Bug running jupyterlab in Docker - "Bad config encountered during initialization"

[morrisalp]

Description

(per request posting this issue here, originally from jupyter/notebook#6630)

When running jupyter-lab in Docker I encounter the following error:

[C 11:15:44.783 LabApp] Bad config encountered during initialization: The 'contents_manager_class' trait of a LabApp instance expected a subclass of notebook.services.contents.manager.ContentsManager or jupyter_server.contents.services.managers.ContentsManage, not the JupytextContentsManager JupytextContentsManager.

Reproduce

I've reproduced a minimal Dockerfile below - reproduce with docker build -t testimg . and docker run testimg.

It appears that this bug is due to Jupyterlab looking for the config file in the wrong location, because it is fixed when adding the flag --config=.jupyter/nbconfig/tree.json (docker run --entrypoint jupyter-lab testimg --config=.jupyter/nbconfig/tree.json --allow-root).

Dockerfile reproducing the bug:

FROM nvcr.io/nvidia/pytorch:22.10-py3
WORKDIR /root
RUN pip install --upgrade pip \
    && pip install jupyterlab
ENTRYPOINT jupyter-lab

Expected behavior

docker run testimg should run without errors.

Context

• Operating System and version: Linux Ubuntu 20.04.5 LTS
• Browser and version: Chrome 107.0.5304.121
• JupyterLab version: 2.3.2 (docker run --entrypoint jupyter-lab testimg --version)

Troubleshoot Output

Output of `jupyter troubleshoot` (`docker run --entrypoint jupyter testimg troubleshoot`):

$PATH: /opt/conda/lib/python3.8/site-packages/torch_tensorrt/bin /opt/conda/bin /usr/local/mpi/bin /usr/local/nvidia/bin /usr/local/cuda/bin /usr/local/sbin /usr/local/bin /usr/sbin /usr/bin /sbin /bin /usr/local/ucx/bin /opt/tensorrt/bin

sys.path:
/opt/conda/bin
/opt/conda/lib/python38.zip
/opt/conda/lib/python3.8
/opt/conda/lib/python3.8/lib-dynload
/opt/conda/lib/python3.8/site-packages
/opt/conda/lib/python3.8/site-packages/torchtext-0.11.0a0-py3.8-linux-x86_64.egg
/opt/conda/lib/python3.8/site-packages/certifi-2022.9.24-py3.8.egg
/opt/conda/lib/python3.8/site-packages/functorch-0.3.0a0-py3.8-linux-x86_64.egg

sys.executable:
/opt/conda/bin/python3.8

sys.version:
3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10)
[GCC 10.3.0]

