Notebook svg output OK in jupyterlab but KO using jupyterhub

[mottelet]

Bug description

Hello, I am curently setting up a jupyterhub server using tljh distribution (https://tljh.jupyter.org/en/latest/) on a Linux Ubuntu 20.04.6 LTS and using the Calysto Scilab kernel (https://github.com/Calysto/scilab_kernel).

On an example notebook run in a jupyterhub session, outputing a graph under svg format, the graph is cropped (some labels and legends do not appear), although running the same notebook outside jupyterhub yields a correct output (graph is not cropped):

Both environments use jupyterlab 4.1.2 and latest Scilab kernel (0.10).

How to reproduce

Install official tljh distribution, install latest scilab 2024.0.0 (www.scilab.org), install the Scilab kernel from within a console in jupyterhub as admin user, add the path to scilab-adv-cli in
/opt/tljh/user/share/jupyter/kernels/scilab/kernel.json:

{
   "argv":[
      "/opt/tljh/user/bin/python",
      "-m",
      "scilab_kernel",
      "-f",
      "{connection_file}"
   ],
   "env":{
      "SCILAB_EXECUTABLE":"PATH_WHERE_SCILAB_WAS_INSTALLED/scilab-2024.0.0/bin/scilab-adv-cli"
   },
   "display_name":"Scilab",
   "language":"scilab",
   "mimetype":"text/x-scilab",
   "name":"scilab"
}

login to the jupyterhub (http://localhost:8080), create a new Scilab notebook and paste the following code in the first cell:

h=10.^-(1:0.05:15)';
hstar=2*sqrt(%eps*cos(1))
clf
plot(h,abs((cos(1+h)-cos(1))./h+sin(1))/sin(1));gca().log_flags="ll";
plot([hstar,hstar],[1e-10,1e-1],'-r')
xstring(hstar,1e-10,"$\LARGE h^*$")
xlabel("$\LARGE h$");ylabel("$\LARGE\left|\frac{f''(1)-D(h)}{f''(1)}\right|$")
isoview

Expected behaviour

when running the same notebook in classical jupyterlab

Actual behaviour

when running the notebook in jupyterhub

Your personal set up

• OS: Linux Ubuntu 20.04.6 LTS
  Below from a console within jupyterhub session

jupyter-mottelet@marguerite:~$ jupyterhub --version
4.0.2
jupyter-mottelet@marguerite:~$ jupyter --version
Selected Jupyter core packages...
IPython          : 8.11.0
ipykernel        : 6.22.0
ipywidgets       : 7.7.4
jupyter_client   : 8.1.0
jupyter_core     : 5.3.0
jupyter_server   : 2.12.5
jupyterlab       : 4.1.2
nbclient         : 0.7.2
nbconvert        : 7.2.10
nbformat         : 5.8.0
notebook         : 7.1.1
qtconsole        : 5.5.1
traitlets        : 5.9.0

