feat: add julia (#84)

Co-authored-by: Emma Jablonski <[email protected]>

.github/workflows/build_and_push_to_docker.yml

@@ -11,11 +11,18 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        RENKU_VERSION: ["", "0.9.1", "0.10.2"]
-        EXTENSIONS: ["py3.7", "r3.6.1", "bioc3_10", "cuda9.2", "cuda10.0-tf1.14"]
-
+        RENKU_VERSION:
+          - ""
+          - "0.9.1"
+          - "0.10.2"
+        EXTENSIONS:
+          - py3.7
+          - r3.6.1
+          - bioc3_10
+          - cuda9.2
+          - cuda10.0-tf1.14
+          - julia1.3.1
     steps:
-
     - name: Docker Login
       uses: Azure/docker-login@v1
       with:

docker/julia1.3.1/Dockerfile

@@ -0,0 +1,125 @@
+ARG JUPYTERHUB_VERSION=1.2
+ARG BASE_IMAGE=jupyterhub/singleuser:$JUPYTERHUB_VERSION
+FROM $BASE_IMAGE as base
+
+LABEL maintainer="Swiss Data Science Center <[email protected]>"
+
+USER root
+# Copied from jupyter-minimal-notebook
+# Install all OS dependencies for fully functional notebook server
+RUN apt-get update && apt-get install -yq --no-install-recommends \
+    build-essential \
+    curl \
+    git \
+    gnupg \
+    graphviz \
+    less \
+    libsm6 \
+    libxext-dev \
+    libxrender1 \
+    lmodern \
+    musl-dev \
+    nano \
+    netcat \
+    python-dev \
+    unzip \
+    vim \
+    && apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# link the musl library needed by psutil
+RUN ln -s /usr/lib/x86_64-linux-musl/libc.so /lib/libc.musl-x86_64.so.1
+
+# install git-lfs
+RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash && sudo apt-get install git-lfs=2.8.0
+
+# Add Tini
+ENV TINI_VERSION v0.18.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini
+
+# Julia dependencies and installation - adapted from https://github.com/jupyter/docker-stacks/blob/master/datascience-notebook/Dockerfile
+# install Julia packages in /opt/julia instead of $HOME
+ENV JULIA_DEPOT_PATH=/opt/julia
+ENV JULIA_PKGDIR=/opt/julia
+ENV JULIA_VERSION=1.3.1
+
+RUN mkdir /opt/julia-${JULIA_VERSION} && \
+    cd /tmp && \
+    wget -q https://julialang-s3.julialang.org/bin/linux/x64/`echo ${JULIA_VERSION} | cut -d. -f 1,2`/julia-${JULIA_VERSION}-linux-x86_64.tar.gz && \
+    echo "faa707c8343780a6fe5eaf13490355e8190acf8e2c189b9e7ecbddb0fa2643ad *julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | sha256sum -c - && \
+    tar xzf julia-${JULIA_VERSION}-linux-x86_64.tar.gz -C /opt/julia-${JULIA_VERSION} --strip-components=1 && \
+    rm /tmp/julia-${JULIA_VERSION}-linux-x86_64.tar.gz
+RUN ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
+
+# Show Julia where conda libraries are \
+RUN mkdir /etc/julia && \
+    echo "push!(Libdl.DL_LOAD_PATH, \"$CONDA_DIR/lib\")" >> /etc/julia/juliarc.jl && \
+    # Create JULIA_PKGDIR \
+    mkdir $JULIA_PKGDIR && \
+    chown $NB_USER $JULIA_PKGDIR && \
+    fix-permissions $JULIA_PKGDIR
+
+# Add a new group with id 1000 and arbitrary name
+# Note: this is to standardize groups between the R and jupyter images
+RUN groupadd -g 1000 jovyan
+
+# switch to the notebook user
+USER $NB_USER
+
+RUN julia -e 'import Pkg; Pkg.update()' && \
+    (test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
+    julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \
+    # move kernelspec out of home \
+    mv $HOME/.local/share/jupyter/kernels/julia* $CONDA_DIR/share/jupyter/kernels/ && \
+    chmod -R go+rx $CONDA_DIR/share/jupyter && \
+    rm -rf $HOME/.local/share/jupyter && \
+    fix-permissions $JULIA_PKGDIR $CONDA_DIR/share/jupyter
+
+# install jupyterlab, papermill, git extension and renku-jupyterlab-ts
+COPY requirements.txt /tmp/requirements.txt
+RUN python3 -m pip install -U pip && \
+    pip install -r /tmp/requirements.txt && \
+    jupyter labextension update @jupyterlab/hub-extension --no-build && \
+    jupyter labextension install @jupyterlab/git --no-build && \
+    jupyter labextension list && \
+    pip install jupyterlab-git && \
+    jupyter serverextension enable --py jupyterlab_git && \
+    jupyter lab build
+
+
+# fix https://github.com/SwissDataScienceCenter/renku-jupyter/issues/14
+RUN conda install gxx_linux-64
+
+# install renku-python
+ENV RENKU_DISABLE_VERSION_CHECK 1
+
+RUN python3 -m pip install "pipx>=0.15.0.0"
+ARG RENKU_PIP_SPEC="renku"
+RUN pipx install ${RENKU_PIP_SPEC} --pip-args="--pre" && \
+    pipx inject renku sentry-sdk && \
+    pipx ensurepath
+
+# configure git
+COPY git-config.bashrc /home/$NB_USER/
+RUN cat /home/$NB_USER/git-config.bashrc >> /home/$NB_USER/.bashrc && rm /home/$NB_USER/git-config.bashrc
+
+# configure powerline
+COPY powerline.bashrc /tmp/powerline.bashrc
+COPY powerline.config /tmp/powerline.config
+
+RUN cat /tmp/powerline.bashrc >> ~/.bashrc && \
+    pip install powerline-shell && \
+    mkdir -p ~/.config/powerline-shell/ && \
+    cat /tmp/powerline.config >> ~/.config/powerline-shell/config.json
+
+# Add user `jovyan` to sudoers (passwordless)
+USER root
+RUN echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers && \
+    rm -rf /wheels
+USER $NB_USER
+
+COPY entrypoint.sh /entrypoint.sh
+ENTRYPOINT [ "/tini", "--", "/entrypoint.sh" ]
+
+CMD '/usr/local/bin/start-singleuser.sh'

