Regarding of Jupyter lab

[hmkim]

Bug description

Expected behaviour

Actual behaviour

[I 20:36:06.448 LabApp] KernelRestarter: restarting kernel (4/5), new random ports
Traceback (most recent call last):
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/ipykernel_launcher.py", line 16, in
app.launch_new_instance()
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/traitlets/config/application.py", line 844, in launch_instance
app.initialize(argv)
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/traitlets/config/application.py", line 87, in inner
return method(app, *args, **kwargs)
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/ipykernel/kernelapp.py", line 582, in initialize
self.init_kernel()
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/ipykernel/kernelapp.py", line 452, in init_kernel
user_ns=self.user_ns,
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/traitlets/config/configurable.py", line 537, in instance
inst = cls(*args, **kwargs)
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/ipykernel/ipkernel.py", line 86, in init
appnope.nope()
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/appnope/_nope.py", line 90, in nope
"Because Reasons"
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/appnope/_nope.py", line 60, in beginActivityWithOptions
NSProcessInfo = C('NSProcessInfo')
File "/Users/brandon/miniconda3/envs/ancestry/lib/python3.7/site-packages/appnope/_nope.py", line 38, in C
assert ret is not None, "Couldn't find Class %s" % classname
AssertionError: Couldn't find Class NSProcessInfo

How to reproduce

1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

Your personal set up

• OS:

• Version: OS X 11.0.1

jupyter --version
jupyter core : 4.7.0
jupyter-notebook : 6.1.5
qtconsole : not installed
ipython : 5.8.0
ipykernel : 5.3.4
jupyter client : 6.1.7
jupyter lab : 2.2.9
nbconvert : 6.0.7
ipywidgets : not installed
nbformat : 5.0.8
traitlets : 5.0.5

Hi!

Could you check the issue please?
(I just found the appnode repository e.g here.)

[jasongrout]

@hmkim - can you fill out the rest of the bug report, like how to reproduce, etc.?

[raeisi]

I have managed to bypass the bug by modifying the /opt/anaconda3/envs/DES37/lib/python3.7/site-packages/appnope/init.py

from:
_if sys.platform != "darwin" or V(platform.mac_ver()[0]) < V("10.9"):
from ._dummy import *
else: from ._nope import *
from .dummy import *

to:
from .dummy import *

[minrk]

This is a Python issue. Python must be rebuilt with patches to work properly on macOS 11 (ctypes and thereby appnope is specifically affected by a change to how dyld libraries are found). I believe the latest conda-forge builds have fixed this (I know 3.9 has). CPython itself hasn't released a fix yet, but 3.9.1 will fix it. I'm not sure what the backport plan is, so it may not come all the way back to 3.7

Also make sure you have appnope >= 0.1.2.

[minrk]

FWIW, I'm also on macOS 11 and have envs working with Python 3.8 and 3.9 (from conda-forge). Python 3.7 is not getting updates, I think.

Python 3.8

$ conda list
# packages in environment at ~/conda/envs/nb38:
#
# Name                    Version                   Build  Channel
appnope                   0.1.2            py38h50d1736_0    conda-forge
argon2-cffi               20.1.0           py38h7e3306e_2    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     20.3.0             pyhd3deb0d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.1                      py_0    conda-forge
bleach                    3.2.1              pyh9f0ad1d_0    conda-forge
ca-certificates           2020.12.5            h033912b_0    conda-forge
certifi                   2020.12.5        py38h50d1736_0    conda-forge
cffi                      1.14.4           py38h979bc6b_1    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3             pyhd8ed1ab_1003    conda-forge
importlib-metadata        3.1.1              pyhd8ed1ab_0    conda-forge
importlib_metadata        3.1.1                hd8ed1ab_0    conda-forge
ipykernel                 5.3.4            py38h9bb44b7_1    conda-forge
ipython                   7.19.0           py38h9bb44b7_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.17.2           py38h50d1736_1    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
jsonschema                3.2.0                      py_2    conda-forge
jupyter_client            6.1.7                      py_0    conda-forge
jupyter_core              4.7.0            py38h50d1736_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
libcxx                    11.0.0               h4c3b8ed_1    conda-forge
libffi                    3.3                  h046ec9c_2    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
markupsafe                1.1.1            py38h94c058a_2    conda-forge
mistune                   0.8.4           py38h7e3306e_1002    conda-forge
nbclient                  0.5.1                      py_0    conda-forge
nbconvert                 6.0.7            py38h50d1736_3    conda-forge
nbformat                  5.0.8                      py_0    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
nest-asyncio              1.4.3              pyhd8ed1ab_0    conda-forge
notebook                  6.1.5            py38h50d1736_0    conda-forge
openssl                   1.1.1h               haf1e3a3_0    conda-forge
packaging                 20.7               pyhd3deb0d_0    conda-forge
pandoc                    2.11.2               hc929b4f_0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.7.1              pyh9f0ad1d_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       20.3.1             pyhd8ed1ab_0    conda-forge
prometheus_client         0.9.0              pyhd3deb0d_0    conda-forge
prompt-toolkit            3.0.8              pyha770c72_0    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygments                  2.7.3              pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyrsistent                0.17.3           py38h7e3306e_1    conda-forge
python                    3.8.6           h3b7b5d6_1_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.8                      1_cp38    conda-forge
pyzmq                     20.0.0           py38h9b3f83f_1    conda-forge
readline                  8.0                  h0678c8f_2    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                49.6.0           py38h5347e94_2    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.34.0               h17101e1_0    conda-forge
terminado                 0.9.1            py38h50d1736_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tk                        8.6.10               hb0a8c7a_1    conda-forge
tornado                   6.1              py38h7e3306e_0    conda-forge
traitlets                 5.0.5                      py_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.36.1             pyhd3deb0d_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.3                h74dc148_3    conda-forge
zipp                      3.4.0                      py_0    conda-forge
zlib                      1.2.11            h7795811_1010    conda-forge

