See #26146 for the general issue report.

When does it add all those dependencies to PATH? Are you using nix-shell?

Indeed, you are using nix-shell. nix-shell opens a shell to develop a package, and therefore runs certain hooks, which you are now not interested in. Until we get a nix run command there's not much we can do about it.

Yes. This is what I did (results without this fix):

$ nix-shell -p nbstripout -p which --pure

Now, python and jupyter have been added to PATH:

$ which python
/nix/store/83xv5vjqs8qxzdsqs8dmni23wfkbx43a-python-2.7.13/bin/python
$ which jupyter
/nix/store/78iqhpa3k46ywjc5b9vm2gm5paarpf9p-python2.7-jupyter_core-4.3.0/bin/jupyter

Also, the Python dependencies are in PYTHONPATH:

$ python -c "import nbformat"; echo $?
0

I'm closing this because this is a "limitation" of nix-shell. The proper solution is either waiting for a nix run command or, preferably, implement a proper buildPythonApplication function that works somewhat like what you wrote and this #16672.

Ok. And you're right, I tested: if I added nbstripout to my pkgs in configuration.nix, the dependencies aren't added to my environment, only nbstripout. I did not know that there is such a difference to nix-shell.