jupyter-mottelet@marguerite:~$ python --version
Python 3.9.7

Full environment

jupyter-mottelet@marguerite:~$ pip freeze
aiofiles==22.1.0
aiosqlite==0.18.0
alembic==1.10.2
anyio==3.6.2
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
arrow==1.2.3
asttokens==2.2.1
async-generator==1.10
async-lru==2.0.4
attrs==22.2.0
Babel==2.12.1
backcall==0.2.0
beautifulsoup4==4.12.0
bleach==6.0.0
brotlipy==0.7.0
certifi==2022.12.7
certipy==0.1.3
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1631636250774/work
chardet @ file:///home/conda/feedstock_root/build_artifacts/chardet_1610093492116/work
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1626371162869/work
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1602866480661/work
comm==0.1.3
conda==4.10.3
conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1618231390031/work
cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography_1633983255347/work
debugpy==1.6.6
decorator==5.1.1
defusedxml==0.7.1
entrypoints==0.4
executing==1.2.0
fastjsonschema==2.16.3
fqdn==1.5.1
greenlet==2.0.2
h11==0.14.0
httpcore==1.0.4
httpx==0.27.0
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1609836280497/work
importlib-metadata==6.1.0
ipykernel==6.22.0
ipython==8.11.0
ipython-genutils==0.2.0
ipywidgets==7.7.4
isoduration==20.11.0
jedi==0.18.2
Jinja2==3.1.2
json5==0.9.11
jsonpointer==2.3
jsonschema==4.21.1
jsonschema-specifications==2023.12.1
jupyter==1.0.0
jupyter-console==6.6.3
jupyter-events==0.9.0
jupyter-lsp==2.2.3
jupyter-resource-usage==0.6.4
jupyter-telemetry==0.1.0
jupyter-ydoc==0.2.3
jupyter_client==8.1.0
jupyter_core==5.3.0
jupyter_server==2.12.5
jupyter_server_fileid==0.8.0
jupyter_server_terminals==0.5.2
jupyter_server_ydoc==0.8.0
jupyterhub==4.0.2
jupyterlab==4.1.2
jupyterlab-pygments==0.2.2
jupyterlab-widgets==1.1.3
jupyterlab_server==2.25.3
Mako==1.2.4
mamba @ file:///home/conda/feedstock_root/build_artifacts/mamba_1632770295204/work
MarkupSafe==2.1.2
matplotlib-inline==0.1.6
metakernel==0.30.1
mistune==2.0.5
nbclassic==0.5.3
nbclient==0.7.2
nbconvert==7.2.10
nbformat==5.8.0
nbgitpuller==1.1.1
nest-asyncio==1.5.6
notebook==7.1.1
notebook_shim==0.2.2
nteract-on-jupyter==2.1.3
oauthlib==3.2.2
overrides==7.7.0
packaging==23.0
pamela==1.0.0
pandocfilters==1.5.0
parso==0.8.3
pexpect==4.8.0
pickleshare==0.7.5
platformdirs==3.2.0
prometheus-client==0.16.0
prompt-toolkit==3.0.38
psutil==5.9.4
ptyprocess==0.7.0
pure-eval==0.2.2
pycosat @ file:///home/conda/feedstock_root/build_artifacts/pycosat_1610094799048/work
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1593275161868/work
Pygments==2.14.0
pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1633192417276/work
pyrsistent==0.19.3
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1610291451001/work
python-dateutil==2.8.2
python-json-logger==2.0.7
PyYAML==6.0
pyzmq==25.0.2
qtconsole==5.5.1
QtPy==2.4.1
referencing==0.33.0
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rpds-py==0.18.0
ruamel-yaml-conda @ file:///home/conda/feedstock_root/build_artifacts/ruamel_yaml_1611943432947/work
ruamel.yaml==0.17.21
ruamel.yaml.clib==0.2.7
scilab-kernel==0.10.0
Send2Trash==1.8.2
six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
sniffio==1.3.0
soupsieve==2.4
SQLAlchemy==1.4.47
stack-data==0.6.2
terminado==0.17.1
tinycss2==1.2.1
tomli==2.0.1
tornado==6.2
tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1632160078689/work
traitlets==5.9.0
typing_extensions==4.5.0
uri-template==1.2.0
urllib3 @ file:///home/conda/feedstock_root/build_artifacts/urllib3_1632350318291/work
wcwidth==0.2.6
webcolors==1.13
webencodings==0.5.1
websocket-client==1.5.1
widgetsnbextension==3.6.3
y-py==0.5.9
ypy-websocket==0.8.2
zipp==3.15.0

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[minrk]

Both screenshots are from the same environment (sys.executable matches) as the same user on the same system?

You might try running https://github.com/minrk/envreport to see if you can spot a difference between the two environments.

It's very unlikely this is related to JupyterHub itself, instead being a difference of environment loading different configuration. For example, launching a server in JupyterHub typically doesn't source your .bash_profile, etc. which may set various environment variables that are relevant.