Add a setup script to install Julia + IJulia (#1927)

datascience-notebook/Dockerfile

@@ -12,12 +12,6 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 USER root
 
-# Julia installation
-# Default values can be overridden at build time
-# (ARGS are in lower case to distinguish them from ENV)
-# Check https://julialang.org/downloads/
-ARG julia_version="1.9.1"
-
 # R pre-requisites
 RUN apt-get update --yes && \
     apt-get install --yes --no-install-recommends \
@@ -29,36 +23,16 @@ RUN apt-get update --yes && \
 # Julia dependencies
 # install Julia packages in /opt/julia instead of ${HOME}
 ENV JULIA_DEPOT_PATH=/opt/julia \
-    JULIA_PKGDIR=/opt/julia \
+    JULIA_PKGDIR=/opt/julia
-    JULIA_VERSION="${julia_version}"
 
-WORKDIR /tmp
+# Setup Julia
-
+RUN /opt/setup-scripts/setup-julia.bash
-# hadolint ignore=SC2046
-RUN set -x && \
-    julia_arch=$(uname -m) && \
-    julia_short_arch="${julia_arch}" && \
-    if [ "${julia_short_arch}" == "x86_64" ]; then \
-      julia_short_arch="x64"; \
-    fi; \
-    julia_installer="julia-${JULIA_VERSION}-linux-${julia_arch}.tar.gz" && \
-    julia_major_minor=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2) && \
-    mkdir "/opt/julia-${JULIA_VERSION}" && \
-    wget --progress=dot:giga "https://julialang-s3.julialang.org/bin/linux/${julia_short_arch}/${julia_major_minor}/${julia_installer}" && \
-    tar xzf "${julia_installer}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
-    rm "${julia_installer}" && \
-    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}"
 
 USER ${NB_UID}
 
+# Setup IJulia kernel & other packages
+RUN /opt/setup-scripts/setup-julia-packages.bash
+
 # R packages including IRKernel which gets installed globally.
 # r-e1071: dependency of the caret R package
 RUN mamba install --yes \
@@ -86,18 +60,3 @@ RUN mamba install --yes \
     mamba clean --all -f -y && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
-
-# Add Julia packages.
-# Install IJulia as jovyan and then move the kernelspec out
-# to the system share location. Avoids problems with runtime UID change not
-# taking effect properly on the .local folder in the jovyan home dir.
-RUN julia -e 'import Pkg; Pkg.update()' && \
-    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" && \
-    fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
-
-WORKDIR "${HOME}"

julia-notebook/Dockerfile

@@ -12,56 +12,15 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 USER root
 
-# Julia installation
-# Default values can be overridden at build time
-# (ARGS are in lower case to distinguish them from ENV)
-# Check https://julialang.org/downloads/
-ARG julia_version="1.9.1"
-
 # Julia dependencies
 # install Julia packages in /opt/julia instead of ${HOME}
 ENV JULIA_DEPOT_PATH=/opt/julia \
-    JULIA_PKGDIR=/opt/julia \
+    JULIA_PKGDIR=/opt/julia
-    JULIA_VERSION="${julia_version}"
 
-WORKDIR /tmp
+# Setup Julia
-
+RUN /opt/setup-scripts/setup-julia.bash
-# hadolint ignore=SC2046
-RUN set -x && \
-    julia_arch=$(uname -m) && \
-    julia_short_arch="${julia_arch}" && \
-    if [ "${julia_short_arch}" == "x86_64" ]; then \
-      julia_short_arch="x64"; \
-    fi; \
-    julia_installer="julia-${JULIA_VERSION}-linux-${julia_arch}.tar.gz" && \
-    julia_major_minor=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2) && \
-    mkdir "/opt/julia-${JULIA_VERSION}" && \
-    wget --progress=dot:giga "https://julialang-s3.julialang.org/bin/linux/${julia_short_arch}/${julia_major_minor}/${julia_installer}" && \
-    tar xzf "${julia_installer}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
-    rm "${julia_installer}" && \
-    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}"
 
 USER ${NB_UID}
 
-# Add Julia packages.
+# Setup IJulia kernel & other packages
-# Install IJulia as jovyan and then move the kernelspec out
+RUN /opt/setup-scripts/setup-julia-packages.bash
-# to the system share location. Avoids problems with runtime UID change not
-# taking effect properly on the .local folder in the jovyan home dir.
-RUN julia -e 'import Pkg; Pkg.update()' && \
-    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" && \
-    fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
-
-WORKDIR "${HOME}"

minimal-notebook/Dockerfile

@@ -43,3 +43,6 @@ USER ${NB_UID}
 
 # Add R mimetype option to specify how the plot returns from R to the browser
 COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
+
+# Add setup scripts that may be used by downstream images or inherited images
+COPY setup-scripts/ /opt/setup-scripts/

minimal-notebook/setup-scripts/setup-julia-packages.bash

@@ -0,0 +1,24 @@
+#!/bin/bash
+# Requirements:
+# - Run as non-root user
+# - Julia is already set up, with the setup-julia.bash command
+set -exuo pipefail
+
+# Install base Julia packages
+julia -e '
+import Pkg;
+Pkg.update();
+Pkg.add([
+    "HDF5",
+    "IJulia"
+]);
+Pkg.precompile();
+'
+
+# Move the kernelspec out to the system share location. Avoids
+# problems with runtime UID change not taking effect properly on the
+# .local folder in the jovyan home dir.  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"
+fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"

minimal-notebook/setup-scripts/setup-julia.bash

@@ -0,0 +1,39 @@
+#!/bin/bash
+set -exuo pipefail
+# Requirements:
+# - This script is run as the root user
+# - The JULIA_PKGDIR environment variable is set
+
+# Default julia version to install if env var is not set
+# Check https://julialang.org/downloads/
+JULIA_VERSION="${JULIA_VERSION:-1.9.1}"
+
+# Figure out what architecture we are installing in
+JULIA_ARCH=$(uname -m)
+JULIA_SHORT_ARCH="${JULIA_ARCH}"
+if [ "${JULIA_SHORT_ARCH}" == "x86_64" ]; then
+    JULIA_SHORT_ARCH="x64"
+fi
+
+# Figure out Julia Installer URL
+JULIA_INSTALLER="julia-${JULIA_VERSION}-linux-${JULIA_ARCH}.tar.gz"
+JULIA_MAJOR_MINOR=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)
+
+# Download and install Julia
+cd /tmp
+mkdir "/opt/julia-${JULIA_VERSION}"
+wget --progress=dot:giga "https://julialang-s3.julialang.org/bin/linux/${JULIA_SHORT_ARCH}/${JULIA_MAJOR_MINOR}/${JULIA_INSTALLER}"
+tar xzf "${JULIA_INSTALLER}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1
+rm "${JULIA_INSTALLER}"
+
+# Link Julia installed version to /usr/local/bin, so julia launches it
+ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
+
+# Tell Julia where conda libraries are
+mkdir -p /etc/julia
+echo "push!(Libdl.DL_LOAD_PATH, \"${CONDA_DIR}/lib\")" >> /etc/julia/juliarc.jl
+
+# Create JULIA_PKGDIR, where user libraries are installed
+mkdir "${JULIA_PKGDIR}"
+chown "${NB_USER}" "${JULIA_PKGDIR}"
+fix-permissions "${JULIA_PKGDIR}"