jupytext
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20 hours ago •
mwouts
mwouts
jupyter lab crashes on startup since jupytext install
After I installed jupytext I cannot run jupyter lab anymore, because of the following error
[I 13:40:30.138 LabApp] [nb_conda_kernels] enabled, 3 kernels found
[I 13:40:31.215 LabApp] JupyterLab extension loaded from ,,, anaconda3\envs\labplot\lib\site-packages\jupyterlab
[I 13:40:31.216 LabApp] JupyterLab application directory is ,,, anaconda3\envs\labplot\share\jupyter\lab
[I 13:40:31.335 LabApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[I 13:40:31.336 LabApp] Serving notebooks from local directory: ,,,,
[I 13:40:31.337 LabApp] The Jupyter Notebook is running at:
[I 13:40:31.337 LabApp] http://localhost:8888/
[I 13:40:31.337 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 13:40:34.496 LabApp] Build is up to date
/[I 13:40:36.629 LabApp] Kernel started: e5dde3c3-dd03-4295-98e6-e4fcd96d6e3d
[I 13:40:36.654 LabApp] Kernel started: 387b94eb-8052-428d-b420-8f670962312a
-[I 13:40:36.714 LabApp] Kernel started: f94070bb-dafe-4de4-b6b1-7704e6ef92fb
[I 13:40:36.745 LabApp] Kernel started: 2fafa0c2-5092-49f3-89fa-5567564647a5
|Active code page: 850
Active code page: 850
/Active code page: 850
[IPKernelApp] WARNING | Parent appears to have exited, shutting down.
Hi @MaximilianHoffmann , thank you for reporting this.
For troubleshooting it would be useful to know a bit more about your environment (which OS, are you using pip or conda, which version of Jupyter, etc). When exactly does the problem occur (when you create a new notebook, open an existing one?). Also, are you able to reproduce the issue in a conda environment with just jupyterlab and jupytext?
Sorry, of course. It's Windows 10, and conda, this is the clean env before I installed jupytext/ i.e. the one that I had to re-install yesterday
#
# Name Version Build Channel
attrs 19.3.0 py_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
bleach 3.1.5 pyh9f0ad1d_0 conda-forge
brotlipy 0.7.0 py38h1e8a9f7_1000 conda-forge
ca-certificates 2020.6.20 hecda079_0 conda-forge
certifi 2020.6.20 py38h32f6830_0 conda-forge
cffi 1.14.0 py38ha419a9e_0 conda-forge
chardet 3.0.4 py38h32f6830_1006 conda-forge
colorama 0.4.3 py_0 conda-forge
cryptography 2.9.2 py38hba49e27_0 conda-forge
cycler 0.10.0 py_2 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
entrypoints 0.3 py38h32f6830_1001 conda-forge
freetype 2.10.2 hd328e21_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
importlib-metadata 1.7.0 py38h32f6830_0 conda-forge
importlib_metadata 1.7.0 0 conda-forge
intel-openmp 2020.1 216
ipykernel 5.3.2 py38h5ca1d4c_0 conda-forge
ipympl 0.5.6 pyh9f0ad1d_1 conda-forge
ipython 7.16.1 py38h23f93f0_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jedi 0.17.1 py38h32f6830_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
json5 0.9.4 pyh9f0ad1d_0 conda-forge
jsonschema 3.2.0 py38h32f6830_1 conda-forge
jupyter_client 6.1.5 py_0 conda-forge
jupyter_core 4.6.3 py38h32f6830_1 conda-forge
jupyterlab 2.1.5 py_0 conda-forge
jupyterlab_server 1.2.0 py_0 conda-forge
kiwisolver 1.2.0 py38heaebd3c_0 conda-forge
libblas 3.8.0 16_mkl conda-forge
libcblas 3.8.0 16_mkl conda-forge
liblapack 3.8.0 16_mkl conda-forge