platform.platform():
Linux-4.15.0-196-generic-x86_64-with-glibc2.10

which -a jupyter:
/opt/conda/bin/jupyter

pip list:
Package Version
----------------------------- ------------------------------
absl-py 1.2.0
alabaster 0.7.12
anyio 3.6.1
apex 0.1
appdirs 1.4.4
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.0.8
attrs 22.1.0
audioread 3.0.0
Babel 2.10.3
backcall 0.2.0
backports.functools-lru-cache 1.6.4
beautifulsoup4 4.11.1
bleach 5.0.1
blis 0.7.8
brotlipy 0.7.0
cachetools 5.2.0
catalogue 2.0.8
certifi 2022.9.24
cffi 1.15.1
chardet 5.0.0
charset-normalizer 2.1.0
click 8.1.3
cloudpickle 2.2.0
codecov 2.1.12
colorama 0.4.5
conda 22.9.0
conda-build 3.22.0
conda-package-handling 1.9.0
contourpy 1.0.5
coverage 6.5.0
cryptography 38.0.2
cuda-python 11.7.0+0.g95a2041.dirty
cudf 22.8.0a0+304.g6ca81bbc78.dirty
cugraph 22.8.0a0+132.g2daa31b6.dirty
cuml 22.8.0a0+52.g73b8d00d0.dirty
cupy-cuda118 11.0.0
cycler 0.11.0
cymem 2.0.6
Cython 0.29.32
dask 2022.7.1
dask-cuda 22.8.0a0+36.g9860cad
dask-cudf 22.8.0a0+304.g6ca81bbc78.dirty
dataclasses 0.8
debugpy 1.6.3
decorator 5.1.1
defusedxml 0.7.1
distributed 2022.7.1
docutils 0.17.1
entrypoints 0.3
executing 1.1.1
expecttest 0.1.3
fastjsonschema 2.16.2
fastrlock 0.8
filelock 3.8.0
flake8 3.7.9
Flask 2.2.2
fonttools 4.37.4
fsspec 2022.8.2
functorch 0.3.0a0
future 0.18.2
glob2 0.7
google-auth 2.12.0
google-auth-oauthlib 0.4.6
graphsurgeon 0.4.6
grpcio 1.49.1
HeapDict 1.0.1
hypothesis 4.50.8
idna 3.3
imagesize 1.4.1
importlib-metadata 5.0.0
importlib-resources 5.10.0
iniconfig 1.1.1
iopath 0.1.10
ipykernel 6.16.0
ipython 8.5.0
ipython-genutils 0.2.0
itsdangerous 2.1.2
jedi 0.18.1
Jinja2 3.1.2
joblib 1.2.0
json5 0.9.10
jsonschema 4.16.0
jupyter_client 7.4.2
jupyter-core 4.11.1
jupyter-server 1.21.0
jupyter-tensorboard 0.2.0
jupyterlab 2.3.2
jupyterlab-pygments 0.2.2
jupyterlab-server 1.2.0
jupytext 1.14.1
kiwisolver 1.4.4
langcodes 3.3.0
libarchive-c 4.0
librosa 0.9.2
llvmlite 0.39.1
lmdb 1.3.0
locket 1.0.0
Markdown 3.4.1
markdown-it-py 2.1.0
MarkupSafe 2.1.1
matplotlib 3.6.1
matplotlib-inline 0.1.6
mccabe 0.6.1
mdit-py-plugins 0.3.1
mdurl 0.1.2
mistune 2.0.4
mock 4.0.3
msgpack 1.0.4
murmurhash 1.0.6
nbclassic 0.4.5
nbclient 0.7.0
nbconvert 7.2.1
nbformat 5.7.0
nest-asyncio 1.5.6
networkx 2.6.3
nltk 3.7
notebook 6.4.10
notebook-shim 0.1.0
numba 0.56.2
numpy 1.22.2
nvidia-dali-cuda110 1.18.0
nvidia-pyindex 1.0.9
nvtx 0.2.5
oauthlib 3.2.1
onnx 1.12.0
packaging 21.3
pandas 1.4.4
pandocfilters 1.5.0
parso 0.8.3
partd 1.3.0
pathy 0.6.2
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.0.1
pip 22.3.1
pkginfo 1.8.3
pkgutil_resolve_name 1.3.10
pluggy 1.0.0
polygraphy 0.42.1
pooch 1.6.0
portalocker 2.5.1
preshed 3.0.6
prettytable 3.4.1
prometheus-client 0.15.0
prompt-toolkit 3.0.31
protobuf 3.20.3
psutil 5.9.2
ptyprocess 0.7.0
pure-eval 0.2.2
py 1.11.0
pyarrow 8.0.0
pyasn1 0.4.8
pyasn1-modules 0.2.8
pybind11 2.10.0
pycocotools 2.0+nv0.6.0
pycodestyle 2.5.0
pycosat 0.6.3
pycparser 2.21
pydantic 1.8.2
pydot 1.4.2
pyflakes 2.1.1
Pygments 2.13.0
pylibcugraph 22.8.0a0+132.g2daa31b6.dirty
pynvml 11.4.1
pyOpenSSL 22.0.0
pyparsing 3.0.9
pyrsistent 0.18.1
PySocks 1.7.1
pytest 6.2.5
pytest-cov 4.0.0
pytest-pythonpath 0.7.4
python-dateutil 2.8.2
python-hostlist 1.22
python-nvd3 0.15.0
python-slugify 6.1.2
pytorch-quantization 2.1.2
pytz 2022.4
PyYAML 6.0
pyzmq 24.0.1
raft 22.8.0a0+70.g9070c30.dirty
regex 2022.9.13
requests 2.28.1
requests-oauthlib 1.3.1
resampy 0.4.2
revtok 0.0.3
rmm 22.8.0a0+62.gf6bf047.dirty
rsa 4.9
ruamel-yaml-conda 0.15.80
sacremoses 0.0.53
scikit-learn 0.24.2
scipy 1.6.3
Send2Trash 1.8.0
setuptools 59.5.0
shellingham 1.5.0
six 1.16.0
smart-open 5.2.1
sniffio 1.3.0
snowballstemmer 2.2.0
sortedcontainers 2.4.0
soundfile 0.11.0
soupsieve 2.3.2.post1
spacy 3.2.2
spacy-legacy 3.0.10
spacy-loggers 1.0.3
Sphinx 5.2.3
sphinx-glpi-theme 0.3
sphinx-rtd-theme 1.0.0
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
srsly 2.4.2
stack-data 0.5.1
tabulate 0.9.0
tblib 1.7.0
tensorboard 2.10.1
tensorboard-data-server 0.6.1
tensorboard-plugin-wit 1.8.1
tensorrt 8.5.0.12
terminado 0.16.0
text-unidecode 1.3
thinc 8.0.13
threadpoolctl 3.1.0
tinycss2 1.1.1
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
torch 1.13.0a0+d0d6b1f
torch-tensorrt 1.3.0a0
torchtext 0.11.0a0
torchvision 0.14.0a0
tornado 6.2
tqdm 4.64.1
traitlets 5.4.0
transformer-engine 0.1.0
treelite 2.4.0
treelite-runtime 2.4.0
typer 0.4.2
typing_extensions 4.4.0
ucx-py 0.27.0a0+29.ge9e81f8
uff 0.6.9
urllib3 1.26.11
wasabi 0.10.0
wcwidth 0.2.5
webencodings 0.5.1
websocket-client 1.4.1
Werkzeug 2.2.2
wheel 0.37.1
xgboost 1.6.1
zict 2.2.0
zipp 3.9.0

