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

[Konrad Hinsen <konrad.hinsen@cnrs.fr>]

Hi Ludo and Simon,

> 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.

> 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.

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.

Some ideas: Simple deployment of a VM running Guix System on a major
cloud provider would be nice to have. Or a service like mybinder.org,
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.

Cheers,
  Konrad
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: konrad DOT hinsen AT cnrs DOT fr
http://dirac.cnrs-orleans.fr/~hinsen/
ORCID: https://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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