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#softwareheritage

0 Beiträge0 Beteiligte0 Beiträge heute
Ludovic Courtès

Yesterday @rougier and I gave an informal #ReproducibleResearch workshop at Inria with ~20 scientists, half of whom working in HPC, the rest of them working on user interfaces, computer graphics, number theory, and robotics—very insightful to see how each community approaches these issues.

@rougier had excellent examples to get the discussion started. I followed up on computational reproducibility with #HPC examples and a touch of #Guix and #SoftwareHeritage:
gitlab.inria.fr/lcourtes/ateli

GitLabLudovic Courtès / Atelier recherche reproductible · GitLabGitlab at Inria
Simon Tournier

Blog post: What Guix could offer in computational medical environments?

French national agency for secure drug and medicine (ANSM) requires for a medical device to have unambiguous identifications:

1. reference of the product
2. reference of the maker
3. serial number

Well, through my lenses applied to software, it reads:

1. #SoftwareHeritage identifier (#SWHID)
2. #Guix

and 3. is redundant. 😁

Well, a quick summary of a 30min talk I gave past week.

Thanks my previous colleague Sam from APHP to give me the opportunity to brainstorm on this topic. 🤩

simon.tournier.info/posts/2025

simon.tournier.infoWhat Guix could offer in computational medical environments?
#ReproducibleResearch#OpenScience#Debian
Simon Tournier

Asking for news from a colleague now in Univ. of Tours – long time, no see.

Nicolas pointed me a recent publication where… guess what? … they archived the source code in #SoftwareHeritage.

pubmed.ncbi.nlm.nih.gov/394876

Section « Open Research, data availability statement » reads:

« Anonymized raw data, the source code of the analyses, instructions to reproduce the computing environment, unformatted analysis reports and figures are available online (gitlab.com/nivall/car-lacates) and long term preserved at Software Heritage (archive.softwareheritage.org/s). »

And guess what else? The computational environment is managed using #Guix.

It makes my day! 😎

I’m happy to see #Guix and #SoftwarHeritage mentioned in the European Journal Of Clinical Investigation.

PubMedGlycolytic activity following anti-CD19 CAR-T cell infusion in non-Hodgkin lymphoma - PubMedEnergy metabolism of chimeric antigen receptor-T cells (CAR-T) activation in humans remains unexplored. As a glycolytic activity surrogate, we investigated the dynamics of peripheral blood (PB) lactate in the first weeks post-CAR-T infusion. In 17 patients treated with CD28 harbording anti-CD19 CAR- …
#ReproducibleResearch#OpenScience#EuropeanJournalOfClinicalInvestigation
Antwortete im Thread
Giacomo Tesio
@ekaitz_zarraga@mastodon.social

Indeed if you were leading #Guix, I'd likely be a user and contributor (I think you know I have the technical skills required).

And I also know other people working there, people I respect despite not being always aligned with their opinion (for example I had a long debate with a friend that work on Guix a few months ago about the right to be mentioned with the preferred name by a transitioned trans developer whose code was archived with their dead-name and #SoftwareHeritage was refusing to update. I think hackers have the right to be named as they wish in their works and no script, tool or hash chain matter more than this right).

Yet there's a huge difference between a technical or even philosophical argument and a (politically motivated) personal attack in form of a shitstorm.

Courtès might even be the best #scheme hacker out there, with a solid architectural vision of how to make #linux more reliable.

But I chose free software for political goals that he actively damaged with that attack to RMS.
Bioinfo-fr.net

📰 @pierrepo , ambas­sa­deur pour @swheritage nous présente l’archive uni­ver­selle dédiée à la col­lecte, la pré­ser­va­tion et le par­tage des codes sources logi­ciels 🖥️ 🔓 ♾️
bioinfo-fr.net/software-herita
#softwareheritage #opensource #bioinfofr

