#Tag
@GuilloteauQ @hannes @Zimm_i48 @zacchiro @luj Amazing work.
Many of us have been repeating “Dockerfiles cannot yield reproducible images” for years, but a thorough literature review and experimental demonstration like this really hits the nail.
> "Our results show that
Docker does not guarantee reproducibility under any tested definition, nor is there a “silver bullet” set of rules for
writing Dockerfiles yielding reproducible images"
Nice paper from @luj @zacchiro @Zimm_i48 on the use of Docker and reproducibility [1]
Somewhat related to what we were trying to show at ACM REP'25 [2], but at different scales (in time and amount of dockerfiles).
The scientific community cannot say that it has not been warned of Docker's reproducibility pitfalls ! :)
[1] https://arxiv.org/pdf/2601.12811
[2] https://dl.acm.org/doi/10.1145/3736731.3746146
@GuilloteauQ @hannes @Zimm_i48 @zacchiro @luj Amazing work.
Many of us have been repeating “Dockerfiles cannot yield reproducible images” for years, but a thorough literature review and experimental demonstration like this really hits the nail.
This code supporting a refereed zoology paper uses #Guix + Guix-CRAN for #ReproducibleResearch 👇
https://forge.inrae.fr/mathieu.laparie/agrilusflight
(HT to @phsw!)
This code supporting a refereed zoology paper uses #Guix + Guix-CRAN for #ReproducibleResearch 👇
https://forge.inrae.fr/mathieu.laparie/agrilusflight
(HT to @phsw!)
☕ Café #Guix is en English today: long-time contributor Arun Isaac will talk about reproducible computations with Guix and #CWL
📅 today Tue. 25th, 1PM CEST
▶ https://meet.univ-grenoble-alpes.fr/b/cel-dyj-m93-arv
☕ Café #Guix is en English today: long-time contributor Arun Isaac will talk about reproducible computations with Guix and #CWL
📅 today Tue. 25th, 1PM CEST
▶ https://meet.univ-grenoble-alpes.fr/b/cel-dyj-m93-arv
• Paper published in 2009.
• Colleague needs release from 5 years ago.
• Python code and C bindings.
Guess what? 🤔
Open Source code isn’t enough! 😱
1. The 5 years old package needs dependencies.
2. These dependencies need options, incompatible with the current ones.
2. The 5 years old package needs specific CPython C API.
🥳 Colleague’s convinced! 🎉
📣 Package managers are one pillar of #OpenScience and #ReproducibleResearch!
And hopefully, it’s a fun challenge with #Guix. 😍
• Paper published in 2009.
• Colleague needs release from 5 years ago.
• Python code and C bindings.
Guess what? 🤔
Open Source code isn’t enough! 😱
1. The 5 years old package needs dependencies.
2. These dependencies need options, incompatible with the current ones.
2. The 5 years old package needs specific CPython C API.
🥳 Colleague’s convinced! 🎉
📣 Package managers are one pillar of #OpenScience and #ReproducibleResearch!
And hopefully, it’s a fun challenge with #Guix. 😍
Using Guix for Reproducible Research—a guide in 4 steps 👇
https://guix.gnu.org/cookbook/en/html_node/Reproducible-Research.html
Cc: @swheritage
Using Guix for Reproducible Research—a guide in 4 steps 👇
https://guix.gnu.org/cookbook/en/html_node/Reproducible-Research.html
Cc: @swheritage
In 2020, I reran computational experiments made in 2006 for my PhD, and packaged the whole analysis-to-paper-production pipeline with Guix:
https://gitlab.inria.fr/lcourtes-phd/edcc-2006-redone
https://dx.doi.org/10.5281/zenodo.3886739
A fellow #Guix hacker reran this Guixified pipeline days ago and it still works as intended.
That’s good news and something to celebrate in my view, as someone who knows well about the speed of the software bitrot process and the work it took to achieve this.
But still, that’s just 5 years. What’s a success for us in the field (5 years was a long time ago on the software time scale!) probably looks like a very small time frame to anyone outside.
But here we are. The promise of reproducible research can only be upheld if one can re-deploy software years
later.
People working in #ReproducibleResearch and #OpenScience should realize how bad the situation is, what solutions
exist, and what promises they can make.
In 2020, I reran computational experiments made in 2006 for my PhD, and packaged the whole analysis-to-paper-production pipeline with Guix:
https://gitlab.inria.fr/lcourtes-phd/edcc-2006-redone
https://dx.doi.org/10.5281/zenodo.3886739
A fellow #Guix hacker reran this Guixified pipeline days ago and it still works as intended.
In 2020, I reran computational experiments made in 2006 for my PhD, and packaged the whole analysis-to-paper-production pipeline with Guix:
https://gitlab.inria.fr/lcourtes-phd/edcc-2006-redone
https://dx.doi.org/10.5281/zenodo.3886739
A fellow #Guix hacker reran this Guixified pipeline days ago and it still works as intended.
New server, new #introduction:
👋 Hi! I'm Eric! I'm a scientific programmer & educator who writes mostly 
code. I currently work part time at #UniversityOfArizona where I help researchers by making R packages, #Shiny apps, automated data workflows, and training them on #ReproducibleResearch practices. I also mentor data scientists for @Posit Academy. I am #OpenToWork as a contractor if any of those skills sound useful to you.
My background is in plant chemical ecology and population ecology and for my PhD I studied #tea and did field work in China. I love tea (although I've been drinking coffee more and more lately) and practice #GongFuCha when I can. I love #foraging and tasting new things.
I currently live in #Tucson but the #BayArea will always be my home.
#rstats #rse #datascience #dataviz #ecology #chemistry #statistics
