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

[zimoun <zimon.toutoune@gmail.com>]

Hi Ludo,

On Tue, 16 Jun 2020 at 14:25, Ludovic Courtès <ludovic.courtes@inria.fr> wrote:
> Hello!
>
> This new post introduces the work I did to have a fully reproducible
> replication (!) of a 13-year old article, using Guix to express the
> whole pipeline:
>
>   https://hpc.guix.info/blog/2020/06/reproducible-research-articles-from-source-code-to-pdf/

Really cool!
IMHO, it even deserves an entry to guix.gnu.org/blog. :-)

Aside, I have learnt the interesting project maneage.org.

As always, it gives me some food for thought.

For example, they are future bridges to think: connect the Guix archive
somehow with zenodo DOI and/or Software Heritage identifier.

When I read this comment in the review [1]:

        As  a final  note,  I  wonder if,  and  how  much, the  author's
        approach to reproducible computation/automated report generation
        is  feasible  for  the  average scientist,  in  particular  when
        compared to tools with a smoother learning curve, such as Docker
        containers,  Jupyter notebooks,  R  Markdown  documents and  the
        like. A brief  analysis of this topic with  a clear presentation
        of the  advantages of  the author's  approach in  the Discussion
        session would be worthwhile.

and then the Konrad's answer [2], I asked myself what pieces are
missing.  And what could be the articulation of "guix pack -f docker",
Guix-Jupyter or other notebooks (RMarkdown, Org)?  And what could be a
practical workflow? (Keeping in mind that the average scientist is not a
Linux guru but often run MacOS or Windows.)

1: https://github.com/ReScience/submissions/issues/32#issuecomment-633739558
2: https://github.com/ReScience/submissions/issues/32#issuecomment-634149030


Half-related to the blog post.  You mention elsewhere this baby channel
[3], maybe it could be worth to link it somewhere in the blog post.
Moreover, totally unrelated, I feel it lacks a list of "Scientific"
channels, as [4] or [5], maybe on hpc.guix.info

3: https://gitlab.inria.fr/guix-hpc/guix-past
4: https://github.com/BIMSBbioinfo/guix-bimsb
5: https://gitlab.inria.fr/guix-hpc/guix-hpc


Thanks,
simon