I use emacs because of org-mode and not the other way around.

I haven't found anything in which I can combine writing, latex, coding (in any language I want), to-do list in one single document/system.

An example of how I do work in the lab. I have one org-mode file per experiment. The experiment is written in org-mode style which is similar (or even simpler) than markdown. One combination exports it to pdf/html/odt, which is a nice thing. This org-mode file is in a folder with all the files and data I generated that are associated with the experiment. Tables are imported and then processes mainly with R. Tables can be generated inside org-mode even with simple spreadsheet capabilities, outputs from code can be embedded directly in the file and exported, the source code can be either hidden or also exported etc.

Now every headline in the file can be turned into a to-do item with a deadline/schedule date, tags etc. The nice thing about org-mode is the Agenda. A place in which you can aggregate all your experiment files and only show the todo items from it.

I find it very powerful to use because the options are endless. I know you like python, check out Scimax which is a version of org-mode that is optimized for all the things I mentioned above. They write their publications with it and they mainly use python...