Ubuntu – ModuleNotFoundError: No module named '_sqlite3' after installing spyder-kernels 3 for Spyder 6.0 IPython console

I am trying to use Spyder 6 IDE on Ubuntu 24.04. After installation of Spyder 6, I changed the default python interpreter to my virtual environment running Python 3.11 and installed spyder-kernels==3.0 in order to have the python console within the IDE. However, instead of the python console showing up, I get the following error:

Traceback (most recent call last):
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/console/__main__.py", line 24, in
start.main()
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/console/start.py", line 151, in main
import_spydercustomize()
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/console/start.py", line 41, in import_spydercustomize
import spydercustomize # noqa
^^^^^^^^^^^^^^^^^^^^^^
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/customize/spydercustomize.py", line 19, in
from spyder_kernels.customize.spyderpdb import SpyderPdb
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/customize/spyderpdb.py", line 22, in
from IPython.core.autocall import ZMQExitAutocall
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/__init__.py", line 55, in
from .terminal.embed import embed
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/terminal/embed.py", line 15, in
from IPython.core.interactiveshell import DummyMod, InteractiveShell
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/core/interactiveshell.py", line 110, in
from IPython.core.history import HistoryManager
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/core/history.py", line 10, in
import sqlite3
File "/home/katmatzidis/.pyenv/versions/3.11.10/lib/python3.11/sqlite3/__init__.py", line 57, in
from sqlite3.dbapi2 import *
File "/home/katmatzidis/.pyenv/versions/3.11.10/lib/python3.11/sqlite3/dbapi2.py", line 27, in
from _sqlite3 import *
ModuleNotFoundError: No module named '_sqlite3'
Traceback (most recent call last):
File "/home/katmatzidis/.pyenv/versions/3.11.10/lib/python3.11/runpy.py", line 198, in _run_module_as_main
return _run_code(code, main_globals, None,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/katmatzidis/.pyenv/versions/3.11.10/lib/python3.11/runpy.py", line 88, in _run_code
exec(code, run_globals)
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/console/__main__.py", line 24, in
start.main()
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/console/start.py", line 151, in main
import_spydercustomize()
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/console/start.py", line 41, in import_spydercustomize
import spydercustomize # noqa
^^^^^^^^^^^^^^^^^^^^^^
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/customize/spydercustomize.py", line 19, in
from spyder_kernels.customize.spyderpdb import SpyderPdb
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/spyder_kernels/customize/spyderpdb.py", line 22, in
from IPython.core.autocall import ZMQExitAutocall
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/__init__.py", line 55, in
from .terminal.embed import embed
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/terminal/embed.py", line 15, in
from IPython.core.interactiveshell import DummyMod, InteractiveShell
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/core/interactiveshell.py", line 110, in
from IPython.core.history import HistoryManager
File "/home/katmatzidis/.virtualenvs/r‑tensorflow/lib/python3.11/site‑packages/IPython/core/history.py", line 10, in
import sqlite3
File "/home/katmatzidis/.pyenv/versions/3.11.10/lib/python3.11/sqlite3/__init__.py", line 57, in
from sqlite3.dbapi2 import *
File "/home/katmatzidis/.pyenv/versions/3.11.10/lib/python3.11/sqlite3/dbapi2.py", line 27, in
from _sqlite3 import *
ModuleNotFoundError: No module named '_sqlite3'

What is this sqlite3 package? It seems I don’t have it in my python virtual environment. How do I install it?

I tried to install the sqlite3 package by running the following command from Ubuntu terminal:

~$ .virtualenvs/r-tensorflow/bin/pip install sqlite3

However, pip is unable to find such a package. I also tried other variants after researching the problem online such as

$ .virtualenvs/r-tensorflow/bin/pip install libsqlite3-dev

but the same problem persists. What am I doing wrong? The default python version that comes with Spyder 6 (the internal python) runs fine in the IPython console, but my virtual environment python has the above error.

I actually found that sqlite3 is in the site-packages of my python virtual environment buried in

Ubuntuhomekatmatzidis.virtualenvsr-tensorflowlibpython3.11site-packagesjedithird_partydjango-stubsdjango-stubsdbbackendssqlite3

Now I’m definitely not sure why it’s not working. I appreciate the help!