Jupyter notebook with poetry give error: [Errno 13] Permission denied: '/home/jovyan/.local/share/jupyter/runtime'

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Hi! I’m trying to create a custom image to use it in singleuser Jupyterhub on k8s.
I would need to create a jupyter image that has Python version 3.12 and create a custom kernel via poetry.
This is the configuration of my Dockerfile:

FROM quay.io/jupyter/minimal-notebook:python-3.12

USER root

RUN apt-get update && apt-get install -y \
    build-essential \
    python3-dev \
    libffi-dev \
    curl \
    postgresql-client \
    libpq-dev \
    gfortran \
    libopenblas-dev \
    iputils-ping \
    git \
    openssh-client \
    && rm -rf /var/lib/apt/lists/*


ENV POETRY_VERSION=1.8.2
ENV POETRY_HOME=/opt/poetry
ENV POETRY_VENV=/opt/poetry-venv

ENV POETRY_CACHE_DIR=/opt/.cache
ENV PATH="${PATH}:${POETRY_VENV}/bin"

RUN python3 -m venv $POETRY_VENV \
    && $POETRY_VENV/bin/pip install -U pip setuptools \
    && $POETRY_VENV/bin/pip install poetry==${POETRY_VERSION} 

RUN mkdir -p /root/.ssh
RUN chmod 0700 /root/.ssh
COPY known_hosts /root/.ssh/known_hosts
COPY id_rsa /root/.ssh/id_rsa
COPY id_rsa.pub /root/.ssh/id_rsa.pub
RUN chmod 600 /root/.ssh/id_rsa
RUN chmod 600 /root/.ssh/id_rsa.pub

COPY poetry.lock pyproject.toml ./

RUN poetry lock --no-update && poetry install --no-interaction --no-cache 

RUN poetry run pip install ipykernel

RUN poetry run python -m ipykernel install --user --name new-kernel --display-name "new-kernel" 

EXPOSE 8888

# CMD ["poetry", "run", "jupyter-lab", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]
CMD ["jupyter", "lab", "--ip=0.0.0.0", "--no-browser", "--allow-root"]

As soon as I start the server, however, I get the following error:

             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/jupyter_server/serverapp.py", line 2813, in initialize
    self.init_configurables()
  File "/opt/conda/lib/python3.12/site-packages/jupyter_server/serverapp.py", line 2087, in init_configurables
    "connection_dir": self.runtime_dir,
                      ^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/traitlets/traitlets.py", line 687, in __get__
    return t.cast(G, self.get(obj, cls))  # the G should encode the Optional
                     ^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/traitlets/traitlets.py", line 635, in get
    default = obj.trait_defaults(self.name)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/traitlets/traitlets.py", line 1897, in trait_defaults
    return t.cast(Sentinel, self._get_trait_default_generator(names[0])(self))
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.12/site-packages/jupyter_core/application.py", line 111, in _runtime_dir_default
    ensure_dir_exists(rd, mode=0o700)
  File "/opt/conda/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 26, in ensure_dir_exists
    Path(path).mkdir(parents=True, mode=mode)
  File "/opt/conda/lib/python3.12/pathlib.py", line 1311, in mkdir
    os.mkdir(self, mode)
PermissionError: [Errno 13] Permission denied: '/home/jovyan/.local/share/jupyter/runtime'

image
image1011×811 32 KB

How can I solve this? are there guides to building an image with poetry and python 3.12?
Building the image from scratch with python3.12 when I start the server I get:

image_480
image_480478×105 18.7 KB

Thanks

2

You’ve switched to USER root at the start which means all your RUN commands will create root owned files/directories. Try switching back to USER ${NB_UID} before running any commands that affect the home directory, or alternatively there’s a fix-permissions "/home/${NB_USER}" script you can run, for example:

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