conda list:
# packages in environment at /opt/conda:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
absl-py 1.2.0 pypi_0 pypi
alabaster 0.7.12 pypi_0 pypi
anyio 3.6.1 pypi_0 pypi
apex 0.1 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
argon2-cffi 21.3.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
asttokens 2.0.8 pyhd8ed1ab_0 conda-forge
attrs 22.1.0 pypi_0 pypi
audioread 3.0.0 pypi_0 pypi
babel 2.10.3 pypi_0 pypi
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bleach 5.0.1 pypi_0 pypi
brotlipy 0.7.0 py38h0a891b7_1004 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.9.24 ha878542_0 conda-forge
cachetools 5.2.0 pypi_0 pypi
catalogue 2.0.8 py38h578d9bd_0 conda-forge
certifi 2022.9.24 pypi_0 pypi
cffi 1.15.1 py38h4a40e3a_0 conda-forge
chardet 5.0.0 py38h578d9bd_0 conda-forge
charset-normalizer 2.1.0 pyhd8ed1ab_0 conda-forge
click 8.1.3 py38h578d9bd_0 conda-forge
cloudpickle 2.2.0 pypi_0 pypi
cmake 3.22.2 h1021d11_0 conda-forge
codecov 2.1.12 pypi_0 pypi
colorama 0.4.5 pyhd8ed1ab_0 conda-forge
conda 22.9.0 py38h578d9bd_1 conda-forge
conda-build 3.22.0 py38h578d9bd_2 conda-forge
conda-package-handling 1.9.0 py38h0a891b7_0 conda-forge
contourpy 1.0.5 pypi_0 pypi
coverage 6.5.0 pypi_0 pypi
cryptography 38.0.2 py38h2b5fc30_0 conda-forge
cuda-python 11.7.0+0.g95a2041.dirty pypi_0 pypi
cudf 22.8.0a0+304.g6ca81bbc78.dirty pypi_0 pypi
cugraph 22.8.0a0+132.g2daa31b6.dirty pypi_0 pypi
cuml 22.8.0a0+52.g73b8d00d0.dirty pypi_0 pypi
cupy-cuda118 11.0.0 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
cymem 2.0.6 py38h709712a_2 conda-forge
cython 0.29.32 pypi_0 pypi
cython-blis 0.7.8 py38h71d37f0_0 conda-forge
dask 2022.7.1 pypi_0 pypi
dask-cuda 22.8.0a0+36.g9860cad pypi_0 pypi
dask-cudf 22.8.0a0+304.g6ca81bbc78.dirty pypi_0 pypi
dataclasses 0.8 pyhc8e2a94_3 conda-forge
debugpy 1.6.3 pypi_0 pypi
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pypi_0 pypi
distributed 2022.7.1 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
entrypoints 0.3 pypi_0 pypi
executing 1.1.1 pyhd8ed1ab_0 conda-forge
expat 2.4.4 h9c3ff4c_0 conda-forge
expecttest 0.1.3 pypi_0 pypi
fastjsonschema 2.16.2 pypi_0 pypi
fastrlock 0.8 pypi_0 pypi
filelock 3.8.0 pyhd8ed1ab_0 conda-forge
flake8 3.7.9 pypi_0 pypi
flask 2.2.2 pypi_0 pypi
fonttools 4.37.4 pypi_0 pypi
fsspec 2022.8.2 pypi_0 pypi
functorch 0.3.0a0 pypi_0 pypi
future 0.18.2 pypi_0 pypi
glob2 0.7 py_0 conda-forge
google-auth 2.12.0 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
graphsurgeon 0.4.6 pypi_0 pypi
grpcio 1.49.1 pypi_0 pypi
heapdict 1.0.1 pypi_0 pypi
hypothesis 4.50.8 pypi_0 pypi
icu 69.1 h9c3ff4c_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 5.0.0 pypi_0 pypi
importlib-resources 5.10.0 pypi_0 pypi
iniconfig 1.1.1 pypi_0 pypi
iopath 0.1.10 pypi_0 pypi
ipykernel 6.16.0 pypi_0 pypi
ipython 8.5.0 pyh41d4057_1 conda-forge
ipython-genutils 0.2.0 pypi_0 pypi
itsdangerous 2.1.2 pypi_0 pypi
jedi 0.18.1 pyhd8ed1ab_2 conda-forge
jinja2 3.1.2 pyhd8ed1ab_1 conda-forge
joblib 1.2.0 pypi_0 pypi
json5 0.9.10 pypi_0 pypi
jsonschema 4.16.0 pypi_0 pypi
jupyter-client 7.4.2 pypi_0 pypi
jupyter-core 4.11.1 pypi_0 pypi
jupyter-server 1.21.0 pypi_0 pypi
jupyter-tensorboard 0.2.0 pypi_0 pypi
jupyterlab 2.3.2 pypi_0 pypi
jupyterlab-pygments 0.2.2 pypi_0 pypi
jupyterlab-server 1.2.0 pypi_0 pypi
jupytext 1.14.1 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
krb5 1.19.2 hcc1bbae_3 conda-forge
