I'm looking for a graph based solution, too. For my master thesis I used diagrams.net, but it's not a long term solution. I need something with markdown support, git, offline mode and hopefully for free.

Obsidian has a graph view, yes. But Zettlr is a much more stable note taking app than Obsidian. Zettlr is also open source. I would recommend you checkout Zettlr.com if possible. It has great set of tools and is stable unlike Obsidian (beta) which is proprietary.

Currently Zettlr doesn't have graph view, But the PR for a graph view is up and soon will come (power of open source?). If cool with it, I would recommend Open Source Software like Zettlr. :)

PR for graph view in Zettlr - https://github.com/Zettlr/Zettlr/pull/921

You keep saying Zettlr is stable, unlike Obsidian? Why? Obsidian is quite stable in my experience, despite being in beta. Do you simply mean the feature set is built out and mostly solidified? Otherwise, I don't see the rationale behind your comment.

Creating graphs, not same as organising your work into one.. If former, with markdown-preview you can write markdown and mermaidJS at the same time and see a live preview of it.

obsidian ticks most of those boxes, it's flat file, markup based, free, offline by design. don't think it has git integration but since its flat file you can likely rig something up.

Notebag also pretty cool.

Thank you for showing obsidian, it was just what I was looking for! Now it just needs vim keybindings!

edit: it has!