scimax VS code-cells.el

Scimax should have out of box setup for bibliography, references etc. Anyway, regardless of what you use Emacs for, one step a time, would be my recommendation. Just start using it and solve problems as you experience them. It is better to add a single thing at a time when you need it, than to add 1000 different things because you think you will need them, and then not know what you have or what causes a problem.

https://github.com/wdavew/org-excalidraw is close. I discovered you can install Excalidraw from Chrome, and then it is like a local program. That is pretty amazing in itself. org-excalidraw indeed offers an org-link and way to make an excalidraw file from emacs, edited natively in an external excalidraw window. The svg preview does not work though if you use freehand lines in your image, and I was unable to install the npm packages on my Mac for some uninteresting reason related to DNS, but it did work in a node docker image. I find writing in excalidraw less advanced than in tools like Notability or PDFExpert. There are some artifacts in excalidraw from smoothing, or dangling pixels that I don't love. I forgot I had previously used https://github.com/lepisma/org-krita. Krita is a full drawing program, and this integrates into org-mode with image previews nicely. I am not that skilled in using it, and as a full drawing program, it has a learning curve. I wrote https://github.com/jkitchin/scimax/blob/master/scimax-inkscape.el to integrate inkscape into org-mode. It works, but I find inkscape slow to open, and I am not that skilled in using it.

Maybe give scimax a go?

Anyway, if you want something geared toward scientific usage, there is Scimax by J. Kitchin. There may be some others, but I am not aware off.

Apart from the ones already mention, John Kitchin's science-focused Scimacs is also an option.

code-cells: Utilities to work with “lightweight notebooks”, that is, source code which is split into cells by special %% comments. Also allows you to transparently edit Jupyter notebook (ipynb) files.

Emacs, Sublime Text 3 and Atom Pulsar can all do this with arbitrary Jupyter kernels with the emacs-jupyter/code-cells, helium and hydrogen packages, respectively.

I've been using code-cells together with emacs-jupyter, the combination of the two lets you work pretty much identically as you would in Atom with Hydrogen, Sublime with Helium, or VSCode with the Jupyter Python extension; you just delimit code cells with #%% and execute in a separate Jupyter REPL buffer. It does require some getting used to the key bindings though (or some tweaking to make it more similar to what you're used to).

I use a similar setup in Emacs with code-cells.el [1]. VSCode had a tendency to choke rendering large interactive graphs in-line, so if I was needing to view in a separate process anyways a little elisp turns "write last IPython output to a tempfile, open, move to workspace N" into a keybind.

[1] https://github.com/astoff/code-cells.el

Try https://github.com/astoff/code-cells.el

I use the simple but very convenient code-cells package to run python cells. E.g. with the Spyder IDE, the cell where the cursor is currently in has a different background color, and I'd love to have that in emacs. Would you have any idea on how to do that?

For scripts with cells there are a couple of packages. Mine is this: https://github.com/astoff/code-cells.el