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

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

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)

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.

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!

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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