From: Brett Viren <bv@bnl.gov>
To: Ken Mankoff <mankoff@gmail.com>
Cc: 'grass-user grass-user' <grass-user@lists.osgeo.org>,
Org Mode <emacs-orgmode@gnu.org>
Subject: Re: Open Peer-Review Reproducible Publication with Org and GRASS
Date: Fri, 03 Jun 2016 10:57:55 -0400 [thread overview]
Message-ID: <ir4fusucob0.fsf@lycastus.phy.bnl.gov> (raw)
In-Reply-To: <m2lh2m4ap0.fsf@gmail.com> (Ken Mankoff's message of "Fri, 03 Jun 2016 10:19:07 -0400")
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Thanks for your example.
A few ideas:
- When you begin developing your paper, or sometime before submission,
make a break from your personal ~/.emacs.d/ environment and begin
processing the .org in an explicitly configured Emacs session. Submit
the needed, minimal, paper-specific Emacs setup as part of the
supplementary material.
- Bundle the document building into a shell script which calls Emacs so
that you can assure that personal ~/.emacs.d/ is excluded and only the
paper-specific Emacs setup is used. It also helps users to rebuild
the paper, especially if they may not yet be Emacs aficionados.
- Instead of multi-GB VM image, provide a few kB Dockerfile which can be
used to build a Linux container with base OS and all required
applications needed to run the Babel code blocks.
- The Dockerfile could go so far as to create a user account, get the
supplementary material from a repository or the publisher's web page,
unpack and run the shell script which calls Emacs to build the
document. If you go this far then in principle just this Dockerfile
is enough to reproduce the paper - but this will rely on some binaries
to remain available (Docker base OS images and OS packages).
The reliance on long-term availability of the Docker base OS image and
binary packages is problematic for long term automated reproducibility.
However, even after those bits disappear from the 'net the Dockerfile
serves as a concise and explicit recipe for future humans to follow.
-Brett.
Ken Mankoff <mankoff@gmail.com> writes:
> Hi Org and GRASS lists,
>
> I just wanted to let these two lists know that I've just posted a
> paper written in Org and using GRASS (text-mode) and Python for the
> analysis. My goal was to create not just an open access publication,
> but a fully reproducible publication. This is an early announcement,
> and the paper may not pass peer review.
>
> The Supplemental Material is the Org file with all the code to
> generate the document, beginning with downloading the 3rd party data
> that is input to our analysis, the GRASS code to perform the analysis,
> and the Python code to regenerate the figures.
>
> I don't think I did a great job on the reproducible part because I
> have a highly customized .emacs, etc. All the information necessary to
> replicate the work should be in the Supplemental Material, but it
> might not be easy to do so. Anyway, I think it is a step in the right
> direction.
>
> To make it easier to reproduce... including my emacs.org seems
> overkill. Including a Virtual Machine that contains everything,
> including my ~/.emacs.d/ and all the software and data seems like the
> right thing to do, but journals don't want to host a 20 GB VM with the
> publication.
>
> Thanks to people on these two lists who have developed the software and helped me use it.
>
> -k.
>
> http://www.the-cryosphere-discuss.net/tc-2016-113/
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next prev parent reply other threads:[~2016-06-03 14:57 UTC|newest]
Thread overview: 6+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-06-03 14:19 Open Peer-Review Reproducible Publication with Org and GRASS Ken Mankoff
2016-06-03 14:57 ` Brett Viren [this message]
2016-06-06 20:12 ` Daniele Pizzolli
2016-06-06 9:08 ` Christian Moe
2016-06-06 20:11 ` Daniele Pizzolli
2016-06-06 23:01 ` Samuel Wales
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