libpng 1.6.37 hfe6a214_1 conda-forge
libsodium 1.0.17 h2fa13f4_0 conda-forge
m2w64-gcc-libgfortran 5.3.0 6
m2w64-gcc-libs 5.3.0 7
m2w64-gcc-libs-core 5.3.0 7
m2w64-gmp 6.1.0 2
m2w64-libwinpthread-git 5.0.0.4634.697f757 2
markupsafe 1.1.1 py38h9de7a3e_1 conda-forge
matplotlib-base 3.2.2 py38hbe5506b_1 conda-forge
mistune 0.8.4 py38h9de7a3e_1001 conda-forge
mkl 2020.1 216
msys2-conda-epoch 20160418 1
nb_conda_kernels 2.2.3 py38_0 conda-forge
nbconvert 5.6.1 py38h32f6830_1 conda-forge
nbformat 5.0.7 py_0 conda-forge
nodejs 13.13.0 0 conda-forge
notebook 6.0.3 py38h32f6830_1 conda-forge
numpy 1.18.5 py38h72c728b_0 conda-forge
openssl 1.1.1g he774522_0 conda-forge
packaging 20.4 pyh9f0ad1d_0 conda-forge
pandoc 2.10 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.7.0 pyh9f0ad1d_0 conda-forge
pickleshare 0.7.5 py38h32f6830_1001 conda-forge
pip 20.1.1 py_1 conda-forge
prometheus_client 0.8.0 pyh9f0ad1d_0 conda-forge
prompt-toolkit 3.0.5 py_1 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pygments 2.6.1 py_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyrsistent 0.16.0 py38h9de7a3e_0 conda-forge
pysocks 1.7.1 py38h32f6830_1 conda-forge
python 3.8.3 cpython_h5fd99cc_0 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.8 1_cp38 conda-forge
pywin32 227 py38hfa6e2cd_0 conda-forge
pywinpty 0.5.7 py38_0 conda-forge
pyzmq 19.0.1 py38h77b9d75_0 conda-forge
requests 2.24.0 pyh9f0ad1d_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 49.2.0 py38h32f6830_0 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlite 3.32.3 he774522_1 conda-forge
terminado 0.8.3 py38h32f6830_1 conda-forge
testpath 0.4.4 py_0 conda-forge
tornado 6.0.4 py38hfa6e2cd_0 conda-forge
traitlets 4.3.3 py38h32f6830_1 conda-forge
urllib3 1.25.9 py_0 conda-forge
vc 14.1 h869be7e_1 conda-forge
vs2015_runtime 14.16.27012 h30e32a0_2 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.34.2 py_1 conda-forge
widgetsnbextension 3.5.1 py38h32f6830_1 conda-forge
win_inet_pton 1.1.0 py38_0 conda-forge
wincertstore 0.2 py38_1003 conda-forge
winpty 0.4.3 4 conda-forge
zeromq 4.3.2 ha925a31_3 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h2fa13f4_1006 conda-forge
The crash directly occurse when I start jupyter lab, allthough it was my existing one, so I guess it would have launched some notebooks on startup. The environment is my plot/lab environment, which pretty much only contains jupyter lab and matplotlib.
Interesting. I just gave it a try with
conda create -n jupytext_566 python=3.8.3 jupyterlab=2.1.5 matplotlib-base=3.2.2 jupytext=1.5.1 nodejs=13.13.0 -c conda-forge
conda activate jupytext_566
jupyter lab
on Windows 10 (Miniconda under powershell), and I didn't get any crash. The logs are
[I 22:39:06.767 LabApp] JupyterLab extension loaded from C:\Users\Marc\Miniconda3\envs\jupytext_566\lib\site-packages\jupyterlab
[I 22:39:06.774 LabApp] JupyterLab application directory is C:\Users\Marc\Miniconda3\envs\jupytext_566\share\jupyter\lab
[I 22:39:07.303 LabApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[I 22:39:07.306 LabApp] Serving notebooks from local directory: C:\Users\Marc
[I 22:39:07.307 LabApp] The Jupyter Notebook is running at:
[I 22:39:07.307 LabApp] http://localhost:8888/?token=...
