[Bioc-devel] jupyter notebooks as vignettes?

[Gabe Becker]

Martin,

I have a package on Github (DynDocModel) that was part of my thesis which
will happily process jupyter notebooks (they were called IPython Notebooks
at the time).  It (IIRC) supports tangling, weaving, restructuring, etc.

I can look at productionizing it if that is something Bioc thinks is
important. Right now it is tied in pretty closely with my caching mechanism
(another part of my thesis), and supports non-linear notebooks (the third
part), but those features are probably "lower priority" for what you want.

~G

On Wed, May 20, 2015 at 10:15 AM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

> I'm forwarding a couple of messages from the support site.
>
> I'd appreciate some discussion.
>
> It seems like jupyter notebooks are becoming increasingly plausible as a
> possible vignette format, and I was wondering whether there is any
> real-world experience with these, including their pros and cons as
> vignettes. For instance...
>
> Developer / build system
>
> - Presumably these notebooks need to be run as part of the package check
> -- no sense distributed non-functional notebooks. Are there facilities for
> this, along the lines of a traditional vignette that builds and potentially
> generates errors during R and / or document processing?
>
> - Are notebooks actually mature enough that, e.g., their format will not
> change dramatically?
>
> End-user
>
> - I guess most end users will get static, evaluated versions of the
> notebooks, unless they install python & friends. Is that right?
>
> - Can the user easily obtain the equivalent of a Stangle'd vignette, i.e.,
> a runnable R script?
>
> - If a typical user only has access to a static version of the notebook,
> then what have we gained relative to traditional vignettes?
>
> -------- Forwarded Message --------
> Subject:        [bioc] A: BiocCheck: REQUIRED: vignette sources in
> vignettes/
> directory (for custom vignet
> Date:   Wed, 20 May 2015 16:32:24 -0000
> From:   Dan Tenenbaum [bioc] <noreply at bioconductor.org>
> Reply-To:       reply+9665d4a8+code at bioconductor.org
> To:     mtmorgan at fhcrc.org
>
>
>
> Activity on a post you are following on support.bioconductor.org
> <https://support.bioconductor.org>
>
> User Dan Tenenbaum <https://support.bioconductor.org/u/4256/> wrote
> Answer:
> BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom
> vignettebuilder) <https://support.bioconductor.org/p/67884/#67885>:
>
> BTW, questions about package development and submission should go to the
> bioc-devel mailing list <http://bioconductor.org/help/support/#bioc-devel
> >.
>
> We don't yet have a policy about .ipynb vignettes and we'd have to make
> sure the
> build system is capable of building them. However, I would ignore the
> error for
> now and you can discuss it with your reviewer when you submit the package.
>
>
> --------------------------------------------------------------------------------
>
> -------- Forwarded Message --------
> Subject:        [bioc] BiocCheck: REQUIRED: vignette sources in vignettes/
> directory
> (for custom vignettebuilder)
> Date:   Wed, 20 May 2015 16:29:49 -0000
> From:   flying-sheep [bioc] <noreply at bioconductor.org>
> Reply-To:       reply+c01911bc+code at bioconductor.org
> To:     mtmorgan at fhcrc.org
>
>
>
> Activity on a post you are following on support.bioconductor.org
> <https://support.bioconductor.org>
>
> User flying-sheep <https://support.bioconductor.org/u/7779/> wrote
> Question:
> BiocCheck: REQUIRED: vignette sources in vignettes/ directory (for custom
> vignettebuilder) <https://support.bioconductor.org/p/67884/>:
>
> I’m using a .ipynb notebook as source for my Vignette, so I created a
> Vignette
> engine inside my package to build it.
>
> That one registers a the necessary extensions, and R CMD build obediently
> creates a vignette from the .ipynb file.
>
> Yet R CMD BiocCheck still says `REQUIRED: vignette sources in vignettes/
> directory`. should I ignore that when submitting my package, or will the
> bioconductor people have to fix that check beforehand?
>
>
> --------------------------------------------------------------------------------
>
> You may reply via email or visit https://support.bioconductor.org/p/67884/
>
> _______________________________________________
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>



-- 
Gabriel Becker, Ph.D
Computational Biologist
Genentech Research

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