langcodes 3.3.0 pyhd8ed1ab_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libarchive 3.5.2 hccf745f_1 conda-forge
libblas 3.9.0 15_linux64_openblas conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libcurl 7.81.0 h2574ce0_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.1.0 h8d9b700_16 conda-forge
libgfortran-ng 12.1.0 h69a702a_16 conda-forge
libgfortran5 12.1.0 hdcd56e2_16 conda-forge
libgomp 12.1.0 h8d9b700_16 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
liblapack 3.9.0 15_linux64_openblas conda-forge
liblief 0.11.5 h9c3ff4c_1 conda-forge
libllvm10 10.0.1 he513fc3_3 conda-forge
libnghttp2 1.46.0 h812cca2_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_1 conda-forge
librosa 0.9.2 pypi_0 pypi
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 9.4.0 h79bfe98_16 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libuv 1.44.2 h166bdaf_0 conda-forge
libxml2 2.9.12 h885dcf4_1 conda-forge
libzlib 1.2.12 h166bdaf_2 conda-forge
llvm-openmp 14.0.4 he0ac6c6_0 conda-forge
llvmlite 0.39.1 pypi_0 pypi
lmdb 1.3.0 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
lzo 2.10 h516909a_1000 conda-forge
markdown 3.4.1 pypi_0 pypi
markdown-it-py 2.1.0 pypi_0 pypi
markupsafe 2.1.1 py38h0a891b7_1 conda-forge
matplotlib 3.6.1 pypi_0 pypi
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
mccabe 0.6.1 pypi_0 pypi
mdit-py-plugins 0.3.1 pypi_0 pypi
mdurl 0.1.2 pypi_0 pypi
mistune 2.0.4 pypi_0 pypi
mkl 2020.4 h726a3e6_304 conda-forge
mkl-include 2020.4 h726a3e6_304 conda-forge
mock 4.0.3 py38h578d9bd_3 conda-forge
msgpack 1.0.4 pypi_0 pypi
murmurhash 1.0.6 py38h709712a_2 conda-forge
nbclassic 0.4.5 pypi_0 pypi
nbclient 0.7.0 pypi_0 pypi
nbconvert 7.2.1 pypi_0 pypi
nbformat 5.7.0 pypi_0 pypi
ncurses 6.3 h27087fc_1 conda-forge
nest-asyncio 1.5.6 pypi_0 pypi
networkx 2.6.3 pypi_0 pypi
ninja 1.10.2 h4bd325d_1 conda-forge
nltk 3.7 pypi_0 pypi
notebook 6.4.10 pypi_0 pypi
notebook-shim 0.1.0 pypi_0 pypi
numba 0.56.2 pypi_0 pypi
numpy 1.22.2 py38h6ae9a64_0 conda-forge
nvidia-dali-cuda110 1.18.0 pypi_0 pypi
nvidia-pyindex 1.0.9 pypi_0 pypi
nvtx 0.2.5 pypi_0 pypi
oauthlib 3.2.1 pypi_0 pypi
onnx 1.12.0 pypi_0 pypi
openblas 0.3.20 pthreads_h320a7e8_1 conda-forge
openssl 1.1.1q h166bdaf_0 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.4.4 pypi_0 pypi
pandocfilters 1.5.0 pypi_0 pypi
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.3.0 pypi_0 pypi
patch 2.7.6 h7f98852_1002 conda-forge
patchelf 0.15.0 h58526e2_0 conda-forge
pathy 0.6.2 pyhd8ed1ab_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 9.0.1 pypi_0 pypi
pip 22.3.1 pypi_0 pypi
pkginfo 1.8.3 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pypi_0 pypi
pluggy 1.0.0 pypi_0 pypi
polygraphy 0.42.1 pypi_0 pypi
pooch 1.6.0 pypi_0 pypi
portalocker 2.5.1 pypi_0 pypi
preshed 3.0.6 py38h709712a_1 conda-forge
prettytable 3.4.1 pypi_0 pypi
prometheus-client 0.15.0 pypi_0 pypi
prompt-toolkit 3.0.31 pyha770c72_0 conda-forge
protobuf 3.20.3 pypi_0 pypi
psutil 5.9.2 py38h0a891b7_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py 1.11.0 pypi_0 pypi
py-lief 0.11.5 py38h709712a_1 conda-forge
pyarrow 8.0.0 pypi_0 pypi
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pybind11 2.10.0 pypi_0 pypi
pycocotools 2.0+nv0.6.0 pypi_0 pypi
pycodestyle 2.5.0 pypi_0 pypi
pycosat 0.6.3 py38h0a891b7_1010 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydantic 1.8.2 py38h497a2fe_2 conda-forge
pydot 1.4.2 pypi_0 pypi
pyflakes 2.1.1 pypi_0 pypi
pygments 2.13.0 pyhd8ed1ab_0 conda-forge