[I 22:39:07.308 LabApp] or http://127.0.0.1:8888/?token=...
[I 22:39:07.309 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 22:39:07.503 LabApp]
To access the notebook, open this file in a browser:
file:///C:/Users/Marc/AppData/Roaming/jupyter/runtime/nbserver-13972-open.html
Or copy and paste one of these URLs:
http://localhost:8888/?token=...
or http://127.0.0.1:8888/?token=...
[W 22:39:11.842 LabApp] Build recommended
[W 22:39:11.843 LabApp] jupyterlab-jupytext needs to be included in build
|[I 22:39:13.326 LabApp] Kernel started: b30ec30f-f349-4955-9cdb-da7100592d8c
/[I 22:39:15.639 LabApp] Building jupyterlab assets (build:dev)
\[I 22:39:43.643 LabApp] Saving file at /Untitled.ipynb
[I 22:39:43.652 LabApp] Saving Untitled.ipynb
[I 22:43:20.811 LabApp] Starting buffering for b30ec30f-f349-4955-9cdb-da7100592d8c:df21de97-6183-447c-bf8e-8bed1f0167df
[I 22:43:20.848 LabApp] Restoring connection for b30ec30f-f349-4955-9cdb-da7100592d8c:df21de97-6183-447c-bf8e-8bed1f0167df
[I 22:43:20.858 LabApp] Starting buffering for b30ec30f-f349-4955-9cdb-da7100592d8c:df21de97-6183-447c-bf8e-8bed1f0167df
[I 22:43:23.857 LabApp] Build is up to date
Compared to your logs, I see that I don't have Active code page: 850 like you. Do you have any idea where this comes from?
Also, if you'd like to compare our environments, here is my conda list. Do you see any difference with yours? Please let me know if you can share the specifications for your env in the form of a single command, or in the form of an environment.yml file.
(jupytext_566) PS C:\Users\Marc> conda list
# packages in environment at C:\Users\Marc\Miniconda3\envs\jupytext_566:
#
# Name Version Build Channel
attrs 19.3.0 py_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
bleach 3.1.5 pyh9f0ad1d_0 conda-forge
brotlipy 0.7.0 py38h1e8a9f7_1000 conda-forge
ca-certificates 2020.6.20 hecda079_0 conda-forge
certifi 2020.6.20 py38h32f6830_0 conda-forge
cffi 1.14.0 py38ha419a9e_0 conda-forge
chardet 3.0.4 py38h32f6830_1006 conda-forge
colorama 0.4.3 py_0 conda-forge
cryptography 2.9.2 py38hba49e27_0 conda-forge
cycler 0.10.0 py_2 conda-forge
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
entrypoints 0.3 py38h32f6830_1001 conda-forge
freetype 2.10.2 hd328e21_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
importlib-metadata 1.7.0 py38h32f6830_0 conda-forge
importlib_metadata 1.7.0 0 conda-forge
intel-openmp 2020.1 216
ipykernel 5.3.2 py38h5ca1d4c_0 conda-forge
ipython 7.16.1 py38h23f93f0_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jedi 0.17.1 py38h32f6830_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
json5 0.9.4 pyh9f0ad1d_0 conda-forge
jsonschema 3.2.0 py38h32f6830_1 conda-forge
jupyter_client 6.1.6 py_0 conda-forge
jupyter_core 4.6.3 py38h32f6830_1 conda-forge
jupyterlab 2.1.5 py_0 conda-forge
jupyterlab_server 1.2.0 py_0 conda-forge
jupytext 1.5.1 pyh9f0ad1d_0 conda-forge
kiwisolver 1.2.0 py38heaebd3c_0 conda-forge
libblas 3.8.0 16_mkl conda-forge
libcblas 3.8.0 16_mkl conda-forge