Python 3.9

$ conda list
# packages in environment at /Users/minrk/conda/envs/nb39:
#
# Name                    Version                   Build  Channel
appnope                   0.1.2            py39h6e9494a_0    conda-forge
argon2-cffi               20.1.0           py39hb5aae12_2    conda-forge
async_generator           1.10                       py_0    conda-forge
attrs                     20.3.0             pyhd3deb0d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.1                      py_0    conda-forge
bleach                    3.2.1              pyh9f0ad1d_0    conda-forge
ca-certificates           2020.12.5            h033912b_0    conda-forge
certifi                   2020.12.5        py39h6e9494a_0    conda-forge
cffi                      1.14.4           py39h7786acb_1    conda-forge
decorator                 4.4.2                      py_0    conda-forge
defusedxml                0.6.0                      py_0    conda-forge
entrypoints               0.3             py39hde42818_1002    conda-forge
importlib-metadata        3.1.1              pyhd8ed1ab_0    conda-forge
importlib_metadata        3.1.1                hd8ed1ab_0    conda-forge
ipykernel                 5.3.4            py39h71a6800_1    conda-forge
ipython                   7.19.0           py39h71a6800_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jedi                      0.17.2           py39hde42818_1    conda-forge
jinja2                    2.11.2             pyh9f0ad1d_0    conda-forge
jsonschema                3.2.0                      py_2    conda-forge
jupyter_client            6.1.7                      py_0    conda-forge
jupyter_core              4.7.0            py39h6e9494a_0    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
libcxx                    11.0.0               h4c3b8ed_1    conda-forge
libffi                    3.3                  h046ec9c_2    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
markupsafe                1.1.1            py39h66d5b7b_2    conda-forge
mistune                   0.8.4           py39hb5aae12_1002    conda-forge
nbclient                  0.5.1                      py_0    conda-forge
nbconvert                 6.0.7            py39h6e9494a_3    conda-forge
nbformat                  5.0.8                      py_0    conda-forge
ncurses                   6.2                  h2e338ed_4    conda-forge
nest-asyncio              1.4.3              pyhd8ed1ab_0    conda-forge
notebook                  6.1.5            py39h6e9494a_0    conda-forge
openssl                   1.1.1h               haf1e3a3_0    conda-forge
packaging                 20.7               pyhd3deb0d_0    conda-forge
pandoc                    2.11.2               hc929b4f_0    conda-forge
pandocfilters             1.4.2                      py_1    conda-forge
parso                     0.7.1              pyh9f0ad1d_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5           py39hde42818_1002    conda-forge
pip                       20.3.1             pyhd8ed1ab_0    conda-forge
prometheus_client         0.9.0              pyhd3deb0d_0    conda-forge
prompt-toolkit            3.0.8              pyha770c72_0    conda-forge
ptyprocess                0.6.0                   py_1001    conda-forge
pycparser                 2.20               pyh9f0ad1d_2    conda-forge
pygments                  2.7.3              pyhd8ed1ab_0    conda-forge
pyparsing                 2.4.7              pyh9f0ad1d_0    conda-forge
pyrsistent                0.17.3           py39hb5aae12_1    conda-forge
python                    3.9.1           h1d169a7_1_cpython    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.9                      1_cp39    conda-forge
pyzmq                     20.0.0           py39h07c395c_1    conda-forge
readline                  8.0                  h0678c8f_2    conda-forge
send2trash                1.5.0                      py_0    conda-forge
setuptools                49.6.0           py39h2c36a5b_2    conda-forge
six                       1.15.0             pyh9f0ad1d_0    conda-forge
sqlite                    3.34.0               h17101e1_0    conda-forge
terminado                 0.9.1            py39hde42818_1    conda-forge
testpath                  0.4.4                      py_0    conda-forge
tk                        8.6.10               hb0a8c7a_1    conda-forge
tornado                   6.1              py39h5a22ff9_0    conda-forge
traitlets                 5.0.5                      py_0    conda-forge
tzdata                    2020d                h516909a_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
wheel                     0.36.1             pyhd3deb0d_0    conda-forge
xz                        5.2.5                haf1e3a3_1    conda-forge
zeromq                    4.3.3                h74dc148_3    conda-forge
zipp                      3.4.0                      py_0    conda-forge
zlib                      1.2.11            h7795811_1010    conda-forge

You can also disable appnope in the IPython kernel by setting:

# ~/.ipython/profile_default/ipython_kernel_config.py
c.Kernel._darwin_app_nap = False

[hmkim]

Thank you @minrk

After upgrade of python (3.7.9 to 3.8.5), I solved the issue.

In my custom conda env (name: ancestry),

(ancestry) $ conda install -c anaconda python=3.8
(ancestry) $ conda update --all

@hmkim - can you fill out the rest of the bug report, like how to reproduce, etc.?

I solved the issue.

[logankilpatrick]

Same, this fixed my issue. Thanks @hmkim!

[Schmidtbit]

Unfortunately I have packages that require Python 3.7. Is there another way to get jupyterlab to work with python 3.7 and BigSur 11.2?

[jasongrout]

Did you try disabling appnope like mentioned above?

[brifordwylie]

For anyone else hitting this thread... I had this and issue, did the fix above (disable appnope) .. and then had another issue (jupyter/notebook#5888). So I simply deleted my Python virtualenv (I used pyenv) and created a new one... both problems completely disappeared.

[Schmidtbit]

@jasongrout I didn't have the configuration file set up, so I created one and disabled appnope and it appears to now be working. Thanks!