pylibcugraph 22.8.0a0+132.g2daa31b6.dirty pypi_0 pypi
pynvml 11.4.1 pypi_0 pypi
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge
pyrsistent 0.18.1 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytest 6.2.5 pypi_0 pypi
pytest-cov 4.0.0 pypi_0 pypi
pytest-pythonpath 0.7.4 pypi_0 pypi
python 3.8.13 h582c2e5_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python-hostlist 1.22 pypi_0 pypi
python-libarchive-c 4.0 py38h578d9bd_1 conda-forge
python-nvd3 0.15.0 pypi_0 pypi
python-slugify 6.1.2 pypi_0 pypi
python_abi 3.8 2_cp38 conda-forge
pytorch-quantization 2.1.2 pypi_0 pypi
pytz 2022.4 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py38h0a891b7_4 conda-forge
pyzmq 24.0.1 pypi_0 pypi
raft 22.8.0a0+70.g9070c30.dirty pypi_0 pypi
readline 8.1.2 h0f457ee_0 conda-forge
regex 2022.9.13 pypi_0 pypi
requests 2.28.1 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pypi_0 pypi
resampy 0.4.2 pypi_0 pypi
revtok 0.0.3 pypi_0 pypi
rhash 1.4.3 h166bdaf_0 conda-forge
ripgrep 13.0.0 h2f28480_2 conda-forge
rmm 22.8.0a0+62.gf6bf047.dirty pypi_0 pypi
rsa 4.9 pypi_0 pypi
ruamel_yaml 0.15.80 py38h0a891b7_1007 conda-forge
sacremoses 0.0.53 pypi_0 pypi
scikit-learn 0.24.2 pypi_0 pypi
scipy 1.6.3 py38h7b17777_0 conda-forge
send2trash 1.8.0 pypi_0 pypi
setuptools 59.5.0 py38h578d9bd_0 conda-forge
shellingham 1.5.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smart_open 5.2.1 pyhd8ed1ab_0 conda-forge
sniffio 1.3.0 pypi_0 pypi
snowballstemmer 2.2.0 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
soundfile 0.11.0 pypi_0 pypi
soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge
spacy 3.2.2 py38h2b96118_0 conda-forge
spacy-legacy 3.0.10 pyhd8ed1ab_0 conda-forge
spacy-loggers 1.0.3 pyhd8ed1ab_0 conda-forge
sphinx 5.2.3 pypi_0 pypi
sphinx-glpi-theme 0.3 pypi_0 pypi
sphinx-rtd-theme 1.0.0 pypi_0 pypi
sphinxcontrib-applehelp 1.0.2 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.3 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi
sqlite 3.39.2 h4ff8645_0 conda-forge
srsly 2.4.2 py38h709712a_1 conda-forge
stack_data 0.5.1 pyhd8ed1ab_0 conda-forge
tabulate 0.9.0 pypi_0 pypi
tblib 1.7.0 pypi_0 pypi
tensorboard 2.10.1 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
tensorrt 8.5.0.12 pypi_0 pypi
terminado 0.16.0 pypi_0 pypi
text-unidecode 1.3 pypi_0 pypi
thinc 8.0.13 py38h2b96118_0 conda-forge
threadpoolctl 3.1.0 pypi_0 pypi
tinycss2 1.1.1 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pypi_0 pypi
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
torch 1.13.0a0+d0d6b1f pypi_0 pypi
torch-tensorrt 1.3.0a0 pypi_0 pypi
torchtext 0.11.0a0 pypi_0 pypi
torchvision 0.14.0a0 pypi_0 pypi
tornado 6.2 pypi_0 pypi
tqdm 4.64.1 pypi_0 pypi
traitlets 5.4.0 pyhd8ed1ab_0 conda-forge
transformer-engine 0.1.0 pypi_0 pypi
treelite 2.4.0 pypi_0 pypi
treelite-runtime 2.4.0 pypi_0 pypi
typer 0.4.2 pyhd8ed1ab_0 conda-forge
typing-extensions 4.4.0 hd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
tzdata 2022a h191b570_0 conda-forge
ucx-py 0.27.0a0+29.ge9e81f8 pypi_0 pypi
uff 0.6.9 pypi_0 pypi
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
wasabi 0.10.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.4.1 pypi_0 pypi
werkzeug 2.2.2 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xgboost 1.6.1 pypi_0 pypi
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zict 2.2.0 pypi_0 pypi
zipp 3.9.0 pypi_0 pypi
zlib 1.2.12 h166bdaf_2 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge

conda env:
name: base
channels:
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_kmp_llvm
- asttokens=2.0.8=pyhd8ed1ab_0
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- beautifulsoup4=4.11.1=pyha770c72_0
- brotlipy=0.7.0=py38h0a891b7_1004
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2022.9.24=ha878542_0
- catalogue=2.0.8=py38h578d9bd_0
- cffi=1.15.1=py38h4a40e3a_0
- chardet=5.0.0=py38h578d9bd_0
- charset-normalizer=2.1.0=pyhd8ed1ab_0
- click=8.1.3=py38h578d9bd_0
- cmake=3.22.2=h1021d11_0
- colorama=0.4.5=pyhd8ed1ab_0
- conda=22.9.0=py38h578d9bd_1
- conda-build=3.22.0=py38h578d9bd_2
- conda-package-handling=1.9.0=py38h0a891b7_0
- cryptography=38.0.2=py38h2b5fc30_0
- cymem=2.0.6=py38h709712a_2
- cython-blis=0.7.8=py38h71d37f0_0
- dataclasses=0.8=pyhc8e2a94_3
- decorator=5.1.1=pyhd8ed1ab_0
- executing=1.1.1=pyhd8ed1ab_0
- expat=2.4.4=h9c3ff4c_0
- filelock=3.8.0=pyhd8ed1ab_0
- glob2=0.7=py_0
- icu=69.1=h9c3ff4c_0
- idna=3.3=pyhd8ed1ab_0
- ipython=8.5.0=pyh41d4057_1
- jedi=0.18.1=pyhd8ed1ab_2
- jinja2=3.1.2=pyhd8ed1ab_1
- krb5=1.19.2=hcc1bbae_3
- langcodes=3.3.0=pyhd8ed1ab_0
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- libarchive=3.5.2=hccf745f_1
- libblas=3.9.0=15_linux64_openblas
- libcblas=3.9.0=15_linux64_openblas
- libcurl=7.81.0=h2574ce0_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libffi=3.4.2=h7f98852_5
- libgcc-ng=12.1.0=h8d9b700_16
- libgfortran-ng=12.1.0=h69a702a_16
- libgfortran5=12.1.0=hdcd56e2_16
- libgomp=12.1.0=h8d9b700_16
- libiconv=1.17=h166bdaf_0
- liblapack=3.9.0=15_linux64_openblas
- liblief=0.11.5=h9c3ff4c_1
- libllvm10=10.0.1=he513fc3_3
- libnghttp2=1.46.0=h812cca2_0
- libnsl=2.0.0=h7f98852_0
- libopenblas=0.3.20=pthreads_h78a6416_1
- libssh2=1.10.0=haa6b8db_3
- libstdcxx-ng=9.4.0=h79bfe98_16
- libuuid=2.32.1=h7f98852_1000
- libuv=1.44.2=h166bdaf_0
- libxml2=2.9.12=h885dcf4_1
- libzlib=1.2.12=h166bdaf_2
- llvm-openmp=14.0.4=he0ac6c6_0
- lz4-c=1.9.3=h9c3ff4c_1
- lzo=2.10=h516909a_1000
- markupsafe=2.1.1=py38h0a891b7_1
- matplotlib-inline=0.1.6=pyhd8ed1ab_0
- mkl=2020.4=h726a3e6_304
- mkl-include=2020.4=h726a3e6_304
- mock=4.0.3=py38h578d9bd_3
- murmurhash=1.0.6=py38h709712a_2
- ncurses=6.3=h27087fc_1
- ninja=1.10.2=h4bd325d_1
- numpy=1.22.2=py38h6ae9a64_0
- openblas=0.3.20=pthreads_h320a7e8_1
- openssl=1.1.1q=h166bdaf_0
- packaging=21.3=pyhd8ed1ab_0
- parso=0.8.3=pyhd8ed1ab_0
- patch=2.7.6=h7f98852_1002
- patchelf=0.15.0=h58526e2_0
- pathy=0.6.2=pyhd8ed1ab_0
- pexpect=4.8.0=pyh9f0ad1d_2
- pickleshare=0.7.5=py_1003
- pkginfo=1.8.3=pyhd8ed1ab_0
- preshed=3.0.6=py38h709712a_1
- prompt-toolkit=3.0.31=pyha770c72_0
- psutil=5.9.2=py38h0a891b7_0
- ptyprocess=0.7.0=pyhd3deb0d_0
- pure_eval=0.2.2=pyhd8ed1ab_0
- py-lief=0.11.5=py38h709712a_1
- pycosat=0.6.3=py38h0a891b7_1010
- pycparser=2.21=pyhd8ed1ab_0
- pydantic=1.8.2=py38h497a2fe_2
- pygments=2.13.0=pyhd8ed1ab_0
- pyopenssl=22.0.0=pyhd8ed1ab_0
- pyparsing=3.0.9=pyhd8ed1ab_0
- pysocks=1.7.1=pyha2e5f31_6
- python=3.8.13=h582c2e5_0_cpython
- python-libarchive-c=4.0=py38h578d9bd_1
- python_abi=3.8=2_cp38
- pytz=2022.4=pyhd8ed1ab_0
- pyyaml=6.0=py38h0a891b7_4
- readline=8.1.2=h0f457ee_0
- requests=2.28.1=pyhd8ed1ab_0
- rhash=1.4.3=h166bdaf_0
- ripgrep=13.0.0=h2f28480_2
- ruamel_yaml=0.15.80=py38h0a891b7_1007
- scipy=1.6.3=py38h7b17777_0
- setuptools=59.5.0=py38h578d9bd_0
- shellingham=1.5.0=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- smart_open=5.2.1=pyhd8ed1ab_0
- soupsieve=2.3.2.post1=pyhd8ed1ab_0
- spacy=3.2.2=py38h2b96118_0
- spacy-legacy=3.0.10=pyhd8ed1ab_0
- spacy-loggers=1.0.3=pyhd8ed1ab_0
- sqlite=3.39.2=h4ff8645_0
- srsly=2.4.2=py38h709712a_1
- stack_data=0.5.1=pyhd8ed1ab_0
- thinc=8.0.13=py38h2b96118_0
- tk=8.6.12=h27826a3_0
- toml=0.10.2=pyhd8ed1ab_0
- toolz=0.12.0=pyhd8ed1ab_0
- traitlets=5.4.0=pyhd8ed1ab_0
- typer=0.4.2=pyhd8ed1ab_0
- typing-extensions=4.4.0=hd8ed1ab_0
- typing_extensions=4.4.0=pyha770c72_0
- tzdata=2022a=h191b570_0
- urllib3=1.26.11=pyhd8ed1ab_0
- wasabi=0.10.0=pyhd8ed1ab_0
- wcwidth=0.2.5=pyh9f0ad1d_2