Bioinfo-fr.net · Software Heritage : l'archive universelle des codes sources logiciels - Bioinfo-fr.netDans cet article, je vous pro­pose de décou­vrir Soft­ware Heri­tage, l’archive uni­ver­selle dédiée à la col­lecte, la pré­ser­va­tion et le par­tage des codes sources logi­ciels. En 2021, je suis deve­nu ambas­sa­deur pour Soft­ware Heri­tage, c’est-à-dire repré­sen­tant de la com­mu­nau­té bio­in­for­ma­tique, dans l’infrastructure Soft­ware Heri­tage. Pourquoi archiver son code source ? Aujourd’hui, les scien­ti­fiques uti­lisent très sou­vent des […]
Simon Tournier

☕ break? #Guix #HPC activity report is out! 🎉

Check it out:

hpc.guix.info/blog/2025/02/gui

The seventh report, time flies! Highlight of key achievements:

• More than 57,000 packages, Guix + related channels for scientific packages;
• Performance and portability: more about MPI;
• ROCm/HIP software stack for AMD GPUs upgrades;
• Migration of Guix-Science channel to Codeberg;
• New version of Guix-Jupyter;
• Common Workflow Language #CWL + Guix = ❤️ : ccwl and ravanan;
• Ensuring Source Code Availability: #SoftwareHeritage rescue mode;
• Re-Deploying Software from the Past;
• Supporting Artifact Evaluation at SuperComputing 2024;
• “Package to Container image” conversion pipeline, #DIAMOND and #DIADEM;
• Digital Electronics Design;
• Reproducible Multiphysics Simulation and Workflows;
• Impact of Hardware Variability;
• Toward Guix on French Tier-1 and EuroHPC Tier-0 machines;
• Pangenome Genetics Research
• Supporting RISC-V
• List of articles, talks, tutorials, events, training sessions.
• … and more…

What a year, isn’t it? 😀

hpc.guix.infoGuix-HPC — Guix-HPC Activity Report, 2024
#ReproducibleResearch#OpenScience
Simon Tournier

The video of my talk about #Guix and @swheritage at #FOSDEM25 is released!

The conclusion is:

• Cite and reference source code using #SoftwareHeritage identifier;

• Use Guix!

Packed in 20 minutes, check out the arguments.

Feel free to raise your questions. 😀

fosdem.org/2025/schedule/event

Thanks @FosdemResearch for the organization of this devroom.

fosdem.orgFOSDEM 2025 - Guix + Software Heritage: Source Code Archiving to the Rescue of Reproducible Deployment
Fortgeführter Thread
*
Stefano Zacchiroli

@zimoun will present « Guix + #SoftwareHeritage Source Code Archiving to the Rescue of Reproducible Deployment » on Saturday: fosdem.org/2025/schedule/event

The presentation is about the work we did to integrate GNU #Guix with the @swheritage archive, so that when users try to (re)build packages whose source code has disappeared from the new, it will still work!

This is key for scientific #reproducibility. See our #ACMREP paper from last year for more details: upsilon.cc/~zack/research/publ

fosdem.orgFOSDEM 2025 - Guix + Software Heritage: Source Code Archiving to the Rescue of Reproducible Deployment
#FOSDEM
*
Simon Tournier

hey @bzg! Thanks for the chat at #SoftwareHeritage symposium.

About #Guix + #SWH = ❤️ ?

A paper authored by @civodul and @zacchiro and Timothy Sample and me.

« Source Code Archiving to the Rescue of Reproducible Deployment »
dl.acm.org/doi/10.1145/3641525

The first bridge: hpc.guix.info/blog/2019/03/con

Then for what it is worth, two blog posts about “real world” attempts about redeploying a computational environment associated to some scientific papers (some issues listed there had been fixed since then 😁).

simon.tournier.info/posts/2023
simon.tournier.info/posts/2023

And also FWIW, a short talk in #FOSDEM this year. 😀

fosdem.org/2025/schedule/event

Well, it could be fun to try something about producing some containers (Docker or else) only using source code from SWH. Heh! 😀

ACM ConferencesSource Code Archiving to the Rescue of Reproducible Deployment | Proceedings of the 2nd ACM Conference on Reproducibility and Replicability
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