Org-mode is the digital lab notebook that I have needed forever. I have a private repo with one folder per general project and one or more org files inside. I mostly treat them as append-only FILO pipes.
PI wants a progress report? Export the relevant headings to a PDF and email it.
I want some literate-programming style "work in progress"? Easy, you can even hook jupyter in, and dump plots out simply. Export it to a PDF if you want, or make it a blog post with some nice HTML styling.
Project documentation? easy.
Paper drafts? Yup.
It's wonderful.