Dockerfile

FROM openjdk:11.0.3-jdk as openjdk

FROM jupyter/r-notebook:lab-3.2.9

ENV CONDA_DIR=/opt/conda \
    SHELL=/bin/bash \
    USER="jovyan" \
    UID=1000 \
    GID=100 \
    LC_ALL=en_US.UTF-8 \
    LANG=en_US.UTF-8 \
    LANGUAGE=en_US.UTF-8
ENV PATH="${CONDA_DIR}/bin:${PATH}" \
    HOME="/home/${USER}"

USER root

RUN apt-get update

USER ${USER}

RUN conda install -y python"<3.8"
RUN conda install -y jupyterlab=2.3.2


# Pycrop2ML and OpenAlea INSTALLATION
RUN conda install -y -c amei -c openalea3 -c conda-forge pycropml


RUN pip install -U urllib3 requests

# Pycrop2ml_ui installation
COPY --chown=${UID} . Pycrop2ml_ui
WORKDIR Pycrop2ml_ui
RUN pip install -r requirements.txt
RUN pip install .
WORKDIR ${HOME}
RUN cp Pycrop2ml_ui/src/pycrop2ml_ui/AppLauncher.ipynb ${HOME}/work/AppLauncher.ipynb
RUN rm -rf Pycrop2ml_ui

# Some parameters must be set to False for MyBinder, according to https://github.com/matplotlib/ipympl/issues/262
RUN jupyter labextension install @jupyter-widgets/jupyterlab-manager@2 qgrid2 --dev-build=False --minimize=False

# C++ KERNEL INSTALLATION
# !! Mamba needs Python>=3.9, which is not compatible with jupyterlab=2.3.2 necessary for qgrid in Pycrop2ml_ui package.
# RUN conda install -y -c conda-forge mamba
# RUN mamba install -y xeus-cling -c conda-forge


RUN conda install -y xeus-cling=0.11.0 -c conda-forge

# install R library
RUN echo 'install.packages(c("gsubfn"),repos="http://cran.us.r-project.org", dependencies=TRUE)' > /tmp/packages.R && Rscript /tmp/packages.R

# JAVA KERNEL INSTALLATION
COPY --from=openjdk /usr/local/openjdk-11 /usr/local/openjdk-11
ENV JAVA_HOME /usr/local/openjdk-11
ENV PATH $JAVA_HOME/bin:$PATH

USER root
RUN apt-get install -y curl unzip

USER ${USER}
RUN curl -L https://github.com/SpencerPark/IJava/releases/download/v1.3.0/ijava-1.3.0.zip > ijava-kernel.zip

# Unpack and install the kernel
RUN unzip ijava-kernel.zip -d ijava-kernel \
    && cd ijava-kernel \
    && python3 install.py --sys-prefix

WORKDIR ${HOME}
RUN rm -rf ijava-kernel ijava-kernel.zip

# FORTRAN KERNEL INSTALLATION

USER root
RUN apt-get install -y git gfortran

#RUN chown ${USER}:users -R /tmp && chmod o+t -R /tmp

USER ${USER}
RUN pip install jupyter-fortran-kernel
RUN git clone https://github.com/ZedThree/jupyter-fortran-kernel.git jupyter-fortran-kernel
WORKDIR jupyter-fortran-kernel
RUN jupyter-kernelspec install --prefix=/opt/conda/ fortran_spec/

WORKDIR ${HOME}
RUN rm -rf jupyter-fortran-kernel
USER root

# DOTNET KERNEL INSTALLATION

ENV \
  # Enable detection of running in a container
  DOTNET_RUNNING_IN_CONTAINER=true \
  # Enable correct mode for dotnet watch (only mode supported in a container)
  DOTNET_USE_POLLING_FILE_WATCHER=true \
  # Skip extraction of XML docs - generally not useful within an image/container - helps performance
  NUGET_XMLDOC_MODE=skip \
  # Opt out of telemetry until after we install jupyter when building the image, this prevents caching of machine id
  DOTNET_INTERACTIVE_CLI_TELEMETRY_OPTOUT=true

