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Re: “Reproducible research articles, from source code to PDF”

From: Ludovic Courtès
Subject: Re: “Reproducible research articles, from source code to PDF”
Date: Thu, 18 Jun 2020 13:42:14 +0200
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux)


Konrad Hinsen <> skribis:

>> I don’t like the phrase “average scientist”, and we’re talking about
>> people with a PhD who definitely know how to learn.
> I didn't take that phrase as a reference to ability, but to prior
> knowledge. I am pretty sure that anyone who uses Python can also learn
> to use Guile, but a computer scientist having experience with ten
> languages will have less effort to do so than an archaeologist or a
> wetlab biologist who has never used anything else but Python.

Yes, I understand and agree with this assessment: making the tools
usable without being an expert will be crucial.

That said, these same people got used to Dockerfiles, CONDA, pip,
Jupyter, CWL, Python, Bash, and whatnot.  I think that stating that all
this, taken together, has a “smooth learning curve”, is inaccurate.

>> Apart from that, I agree with the comments above: putting it in the
>> hands of scientists will be the real challenge.  I think providing
>> modules and ready-to-use “templates” for people who use R+RMarkdown, or
>> LaTeX, or Jupyter, etc. is a necessary step.
> I'd start somewhat differently: generate diverse use case examples.  The
> contributions to the ReScience reproducibility challenge could be a nice
> starting point: go through them, one by one, and try to re-implement the
> authors' various approaches with Guix.  Then, in a second step, try to
> identify additional tooling support in Guix that would make the recipes
> simpler to implement. That might well lead to the development of ready
> to use templates, but I prefer starting from a use case analysis to see
> what is needed in real life.

Yes, sounds like a good plan!

> Another obstacle to adoption is the difficulty of deployment. Right now,
> if I use Guix to make my work reproducible, I require my readers to
> install Guix on their computers, which is a lot of work for Linux users
> and a major headache for Windows/macOS users. We really need to reduce
> that barrier to deployment.

On Debian and derivatives, it should be possible to run “apt-get install
guix” soonish, which should help.

For Windows and macOS, I don’t know (I’m personally less interested in
that but I agree it would be useful to improve the situation there.)

> Some ideas: Simple deployment of a VM running Guix System on a major
> cloud provider would be nice to have. Or a service like,
> but based on Guix rather than Docker. Or, for local execution, a Docker
> image containing Guix plus some tooling to do the equivalent of "guix
> time-machine –commit=xxx – build -f guix.scm" plus copying the contents
> of the generated package into the user's directory.

Yes, we should discuss individual solutions along these lines.


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