python notebook in emacs org-mode

Take away: If you are using doomemacs, you need to have your virtual environment set before the first time you enter a session, i.e. when the python shell process is started, ideally with pyvenv package.(I don’t know any other way)

For some reason, vanilla emacs (emacs -q) spawned python inferior process (where your sessioned python codes are run) would inherent shell’s python virtual environment, while doomemacs spawned python inferior process won’t.

To test, in terminal activate a venv with source path/to/activate and open an org-mode file with the following source block, with emacs -q and your doomemacs command respectively, babel-execute the the following source block, and you can tell if the venv is loaded by checking if the venv path is present in the output.

#+begin_src python :session
import sys
sys.path
#+end_src

On my side, with no user-configuration to org-babel, the venv path is present with emacs -q but not emacs (my doomemacs command).