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Dev jupyter kernel fix #118

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Merged
gaelforget merged 2 commits into from
Oct 5, 2025
Merged

Dev jupyter kernel fix #118

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2c457b8
fix jupyter kernel issue, rm Manifest.toml
gaelforget Oct 3, 2025
9300561
update Dockerfile after ECCO-Docker
gaelforget Oct 5, 2025
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47 changes: 19 additions & 28 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -2,28 +2,18 @@ FROM jupyter/base-notebook:latest

USER root

RUN apt-get update && \
apt-get install -y --no-install-recommends build-essential && \
apt-get install -y --no-install-recommends vim && \
apt-get install -y --no-install-recommends curl && \
apt-get install -y --no-install-recommends git-all && \
apt-get install -y --no-install-recommends unzip && \
apt-get install -y --no-install-recommends gfortran && \
apt-get install -y --no-install-recommends openmpi-bin && \
apt-get install -y --no-install-recommends libopenmpi-dev && \
apt-get install -y --no-install-recommends libnetcdf-dev && \
apt-get install -y --no-install-recommends libnetcdff-dev && \
apt-get clean && rm -rf /var/lib/apt/lists/*
ENV mainpath=/home/jovyan/
RUN mkdir -p ${mainpath}

USER ${NB_USER}
RUN apt-get update

ENV mainpath=/home/${NB_USER}
RUN apt-get install -y --no-install-recommends build-essential && \
apt-get install -y --no-install-recommends vim && \
apt-get install -y --no-install-recommends git && \
apt-get install -y --no-install-recommends curl && \
apt-get install -y --no-install-recommends unzip

RUN echo 'alias julia="${mainpath}/.juliaup/bin/julia --project=${mainpath}"' >> ~/.bashrc
RUN curl -fsSL https://install.julialang.org | sh -s -- --yes

USER root
RUN ln -s ${mainpath}/.juliaup/bin/julia /usr/local/bin/julia
RUN apt-get clean && rm -rf /var/lib/apt/lists/*

USER ${NB_USER}

Expand All @@ -32,20 +22,21 @@ COPY --chown=${NB_USER}:users ./src/plutoserver ${mainpath}/plutoserver

RUN cp ${mainpath}/src/setup.py ${mainpath}/setup.py
RUN cp ${mainpath}/src/runpluto.sh ${mainpath}/runpluto.sh
RUN cp ${mainpath}/src/environment.yml ${mainpath}/environment.yml
RUN cp ${mainpath}/src/Project.toml ${mainpath}/Project.toml
RUN cp ${mainpath}/src/Manifest.toml ${mainpath}/Manifest.toml

RUN echo 'alias julia="${mainpath}/.juliaup/bin/julia --project=${mainpath}"' >> ~/.bashrc

RUN ${mainpath}/.juliaup/bin/julia -e "import Pkg; Pkg.update(); Pkg.instantiate();"
RUN conda config --env --add channels conda-forge
RUN conda config --env --add channels r

RUN curl -fsSL https://install.julialang.org | sh -s -- --yes

RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} -e "import Pkg; Pkg.update(); Pkg.instantiate();"
RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} ${mainpath}/src/download_notebooks.jl
RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath} ${mainpath}/src/warmup1.jl

RUN jupyter lab build && \
jupyter lab clean && \
pip install ${mainpath} --no-cache-dir && \
rm -rf ~/.cache

RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath}/src ${mainpath}/src/warmup1.jl
RUN ${mainpath}/.juliaup/bin/julia --project=${mainpath}/src ${mainpath}/src/download_notebooks.jl

RUN mkdir .dev
RUN mv build plutoserver.egg-info .dev

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