Cannot open Jupyter notebook using Anaconda python 3.6.1 - python

When I use the command jupyter notebook I get the following error and traceback:
Error in sitecustomize; set PYTHONVERBOSE for traceback:
KeyError: 'PYTHONPATH'
Error in sitecustomize; set PYTHONVERBOSE for traceback:
KeyError: 'PYTHONPATH'
Traceback (most recent call last):
File "/Users/hamedbh/anaconda3/bin/jupyter-notebook", line 4, in <module>
import notebook.notebookapp
File "/usr/local/lib/python2.7/site-packages/notebook/notebookapp.py", line 31, in <module>
from zmq.eventloop import ioloop
File "/usr/local/lib/python2.7/site-packages/zmq/__init__.py", line 34, in <module>
from zmq import backend
File "/usr/local/lib/python2.7/site-packages/zmq/backend/__init__.py", line 40, in <module>
reraise(*exc_info)
File "/usr/local/lib/python2.7/site-packages/zmq/utils/sixcerpt.py", line 34, in reraise
raise value
File "/usr/local/lib/python2.7/site-packages/zmq/backend/__init__.py", line 27, in <module>
_ns = select_backend(first)
File "/usr/local/lib/python2.7/site-packages/zmq/backend/select.py", line 27, in select_backend
mod = __import__(name, fromlist=public_api)
ModuleNotFoundError: No module named 'zmq.backend.cython'
I am using the full Anaconda distribution, and although I have created an environment I did this from the root Anaconda env (i.e. /Users/me/anaconda3) and not within an env.
Some quick details that may help with figuring out the problem:
python --version = Python 3.6.1 :: Anaconda 4.4.0 (x86_64)
OS is MacOS Sierra 10.12.6
I don't know whether the same thing that is causing the KeyError: PYTHONPATH is also causing jupyter notebook to fail.

It seems that pyzmq is the problem. Run pip install pyzmq --upgrade or pip unistall pyzmq & pip install pyzmq to make sure you're on the latest version of it.

Related

Jupiter notebook won't start - Symbol not found error

A while back, I upgraded my python version via brew to 3.9.0 and now, whenever I try to start Jupiter notebook, I get this error:
Traceback (most recent call last):
File "/Users/me/Library/Python/3.9/bin/jupyter-notebook", line 5, in <module>
from notebook.notebookapp import main
File "/Users/me/Library/Python/3.9/lib/python/site-packages/notebook/notebookapp.py", line 49, in <module>
from zmq.eventloop import ioloop
File "/usr/local/lib/python3.9/site-packages/zmq/__init__.py", line 62, in <module>
from zmq import backend
File "/usr/local/lib/python3.9/site-packages/zmq/backend/__init__.py", line 32, in <module>
raise original_error from None
File "/usr/local/lib/python3.9/site-packages/zmq/backend/__init__.py", line 27, in <module>
_ns = select_backend(first)
File "/usr/local/lib/python3.9/site-packages/zmq/backend/select.py", line 32, in select_backend
mod = import_module(name)
File "/usr/local/Cellar/python#3.9/3.9.0_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/usr/local/lib/python3.9/site-packages/zmq/backend/cython/__init__.py", line 6, in <module>
from . import (
ImportError: dlopen(/usr/local/lib/python3.9/site-packages/zmq/backend/cython/constants.cpython-39-darwin.so, 2): Symbol not found: ____chkstk_darwin
Referenced from: /usr/local/lib/python3.9/site-packages/zmq/backend/cython/../../.dylibs/libsodium.23.dylib (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
in /usr/local/lib/python3.9/site-packages/zmq/backend/cython/../../.dylibs/libsodium.23.dylib
I've tried completely uninstalling and reinstalling jupiter to no avail. I've also tried reinstalling the zmq module that seems to be a part of this error chain. My thought is that there must be some component that's avoiding my uninstalls that needs to be fixed/updated, but I'm not sure what it could be.
I'm also running MacOS 10.13.6. I notice it states that one of these modules was built for Mac OS X 10.15. Could this instead be the issue?
The answer provided in this link worked for me:
Cannot run jupyter everywhere (terminal, anaconda distributer) Mac os 10.12.6
"downgraded pyzmq to 20.0.0 and it worked fine. pip install pyzmq==20.0.0
I believe the issue is in pyzmq's cython packaging - and should be raised as a bug to them."
The bug has been raised and is expected to be fixed by release 21.0.2