- wheel=0.37.1=pyhd8ed1ab_0
- xz=5.2.5=h516909a_1
- yaml=0.2.5=h7f98852_2
- zlib=1.2.12=h166bdaf_2
- zstd=1.5.2=ha95c52a_0
- pip:
- absl-py==1.2.0
- alabaster==0.7.12
- anyio==3.6.1
- apex==0.1
- appdirs==1.4.4
- argon2-cffi==21.3.0
- argon2-cffi-bindings==21.2.0
- attrs==22.1.0
- audioread==3.0.0
- babel==2.10.3
- bleach==5.0.1
- cachetools==5.2.0
- certifi==2022.9.24
- cloudpickle==2.2.0
- codecov==2.1.12
- contourpy==1.0.5
- coverage==6.5.0
- cuda-python==11.7.0+0.g95a2041.dirty
- cudf==22.8.0a0+304.g6ca81bbc78.dirty
- cugraph==22.8.0a0+132.g2daa31b6.dirty
- cuml==22.8.0a0+52.g73b8d00d0.dirty
- cupy-cuda118==11.0.0
- cycler==0.11.0
- cython==0.29.32
- dask==2022.7.1
- dask-cuda==22.8.0a0+36.g9860cad
- dask-cudf==22.8.0a0+304.g6ca81bbc78.dirty
- debugpy==1.6.3
- defusedxml==0.7.1
- distributed==2022.7.1
- docutils==0.17.1
- entrypoints==0.3
- expecttest==0.1.3
- fastjsonschema==2.16.2
- fastrlock==0.8
- flake8==3.7.9
- flask==2.2.2
- fonttools==4.37.4
- fsspec==2022.8.2
- functorch==0.3.0a0
- future==0.18.2
- google-auth==2.12.0
- google-auth-oauthlib==0.4.6
- graphsurgeon==0.4.6
- grpcio==1.49.1
- heapdict==1.0.1
- hypothesis==4.50.8
- imagesize==1.4.1
- importlib-metadata==5.0.0
- importlib-resources==5.10.0
- iniconfig==1.1.1
- iopath==0.1.10
- ipykernel==6.16.0
- ipython-genutils==0.2.0
- itsdangerous==2.1.2
- joblib==1.2.0
- json5==0.9.10
- jsonschema==4.16.0
- jupyter-client==7.4.2
- jupyter-core==4.11.1
- jupyter-server==1.21.0
- jupyter-tensorboard==0.2.0
- jupyterlab==2.3.2
- jupyterlab-pygments==0.2.2
- jupyterlab-server==1.2.0
- jupytext==1.14.1
- kiwisolver==1.4.4
- librosa==0.9.2
- llvmlite==0.39.1
- lmdb==1.3.0
- locket==1.0.0
- markdown==3.4.1
- markdown-it-py==2.1.0
- matplotlib==3.6.1
- mccabe==0.6.1
- mdit-py-plugins==0.3.1
- mdurl==0.1.2
- mistune==2.0.4
- msgpack==1.0.4
- nbclassic==0.4.5
- nbclient==0.7.0
- nbconvert==7.2.1
- nbformat==5.7.0
- nest-asyncio==1.5.6
- networkx==2.6.3
- nltk==3.7
- notebook==6.4.10
- notebook-shim==0.1.0
- numba==0.56.2
- nvidia-dali-cuda110==1.18.0
- nvidia-pyindex==1.0.9
- nvtx==0.2.5
- oauthlib==3.2.1
- onnx==1.12.0
- pandas==1.4.4
- pandocfilters==1.5.0
- partd==1.3.0
- pillow==9.0.1
- pip==22.3.1
- pkgutil-resolve-name==1.3.10
- pluggy==1.0.0
- polygraphy==0.42.1
- pooch==1.6.0
- portalocker==2.5.1
- prettytable==3.4.1
- prometheus-client==0.15.0
- protobuf==3.20.3
- py==1.11.0
- pyarrow==8.0.0
- pyasn1==0.4.8
- pyasn1-modules==0.2.8
- pybind11==2.10.0
- pycocotools==2.0+nv0.6.0
- pycodestyle==2.5.0
- pydot==1.4.2
- pyflakes==2.1.1
- pylibcugraph==22.8.0a0+132.g2daa31b6.dirty
- pynvml==11.4.1
- pyrsistent==0.18.1
- pytest==6.2.5
- pytest-cov==4.0.0
- pytest-pythonpath==0.7.4
- python-dateutil==2.8.2
- python-hostlist==1.22
- python-nvd3==0.15.0
- python-slugify==6.1.2
- pytorch-quantization==2.1.2
- pyzmq==24.0.1
- raft==22.8.0a0+70.g9070c30.dirty
- regex==2022.9.13
- requests-oauthlib==1.3.1
- resampy==0.4.2
- revtok==0.0.3
- rmm==22.8.0a0+62.gf6bf047.dirty
- rsa==4.9
- sacremoses==0.0.53
- scikit-learn==0.24.2
- send2trash==1.8.0
- sniffio==1.3.0
- snowballstemmer==2.2.0
- sortedcontainers==2.4.0
- soundfile==0.11.0
- sphinx==5.2.3
- sphinx-glpi-theme==0.3
- sphinx-rtd-theme==1.0.0
- sphinxcontrib-applehelp==1.0.2
- sphinxcontrib-devhelp==1.0.2
- sphinxcontrib-htmlhelp==2.0.0
- sphinxcontrib-jsmath==1.0.1
- sphinxcontrib-qthelp==1.0.3
- sphinxcontrib-serializinghtml==1.1.5
- tabulate==0.9.0
- tblib==1.7.0
- tensorboard==2.10.1
- tensorboard-data-server==0.6.1
- tensorboard-plugin-wit==1.8.1
- tensorrt==8.5.0.12
- terminado==0.16.0
- text-unidecode==1.3
- threadpoolctl==3.1.0
- tinycss2==1.1.1
- tomli==2.0.1
- torch==1.13.0a0+d0d6b1f
- torch-tensorrt==1.3.0a0
- torchtext==0.11.0a0
- torchvision==0.14.0a0
- tornado==6.2
- tqdm==4.64.1
- transformer-engine==0.1.0
- treelite==2.4.0
- treelite-runtime==2.4.0
- ucx-py==0.27.0a0+29.ge9e81f8
- uff==0.6.9
- webencodings==0.5.1
- websocket-client==1.4.1
- werkzeug==2.2.2
- xgboost==1.6.1
- zict==2.2.0
- zipp==3.9.0
prefix: /opt/conda

