From: "Ludovic Courtès" <ludovic.courtes@inria.fr>
To: Konrad Hinsen <konrad.hinsen@cnrs.fr>
Cc: guix-devel <guix-devel@gnu.org>, guix-hpc@gnu.org
Subject: Re: “Reproducible research articles, from source code to PDF”
Date: Thu, 18 Jun 2020 13:42:14 +0200 [thread overview]
Message-ID: <87r1ucmwh5.fsf@inria.fr> (raw)
In-Reply-To: <m1a710g1ea.fsf@fastmail.net> (Konrad Hinsen's message of "Thu, 18 Jun 2020 11:37:49 +0200")
Hi,
Konrad Hinsen <konrad.hinsen@cnrs.fr> 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 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.
Yes, we should discuss individual solutions along these lines.
Thanks,
Ludo’.
next prev parent reply other threads:[~2020-06-18 11:43 UTC|newest]
Thread overview: 15+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-06-16 12:25 “Reproducible research articles, from source code to PDF” Ludovic Courtès
2020-06-17 7:06 ` zimoun
2020-06-18 7:31 ` Ludovic Courtès
2020-06-18 9:37 ` Konrad Hinsen
2020-06-18 11:42 ` Ludovic Courtès [this message]
2020-06-18 12:56 ` zimoun
2020-06-18 13:05 ` Ludovic Courtès
2020-06-18 16:28 ` Konrad Hinsen
2020-06-19 12:04 ` Ludovic Courtès
2020-06-19 12:14 ` zimoun
2020-06-19 13:21 ` Ludovic Courtès
2020-06-21 14:50 ` Konrad Hinsen
2020-06-22 7:38 ` Ludovic Courtès
2020-06-18 16:39 ` Pjotr Prins
2020-06-18 2:33 ` Maxim Cournoyer
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