# Install .NET CLI dependencies
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
        libc6 \
        libgcc1 \
        libgssapi-krb5-2 \
        libicu66 \
        libssl1.1 \
        libstdc++6 \
        zlib1g

# Install .NET Core SDK

# When updating the SDK version, the sha512 value a few lines down must also be updated.
ENV DOTNET_SDK_VERSION 5.0.102

RUN dotnet_sdk_version=5.0.102 \
    && curl -SL --output dotnet.tar.gz https://dotnetcli.azureedge.net/dotnet/Sdk/$dotnet_sdk_version/dotnet-sdk-$dotnet_sdk_version-linux-x64.tar.gz \
    && dotnet_sha512='0ce2d5365ca39808fb71baec4584d4ec786491c3735543dc93244604ea97e242377d0987cd8b1e529258dee68f203b5780559201e7ea6d84487d6d8d433329b3' \
    && echo "$dotnet_sha512 dotnet.tar.gz" | sha512sum -c - \
    && mkdir -p /usr/share/dotnet \
    && tar -ozxf dotnet.tar.gz -C /usr/share/dotnet \
    && rm dotnet.tar.gz \
    && ln -s /usr/share/dotnet/dotnet /usr/bin/dotnet \
    # Trigger first run experience by running arbitrary cmd
    && dotnet help


# Add package sources
RUN echo "\
<configuration>\
  <solution>\
    <add key=\"disableSourceControlIntegration\" value=\"true\" />\
  </solution>\
  <packageSources>\
    <clear />\
    <add key=\"dotnet-public\" value=\"https://pkgs.dev.azure.com/dnceng/public/_packaging/dotnet-public/nuget/v3/index.json\" />\
    <add key=\"dotnet-eng\" value=\"https://pkgs.dev.azure.com/dnceng/public/_packaging/dotnet-eng/nuget/v3/index.json\" />\
    <add key=\"dotnet-tools\" value=\"https://pkgs.dev.azure.com/dnceng/public/_packaging/dotnet-tools/nuget/v3/index.json\" />\
    <add key=\"dotnet-libraries\" value=\"https://pkgs.dev.azure.com/dnceng/public/_packaging/dotnet-libraries/nuget/v3/index.json\" />\
    <add key=\"dotnet5\" value=\"https://pkgs.dev.azure.com/dnceng/public/_packaging/dotnet5/nuget/v3/index.json\" />\
    <add key=\"MachineLearning\" value=\"https://pkgs.dev.azure.com/dnceng/public/_packaging/MachineLearning/nuget/v3/index.json\" />\
  </packageSources>\
  <disabledPackageSources />\
</configuration>\
" > ${HOME}/NuGet.config

RUN chown -R ${UID} ${HOME}
USER ${USER}

#Install nteract 
RUN pip install nteract_on_jupyter


# Install lastest build of Microsoft.DotNet.Interactive
#RUN dotnet tool install -g Microsoft.dotnet-interactive --add-source "https://pkgs.dev.azure.com/dnceng/public/_packaging/dotnet-experimental/nuget/v3/index.json"

RUN dotnet tool install -g --ignore-failed-sources Microsoft.dotnet-interactive --version 1.0.255902

ENV PATH="${PATH}:${HOME}/.dotnet/tools"
RUN echo "$PATH"

# Install kernel specs
RUN dotnet interactive jupyter install


# Enable telemetry once we install jupyter for the image
ENV DOTNET_INTERACTIVE_CLI_TELEMETRY_OPTOUT=false


USER root
RUN rm -rf /var/lib/apt/lists/*
USER ${USER}

# Set root directory to /home/joyvan/work
WORKDIR ${HOME}/work/
CMD ["/usr/local/bin/start.sh", "jupyter", "lab", "AppLauncher.ipynb"]