[Bioc-devel] Package reference manuals in html
They are "orphan" branches, so they don't follow the parent. This was the original protocol for creating project pages on github for the longest time, you can see an example in the documentation here: https://help.github.com/articles/creating-project-pages-using-the-command-line/ They are a pain in the butt to work with, for sure. When I've done deploying vignettes from travis, my solution was to create a separate repo entirely, and then push from the master to gh-pages, as shown in this shell script: https://github.com/rmflight/categoryCompare/blob/master/.push_gh_pages.sh I'm sure the same could be done using pkgdown. If you don't like the idea of overwriting, Steph Locke has a guide to keeping up with changes, but still autodeploying the docs https://itsalocke.com/auto-deploying-documentation-better-change-tracking-artefacts/ HTH Robert
On Fri, Dec 23, 2016 at 1:14 PM Laurent Gatto <lg390 at cam.ac.uk> wrote:
Dear Sean and Robert, On 23 December 2016 17:24, Robert M. Flight 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.
It's not clear to me how a separate branch is the solution. In git-svn, devel, release_3_4, ... are just that, different branches. How would you set a gh-pages branch that contains a single dir so that it doesn't conflict with master? If I could set branch-specific directives in my .gitignore file, then I would set this up for the Bioc branches. This seems to suggest it is possible, but I haven't tried yet http://stackoverflow.com/questions/1836742/using-git-how-do-i-ignore-a-file-in-one-branch-but-have-it-committed-in-another Would it be possible to set something on the svn side to ignore/delete the docs dir automatically, independently of what git does? Laurent
-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 Ole? 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 Ole? <
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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