docker/julia1.3.1/entrypoint.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# Setup git user
+if [ -z "$(git config --global --get user.name)" ]; then
+    git config --global user.name "$GIT_AUTHOR_NAME"
+fi
+if [ -z "$(git config --global --get user.email)" ]; then
+    git config --global user.email "$EMAIL"
+fi
+
+#
+# copy the environment from renku-env repo
+#
+
+# clone the repo
+proto=$(echo $GITLAB_URL | sed -e's,^\(.*://\).*,\1,g')
+url=$(echo ${GITLAB_URL/$proto/})
+user=$(echo ${CI_REPOSITORY_URL/$proto/} | grep @ | cut -d@ -f1)
+
+git clone --depth 1 ${proto}${user}@${url}/${JUPYTERHUB_USER}/renku-env.git /tmp/renku-env || true
+
+# append the contents of all the files to same files in ${HOME}
+find /tmp/renku-env -not -path '*.git*' -type f -print0 | xargs --null -I{} sh -c 'cat {} >> ${HOME}/$(basename "{}")' || true
+
+# run the command
+$@

docker/julia1.3.1/git-config.bashrc

@@ -0,0 +1,8 @@
+
+# Setup git user
+if [ -z "$(git config --global --get user.name)" ]; then
+    git config --global user.name "$GIT_AUTHOR_NAME"
+fi
+if [ -z "$(git config --global --get user.email)" ]; then
+    git config --global user.email "$EMAIL"
+fi

docker/julia1.3.1/powerline.bashrc

@@ -0,0 +1,7 @@
+function _update_ps1() {
+    PS1=$(powerline-shell $?)
+}
+
+if [[ $TERM != linux && ! $PROMPT_COMMAND =~ _update_ps1 ]]; then
+    PROMPT_COMMAND="_update_ps1; $PROMPT_COMMAND"
+fi

docker/julia1.3.1/powerline.config

@@ -0,0 +1,9 @@
+{
+  "segments": [
+    "virtual_env",
+    "cwd",
+    "git",
+    "root"
+  ],
+  "mode": "compatible"
+}

docker/julia1.3.1/requirements.txt

@@ -0,0 +1,4 @@
+papermill<1.2.0
+requests>=2.20.0
+jupyterlab==1.2.6
+jupyterhub==1.1.0