liblapack 3.8.0 16_mkl conda-forge
libpng 1.6.37 hfe6a214_1 conda-forge
libsodium 1.0.17 h2fa13f4_0 conda-forge
m2w64-gcc-libgfortran 5.3.0 6
m2w64-gcc-libs 5.3.0 7
m2w64-gcc-libs-core 5.3.0 7
m2w64-gmp 6.1.0 2
m2w64-libwinpthread-git 5.0.0.4634.697f757 2
markupsafe 1.1.1 py38h9de7a3e_1 conda-forge
matplotlib-base 3.2.2 py38hbe5506b_1 conda-forge
mistune 0.8.4 py38h9de7a3e_1001 conda-forge
mkl 2020.1 216
msys2-conda-epoch 20160418 1
nbconvert 5.6.1 py38h32f6830_1 conda-forge
nbformat 5.0.7 py_0 conda-forge
nodejs 13.13.0 0 conda-forge
notebook 6.0.3 py38h32f6830_1 conda-forge
numpy 1.18.5 py38h72c728b_0 conda-forge
openssl 1.1.1g he774522_0 conda-forge
packaging 20.4 pyh9f0ad1d_0 conda-forge
pandoc 2.10 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.7.0 pyh9f0ad1d_0 conda-forge
pickleshare 0.7.5 py38h32f6830_1001 conda-forge
pip 20.1.1 py_1 conda-forge
prometheus_client 0.8.0 pyh9f0ad1d_0 conda-forge
prompt-toolkit 3.0.5 py_1 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pygments 2.6.1 py_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyrsistent 0.16.0 py38h9de7a3e_0 conda-forge
pysocks 1.7.1 py38h32f6830_1 conda-forge
python 3.8.3 cpython_h5fd99cc_0 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.8 1_cp38 conda-forge
pywin32 227 py38hfa6e2cd_0 conda-forge
pywinpty 0.5.7 py38_0 conda-forge
pyyaml 5.3.1 py38h9de7a3e_0 conda-forge
pyzmq 19.0.1 py38h77b9d75_0 conda-forge
requests 2.24.0 pyh9f0ad1d_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 49.2.0 py38h32f6830_0 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sqlite 3.32.3 he774522_1 conda-forge
terminado 0.8.3 py38h32f6830_1 conda-forge
testpath 0.4.4 py_0 conda-forge
toml 0.10.1 pyh9f0ad1d_0 conda-forge
tornado 6.0.4 py38hfa6e2cd_0 conda-forge
traitlets 4.3.3 py38h32f6830_1 conda-forge
urllib3 1.25.9 py_0 conda-forge
vc 14.1 h869be7e_1 conda-forge
vs2015_runtime 14.16.27012 h30e32a0_2 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.34.2 py_1 conda-forge
win_inet_pton 1.1.0 py38_0 conda-forge
wincertstore 0.2 py38_1003 conda-forge
winpty 0.4.3 4 conda-forge
yaml 0.2.5 he774522_0 conda-forge
zeromq 4.3.2 ha925a31_3 conda-forge
zipp 3.1.0 py_0 conda-forge
zlib 1.2.11 h2fa13f4_1006 conda-forge
(jupytext_566) PS C:\Users\Marc>
I am getting closer to your env with
conda create -n jupytext_566 python=3.8.3 jupyterlab=2.1.5 matplotlib-base=3.2.2 jupytext=1.5.1 nodejs=13.13.0 jupyter_client=6.1.5 ipympl=0.5.6 ipywidgets=7.5.1 nb_conda_kernels=2.2.3 widgetsnbextension=3.5.1 -c conda-forge
Now the only differences are that
- I have
jupytextand its dependencies (toml,pyyaml,yaml) - I have
jupyter_client=6.1.5fromdefaultwhile you have it fromconda-forge.
Still no crash, and still no Active code page: 850 message, which makes me think that the message/crash may be specific to something you have in your notebook? Also, it is a bit strange that I can't get the same jupyter_client as you, maybe that is because a new version was published yesterday?