Dockerfile-jupyter

ARG BASE_IMAGE_TAG

FROM 527538141574.dkr.ecr.eu-central-1.amazonaws.com/eoxhub-jupyterlab:${BASE_IMAGE_TAG}

# NOTE: this is not a duplication, but a documented workaround
# https://docs.docker.com/engine/reference/builder/#understand-how-arg-and-from-interact
ARG BASE_IMAGE_TAG

ENV BASE_IMAGE_TAG=${BASE_IMAGE_TAG}

ARG NB_USER="jovyan"
ARG NB_UID="1000"
ARG NB_GID="100"

RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
    useradd -m -s /bin/bash -N -u $NB_UID -g $NB_GID $NB_USER && \
    chmod g+w /etc/passwd && \
    chown $NB_USER $HOME

# add group for nfs provisioner
RUN groupadd users-nfs -g 2005

# allow user kernels here
RUN mkdir /opt/conda/pkgs \
    && chown $NB_USER:$NB_GID /opt/conda/pkgs /opt/conda/envs

USER $NB_UID

ADD --chown=1000 kernel-jupyter.yaml /tmp

RUN pip config set global.cache-dir false && \
    mamba env create \
      -p /opt/conda/envs/edc-default-${BASE_IMAGE_TAG} \
      -f /tmp/kernel-jupyter.yaml && \
    mamba clean --all -f -y && \
    rm /tmp/kernel-jupyter.yaml && \
    pip config set global.cache-dir true

USER root

RUN echo "source activate edc-default-${BASE_IMAGE_TAG}" >> /etc/bash.bashrc

# remove kernel from default env, only jupyter server runs there
RUN /opt/conda/envs/default/bin/python3 -m nb_conda_kernels remove -y python3

# install current conda kernel such that papermill can use it
# https://github.com/Anaconda-Platform/nb_conda_kernels#use-with-nbconvert-voila-papermill
RUN mkdir /etc/jupyter \
    && echo '{"CondaKernelSpecManager": {"kernelspec_path": "--user" }}' > /etc/jupyter/jupyter_config.json \
    && /opt/conda/envs/default/bin/python3 -m nb_conda_kernels list
# NOTE: "nb_conda_kernels list" will create kernel config file
# NOTE: setting kernelspec_path to "" will install it globally

# Need to downgrade edc-jlab in jupyterlab conda env from base image
RUN mamba run -n default python3 -m pip install https://github.com/eurodatacube/edc-jlab/raw/master/dist/edc_jlab-0.5.15-py3-none-any.whl

USER $NB_UID