Preskoči na sadržaj

2026

  • 8 minut(a/e) čitanja

This is academia; everybody has to get something

A tree in the middle of a snowy field

Photo source: Lukas Seitz (@lukasseitz) | Unsplash

It has been three months since we published our preprint, and it has now passed 500 downloads. That seems like a good occasion to write about how I ended up working on molecular simulations and scientific software after leaving a promising assistant professorship.

I have tried to write about that decision several times, but the drafts kept growing and none reached publication. There was always more to explain. This time, I will focus on what led to the decision and what came of it.

  • 10 minut(a/e) čitanja

AI coding agents and a rerun of the operating-system wars

brown train vehicle machine

Photo source: Rod Long (@rodlong) | Unsplash

Attending the Agentic AI for Science workshop at MPCDF in Garching got me thinking about the platforms we are starting to build our scientific workflows around. The workshop programme brings together hands-on work with agents, examples from scientific software development and materials simulations, and perspectives from industry. For someone interested in free and open-source software, this raises some familiar questions: who controls those platforms, what can we change ourselves, and how much of our work can we take elsewhere?

What interests me here is the software around the model. An agent harness gives the model tools, supplies context, and controls what it can do. The flagship GPT, Claude, and Gemini models are proprietary, but the software using them does not have to be (and often isn't). We can use the same model through different harnesses, with different licenses, tools, and restrictions. Choosing the model, deciding where it runs, and choosing the harness are separate decisions, even when a product offering bundles them together.

A few harnesses and development environments for programming, scientific workflows, and other tasks illustrate these differences. This is only part of the picture: agents embedded in enterprise applications bring their own integrations and dependencies.

This led me to a somewhat loose comparison: Claude Code reminds me of Windows, Codex CLI of BSD, OpenCode and the like of Linux, and Antigravity of the Macintosh. Each comparison emphasizes something different: compatibility, permissive reuse, independence from suppliers, or the appeal of an integrated experience.

If you have used Claude Code in a terminal, the first part probably sounds wrong already. How does a program that reads files, invokes shell tools, and fits into a Unix workflow resemble Windows? Bear with me. The resemblance is in how people build tools and workflows around the software, rather than how its interface looks.

  • 4 minut(a/e) čitanja

The future of MkDocs: ProperDocs and Zensical

black and white penguin toy

Photo source: Roman Synkevych (@synkevych) | Unsplash

We have relied on MkDocs for our teaching materials and this website for several years, so its future is more than a passing interest for us.

The slow collapse of MkDocs is, by now, well documented and worth reading if you are interested in the details of it.

In summary, MkDocs is unlikely to get future releases compatible with its current version, which makes the instructions for setting up a GitHub Action for MkDocs deployment in need of an update. Without further ado, here are two good options to move forward.