problem when installing with jupyter notebook

[DanielaPamplona]

I created a new env. in conda, installed plenoptic and jupyter notebook. When I tried to launch the notebook I got an error and it did not launch. I repeated the process without installing plenoptic and it worked.

Error below (copy-paste):

---

(p2) daniela@Vietnam:~$ jupyter notebook
Traceback (most recent call last):
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/requests/compat.py", line 11, in
import chardet
ModuleNotFoundError: No module named 'chardet'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/daniela/anaconda3/envs/p2/bin/jupyter-notebook", line 7, in
from notebook.app import main
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/notebook/app.py", line 20, in
from jupyterlab.commands import ( # type:ignore[import-untyped]
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/jupyterlab/init.py", line 8, in
from .handlers.announcements import (
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/jupyterlab/handlers/announcements.py", line 15, in
from jupyterlab_server.translation_utils import translator
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/jupyterlab_server/init.py", line 6, in
from .app import LabServerApp
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/jupyterlab_server/app.py", line 15, in
from .handlers import LabConfig, add_handlers
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/jupyterlab_server/handlers.py", line 21, in
from .listings_handler import ListingsHandler, fetch_listings
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/jupyterlab_server/listings_handler.py", line 10, in
import requests
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/requests/init.py", line 45, in
from .exceptions import RequestsDependencyWarning
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/requests/exceptions.py", line 9, in
from .compat import JSONDecodeError as CompatJSONDecodeError
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/requests/compat.py", line 13, in
import charset_normalizer as chardet
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/charset_normalizer/init.py", line 23, in
from charset_normalizer.api import from_fp, from_path, from_bytes, normalize
File "/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/charset_normalizer/api.py", line 10, in
from charset_normalizer.md import mess_ratio
File "charset_normalizer/md.py", line 5, in
ImportError: cannot import name 'COMMON_SAFE_ASCII_CHARACTERS' from 'charset_normalizer.constant' (/home/daniela/anaconda3/envs/p2/lib/python3.9/site-packages/charset_normalizer/constant.py)

---

System (please complete the following information):

• Ubuntu
• Python version (as in the installation guide)
• Pytorch version (as in the installation guide)
• Plenoptic version (as in the installation guide)

[billbrod]

Huh, I have never seen that kind of error. I can't reproduce this on my (Fedora) machine using micromamba, where I did the following:

micromamba create -n plen_nb 'python==3.9' -c conda-forge
# install from local copy
cd plenoptic/
pip install .
micromamba install -c conda-forge jupyterlab ipywidgets torchvision
jupyter lab

and that works. My understanding is that jupyter is encouraging everyone to go through jupyter lab now, not notebook, but running micromamba install -c conda-forge notebook after the above and then jupyter notebook works as well.

I'm not quite sure how to best debug this -- I'm not sure why there would be a chardet problem, which looks like it's a requests dependency, so maybe there's an incompatibility in the requests versions that end up getting used between the two? If so, then this is probably what I get for encouraging people to use conda for jupyter and pip for plenoptic, as you and @NickleDave pointed out.

A couple of possible ideas:

• Can you paste the exact sequence of commands you ran checking the version of requests after each of the install commands?
• If you try installing jupyterlab rather than notebook, as I did above, does that work?
• If you install jupyter (try both notebook and lab) and then plenoptic, do you get the same issues?

[DanielaPamplona]

Hi,
The commands were:

---

conda create --name p2 pip python=3.9
conda activate p2
pip install plenoptic
conda install jupyter notebook
jupyter notebook

If jupyter encourages to use lab instead of notebook, then I think that you can just write a statement in the installation saying that it must be installed lab. However, this solution must be discussed with the editor.

I also think that this might result from mixing pip and conda.

[billbrod]

Okay, I'm still unable to reproduce this error following these steps. I'm using conda-forge as the only channel, so maybe that's the difference?

If you have time and can check the bullet points I wrote above, as well as what channels you're conda is using, that might help us get more specific.

But I think for now we assume it's a mixing of pip/conda issue (see related #104). I don't think it won't work with notebook, because I'm able to get it working with notebook locally. but lab might make it easier to get a working environment(?). Not really sure.

[DanielaPamplona]

So, I checked and if I install first the notebook and then plenoptic there is no problem. There is also no problem when installing with jupyter lab. So, I would say, we just check this again after solving the pip issue.

[sneakers-the-rat]

I was able to reproduce the issue (on a mac, if that matters). It's also not specific to jupyter (or plenoptic, for that matter) - if one tries to import requests after doing this, you get the same error.

This looks like a requests problem initially:
psf/requests#6384

but it turns out to be a jupyter problem.

requests tries to import either chardet or charset_normalizer:
https://github.com/psf/requests/blob/147c8511ddbfa5e8f71bbf5c18ede0c4ceb3bba4/requests/compat.py#L10-L15

they require >=2,<4: https://github.com/psf/requests/blob/147c8511ddbfa5e8f71bbf5c18ede0c4ceb3bba4/setup.cfg#L8

but the version that is installed is 2.0.4 - notably older than the current 3.3.2.

Inspecting the jupyter and notebook conda packages, they both pin charset-normalizer 2.0.4 (download the .tar.gz's from conda (anaconda), uncompress, see info > about.json).

uninstalling requests and reinstalling jupyter or notebook from pip resolved the problem.

It also seems to be just a problem with the jupyter and notebook packages in the default anaconda package source. using conda-forge also resolves the problem (conda install -c conda-forge jupyter notebook)

So I think adding the -c conda-forge resolves this

[billbrod]

@DanielaPamplona Can you try following our new installation instructions? In particular, the conda instructions.

[DanielaPamplona]

Hi, I am about to leave on vacations. See you in September!  

…

---------------------------------------------------------------------------------------------- Daniela Pamplona Researcher and Lecturer at Université Paris-Est Créteil Val de Marne https://danielapamplona.github.io/     Sent: Friday, August 23, 2024 at 5:29 PM From: "William F. Broderick" ***@***.***> To: "plenoptic-org/plenoptic" ***@***.***> Cc: "Daniela Pamplona" ***@***.***>, "Mention" ***@***.***> Subject: Re: [plenoptic-org/plenoptic] problem when installing with jupyter notebook (Issue #242)   @DanielaPamplona Can you try following our new installation instructions? In particular, the conda instructions. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>