[Bioc-devel] Package reference manuals in html
Sean Davis
seandavi at gmail.com
Fri Dec 23 18:19:03 CET 2016
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
>>>
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>
>
> --
> Laurent Gatto | @lgatt0
> http://cpu.sysbiol.cam.ac.uk/
> http://lgatto.github.io/
>
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