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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: |
Mon, 22 Jun 2020 09:38:23 +0200 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) |
Hi Konrad,
Konrad Hinsen <konrad.hinsen@cnrs.fr> skribis:
> Konrad Hinsen <konrad.hinsen@cnrs.fr> writes:
>
>> Sounds fine. I am not much of a hackathon expert, so I don't propose
>> myself for organizing this, but I can make a preselection of suitable
>> submissions to the ReScience challenge (no proprietary software etc.)
>> with comments about the specific challenges.
>
> Here is my list of candidate projects. There are three general
> categories:
>
> 1) Package old software that is of sufficiently wide interest
> (i.e. add to guix-past)
> - g77 (used in https://github.com/ReScience/submissions/issues/41)
> - SciPy ecosystem from 2007 (at least Python, NumPy, matplotlib)
> (used in https://github.com/ReScience/submissions/issues/14)
Makes sense.
> 2) Package highly specialized research software
>
> These programs are too specialized for the Guix distribution, so
> "packaging" means writing a guix.scm. The long-term goal is to learn how
> to make this kind of packaging easier, to the point that scientists are
> willing to do it themselves. This means it must be doable with minimal
> Guile competence, ideally by modifying templates provided by experts.
>
> I have picked four cases, listed by increasing level of difficulty:
>
> a) https://github.com/ReScience/submissions/issues/42
>
> A rather standard Fortran code, with only the popular BLAS and LAPACK
> libraries as dependencies. Instructions are given for manual
> compilation.
>
> b) https://github.com/ReScience/submissions/issues/36
>
> A medium-sized Fortran program with a Makefile.
>
> c) https://github.com/ReScience/submissions/issues/41
>
> A mixed C-Fortran code from 2008, built with autotools. Looks simple,
> but the author did not succeed in compiling it on a modern machine
> because it requires the abandoned g77 compiler.
>
> d) https://github.com/ReScience/submissions/issues/20
>
> A medium-sized Fortran library with a Makefile. Tricky because it adds
> its own wrappers around the Fortran compiler.
That’s going to be less fun but I agree it’s important to do something
for this use case.
> 3) Fully automated reproductions of results (typically figures)
>
> There is only one case (other than Ludo's which already uses Guix):
>
> - https://github.com/ReScience/submissions/issues/39
>
> A fully reproducible reproduction of two Open Source simulation software
> packages (C/C++), based on Debian and its debuerreotype system. The
> challenge is to demonstrate how Guix can do it better!
Heh, nice! <https://github.com/debuerreotype/debuerreotype> is
interesting.
Thanks for sharing this overview, I guess we have enough on our plate now!
:-)
Ludo’.
- Re: “Reproducible research articles, from source code to PDF”, (continued)
- Re: “Reproducible research articles, from source code to PDF”, Ludovic Courtès, 2020/06/18
- Re: “Reproducible research articles, from source code to PDF”, Konrad Hinsen, 2020/06/18
- Re: “Reproducible research articles, from source code to PDF”, Ludovic Courtès, 2020/06/18
- Re: “Reproducible research articles, from source code to PDF”, zimoun, 2020/06/18
- Re: “Reproducible research articles, from source code to PDF”, Ludovic Courtès, 2020/06/18
- Re: “Reproducible research articles, from source code to PDF”, Konrad Hinsen, 2020/06/18
- Re: “Reproducible research articles, from source code to PDF”, Ludovic Courtès, 2020/06/19
- Re: “Reproducible research articles, from source code to PDF”, zimoun, 2020/06/19
- Re: “Reproducible research articles, from source code to PDF”, Ludovic Courtès, 2020/06/19
- Re: “Reproducible research articles, from source code to PDF”, Konrad Hinsen, 2020/06/21
- Re: “Reproducible research articles, from source code to PDF”,
Ludovic Courtès <=
- Re: “Reproducible research articles, from source code to PDF”, Pjotr Prins, 2020/06/18
Re: “Reproducible research articles, from source code to PDF”, Maxim Cournoyer, 2020/06/17