just poor form.
> > >>>
> > >>> Yihui, the creator of knitr, has a blog post where he shows
> how
> > >>> to do this. There are a lot of ways to do this, and it's
> > >>> generally pretty straightforward.
> > >>> http://yihui.name/en/2012/10/build-static-html-help/
> > >>>
> > >>> You can also use a function in knitr, knit_rd(), which builds
> > >>> the examples as well and inserts the output right onto the
> > >>> page. That's what I used to make the docs for QoRTs (http://
> > >>> hartleys.github.io/QoRTs/Rhtml/index.html) and JunctionSeq (
> > >>> http://hartleys.github.io/JunctionSeq/Rhtml/index.html).
> > >>>
> > >>> Or you can use the staticdocs package, which does the same
> > >>> basic thing but prettier (see ggplot2's docs: http://
> > >>> docs.ggplot2.org/current/)
> > >>>
> > >>> The nuclear option, of course, is to do what CRAN does and
> > >>> rebuild R on (one of) the servers using the
> > >>> --enable-prebuilt-html configure option. That might affect
> > >>> other things, though, and might not be ideal.
> > >>>
> > >>> Does any of this seem like a viable option for Bioconductor? I
> > >>> think it could be an incredibly valuable resource for the
> > >>> community. Are there any technical issues that haven't been
> > >>> considered in the above?
> > >>>
> > >>> Regards,
> > >>> Steve Hartley
> > >>>
> > >>> -----Original Message-----
> > >>> From: Laurent Gatto [mailto:lg390 at cam.ac.uk]
> > >>> Sent: Tuesday, March 01, 2016 6:42 AM
> > >>> To: bioc-devel
> > >>> Subject: [Bioc-devel] Package reference manuals in html
> > >>>
> > >>>
> > >>> Dear all,
> > >>>
> > >>> I find the http://www.rdocumentation.org/ site very useful to
> > >>> refer to nicely formatted online man pages individually.
> > >>> Unfortunately, this resource is terribly outdated and not
> > >>> maintained anymore.
> > >>>
> > >>> I was wondering if Bioconductor had any interest in serving an
> > >>> html version of individual reference manuals in addition to
> the
> > >>> pdf that are already available on the package landing pages.
> > >>>
> > >>> Is there anything I or any other members of the community
> could
> > >>> help with to get this up and running?
> > >>>
> > >>> Best wishes,
> > >>>
> > >>> Laurent
> > >>>
> > >>> _______________________________________________
> > >>> Bioc-devel at r-project.org mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>
> > >>> _______________________________________________
> > >>> Bioc-devel at r-project.org mailing list
> > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>
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> > >
> > > --
> > > Laurent Gatto | @lgatt0
> > > http://cpu.sysbiol.cam.ac.uk/
> > > http://lgatto.github.io/
> > >
> > > _______________________________________________
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> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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