Create a virtualenv to run jupyter

I have created a new virtualenv and named it python with command virtualenv python.
output:
Using base prefix '/Library/Frameworks/Python.framework/Versions/3.7'
New python executable in /Users/dema/python/bin/python3.7
Also creating executable in /Users/dema/python/bin/python
Installing setuptools, pip, wheel...
done.
Then I activate it with commande source python/bin/activate
Then I installed jupyter notebook with commande pip3 install notebook
Then I try running the notebook with command jupyter notebook
The error:
Traceback (most recent call last):
File "/anaconda2/bin/jupyter-notebook", line 7, in <module>
from notebook.notebookapp import main
File "/anaconda2/lib/python2.7/site-packages/notebook/notebookapp.py", line 60, in <module>
from tornado import httpserver
File "/anaconda2/lib/python2.7/site-packages/tornado/httpserver.py", line 33, in <module>
from tornado.http1connection import HTTP1ServerConnection, HTTP1ConnectionParameters
File "/anaconda2/lib/python2.7/site-packages/tornado/http1connection.py", line 30, in <module>
from tornado import iostream
File "/anaconda2/lib/python2.7/site-packages/tornado/iostream.py", line 40, in <module>
from tornado.netutil import ssl_wrap_socket, _client_ssl_defaults, _server_ssl_defaults
File "/anaconda2/lib/python2.7/site-packages/tornado/netutil.py", line 44, in <module>
_client_ssl_defaults = ssl.create_default_context(
AttributeError: 'module' object has no attribute 'create_default_context'
Why do Anaconda and python2.7 come into this when I am using an active env with python3.7? I am totally unable to understand.

Jupiter notebook run error: AttributeError: module 'importlib_metadata' has no attribute 'version'

Originally, Jupyter notebook was running well without any problems.
But after installing tensorflow and keras today, it doesn't work.
Error message:
Traceback (most recent call last):
File "C:\Anaconda3\Scripts\jupyter-notebook-script.py", line 6, in <module>
from notebook.notebookapp import main
File "C:\Anaconda3\lib\site-packages\notebook\notebookapp.py", line 85, in <module>
from .services.contents.manager import ContentsManager
File "C:\Anaconda3\lib\site-packages\notebook\services\contents\manager.py", line 17, in <module>
from nbformat import sign, validate as validate_nb, ValidationError
File "C:\Anaconda3\lib\site-packages\nbformat\__init__.py", line 32, in <module>
from .validator import validate, ValidationError
File "C:\Anaconda3\lib\site-packages\nbformat\validator.py", line 12, in <module>
from .json_compat import get_current_validator, ValidationError
File "C:\Anaconda3\lib\site-packages\nbformat\json_compat.py", line 10, in <module>
import jsonschema
File "C:\Anaconda3\lib\site-packages\jsonschema\__init__.py", line 34, in <module>
__version__ = metadata.version("jsonschema")
AttributeError: module 'importlib_metadata' has no attribute 'version'
There is a problem with your importlib_metadata package, you can try uninstall it first and then forcing out a new installation with the following commands:
pip uninstall importlib_metadata
pip install importlib_metadata --force-reinstall
It worked for me.
This is a problem with the Anaconda version upgrade.
You can solve this with the following command that worked for me.
conda install -c conda-forge importlib_metadata
For me, the same error happened after VSCode proposed me to install a tensorboard plugin and I pressed yes. (MacOS 11.4, Conda 4.10.3)
It appears that it introduced some kind of version mismatch for multiple packages in the environment.
The following fixed the problem:
conda update --all