Command Line Output

Output of `jupyter lab` (`docker run --entrypoint jupyter testimg lab`):

`[C 18:37:00.726 LabApp] Bad config encountered during initialization: The 'contents_manager_class' trait of a LabApp instance expected a subclass of notebook.services.contents.manager.ContentsManager or jupyter_server.contents.services.managers.ContentsManage, not the JupytextContentsManager JupytextContentsManager.`

[welcome]

Thank you for opening your first issue in this project! Engagement like this is essential for open source projects! 🤗

If you haven't done so already, check out Jupyter's Code of Conduct. Also, please try to follow the issue template as it helps other other community members to contribute more effectively.

You can meet the other Jovyans by joining our Discourse forum. There is also an intro thread there where you can stop by and say Hi! 👋

Welcome to the Jupyter community! 🎉

[krassowski]

• JupytextContentsManager comes from https://github.com/mwouts/jupytext extension, not JupyterLab itself. Does the problem remain when excluding third-party extensions from the docker build?
• Is the version of jupytext that you install (/is installed in the docker base image that you derive from) compatible with JupyterLab 2.x?
• Can you try with JupyterLab 3.x?

[JasonWeill]

@morrisalp Can you please add a comment answering the questions that @krassowski asked earlier? Thanks!

[morrisalp]

It appears this is fixed with JL v3.5.2. In particular, the base image nvcr.io/nvidia/pytorch:22.10-py3 which my Dockerfile used already contained JL v2 and hence the pip install jupyterlab in the Dockerfile was a no-op, changing it to pip install --update jupyterlab installs v3 and resolves this issue.