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/
[Bioc-devel] jupyter notebooks as vignettes?
3 messages · Martin Morgan, Gabriel Becker, Michael Lawrence
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 [[alternative HTML version deleted]]
I would guess a potential major gain for the users would be the ability to interact with the vignette on the Bioc site, where notebooks would run inside Docker containers or something. Beyond software demonstration, this would be very useful for reproducible research. 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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