Import error while trying to run jupyter notebook

An import error occurs when trying to run jupyter notebook
I'm trying to run jupyter notebook using anaconda (git bash platform), and as I type in jupyter notebook, an import error occurs every time. I tried to lauch it inside an environment, but the same error occured.
$ jupyter notebook
Traceback (most recent call last):
File "C:\Users\User\Anaconda3\Scripts\jupyter-notebook-script.py", line 6, in
<module>
from notebook.notebookapp import main
File "C:\Users\User\Anaconda3\lib\site-packages\notebook\notebookapp.py", line 47, in <module>
from zmq.eventloop import ioloop
File "C:\Users\User\Anaconda3\lib\site-packages\zmq\__init__.py", line 47, in <module>
from zmq import backend
File "C:\Users\User\Anaconda3\lib\site-packages\zmq\backend\__init__.py", line 40, in <module>
reraise(*exc_info)
File "C:\Users\User\Anaconda3\lib\site-packages\zmq\utils\sixcerpt.py", line 34, in reraise
raise value
File "C:\Users\User\Anaconda3\lib\site-packages\zmq\backend\__init__.py", line 27, in <module>
_ns = select_backend(first)
File "C:\Users\User\Anaconda3\lib\site-packages\zmq\backend\select.py", line 27, in select_backend
mod = __import__(name, fromlist=public_api)
File "C:\Users\User\Anaconda3\lib\site-packages\zmq\backend\cython\__init__.py", line 6, in <module>
from . import (constants, error, message, context,
ImportError: DLL load failed: The specified module could not be found.
EDITED
After reinstalling pyzmq (and I tried reinstalling conda too), the following error occurs:
$ jupyter notebook
Traceback (most recent call last): File
"C:\Users\User\Anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py",
line 10, in
import sqlite3
File "C:\Users\User\Anaconda3\lib\sqlite3__init__.py", line 23, in
from sqlite3.dbapi2 import *
File "C:\Users\User\Anaconda3\lib\sqlite3\dbapi2.py", line 27, in
from _sqlite3 import *
ImportError: DLL load failed: The specified module could not be found.
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File
"C:\Users\User\Anaconda3\Scripts\jupyter-notebook-script.py", line 6,
in
from notebook.notebookapp import main
File
"C:\Users\User\Anaconda3\lib\site-packages\notebook\notebookapp.py",
line 86, in
from .services.sessions.sessionmanager import SessionManager
File
"C:\Users\User\Anaconda3\lib\site-packages\notebook\services\sessions\sessionmanager.py",
line 13, in
from pysqlite2 import dbapi2 as sqlite3
ModuleNotFoundError: No module named 'pysqlite2'
I found a similar issue open on GitHub for zmq. The recommendation by GitHub user harsh23tyagi that seems to work for most is to run the following:
pip uninstall pyzmq
pip install pyzmq
Working with conda env, jupyter notebook worked in (base) env but gave the .libzmq error in (my_env).
To be able to run notebooks from my_env, this worked for me :
pip uninstall pyzmq
pip install pyzmq==20 (no version for pyzmq didn't fix the issue for me)
It seems that updating pyzmq to the latest version fixes this problem for me.
conda install pyzmq=22

Error In Spyder After Anaconda Install

I just installed Anaconda. I already had Spyder 3.0.0 installed on my Windows 8.1 (64 bit). I also already had Python 3.4 installed. But, after installing Anaconda, I went into Preferences and pointed the Python executable to the Anaconda3 folder to utilize the 3.5 version. But when I started up Spyder again, got the following error:
An error ocurred while starting the kernel
C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\PIL\Image.py:81: RuntimeWarning: The _imaging extension was built for another version of Python.
RuntimeWarning
C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\PIL\Image.py:81: RuntimeWarning: The _imaging extension was built for another version of Python.
RuntimeWarning
Traceback (most recent call last):
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\spyderlib\widgets\externalshell\start_ipython_kernel.py", line 187, in
from ipykernel.kernelapp import IPKernelApp
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\ipykernel\__init__.py", line 2, in
from .connect import *
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\ipykernel\connect.py", line 18, in
import jupyter_client
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\jupyter_client\__init__.py", line 4, in
from .connect import *
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\jupyter_client\connect.py", line 21, in
import zmq
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\zmq\__init__.py", line 66, in
from zmq import backend
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\zmq\backend\__init__.py", line 40, in
reraise(*exc_info)
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\zmq\utils\sixcerpt.py", line 34, in reraise
raise value
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\zmq\backend\__init__.py", line 27, in
_ns = select_backend(first)
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\zmq\backend\select.py", line 27, in select_backend
mod = __import__(name, fromlist=public_api)
File "C:\WinPython󈛤bit𔂭.4.4.2\python𔂭.4.4.amd64\lib\site‑packages\zmq\backend\cython\__init__.py", line 6, in
from . import (constants, error, message, context,
ImportError: Module use of python34.dll conflicts with this version of Python.
Any ideas?
Suggestion:
rename your directory "C:\WinPython-64bit-3.4.4.2" in "C:\WinPython-64bit-3.4.4.2bis"
relaunch your Anaconda Spyder
if it doesn't help, rename it back to "C:\WinPython-64bit-3.4.4.2"

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