update julia packages

Signed-off-by: Greg Werner <[email protected]>

umich-notebook/Dockerfile

@@ -1,5 +1,5 @@
 # Based mostly off of https://github.com/jupyter/docker-stacks/datascience-notebook image
-ARG TAG=julia-1.6.1
+ARG TAG=julia-1.9.0
 ARG BASE_IMAGE=jupyter/datascience-notebook
 FROM $BASE_IMAGE:$TAG
 
@@ -9,34 +9,12 @@ ENV NB_GID=100
 USER "${NB_UID}"
 
 # Install julia packages
-COPY install.jl /tmp/install.jl
-RUN julia /tmp/install.jl \
- && fix-permissions "${JULIA_PKGDIR}" \
+RUN curl https://s3.us-west-2.amazonaws.com/configs.illumidesk.com/docker/install.jl --output /tmp/install.jl
+RUN julia /tmp/install.jl
+RUN fix-permissions "${JULIA_PKGDIR}" \
  && fix-permissions "${HOME}"
 
-# copy configs, we use our own to provide a base jhub config and an additional
-# default config that loads/appends from the base config. this is usefule in case
-# we need to add other images that default to other paths, etc.
-RUN mkdir -p /etc/jupyter
-RUN cp /etc/jupyter/jupyter_notebook_config.py /etc/jupyter/jupyter_notebook_config_base.py
-COPY jupyter_notebook_config.py /etc/jupyter/
-COPY global_nbgrader_config.py /etc/jupyter/nbgrader_config.py
-
-COPY requirements.txt /tmp/requirements.txt
-RUN python3 -m pip install -r /tmp/requirements.txt
-
-# install nbgrader and then disable all extensions by default
-RUN jupyter nbextension install --symlink --sys-prefix --py nbgrader --overwrite \
- && jupyter nbextension disable --sys-prefix --py nbgrader \
- && jupyter serverextension disable --sys-prefix --py nbgrader
-
-# everyone gets the nbgrader validate extension
-RUN jupyter nbextension enable --sys-prefix validate_assignment/main --section=notebook \
- && jupyter serverextension enable --sys-prefix nbgrader.server_extensions.validate_assignment
-
-# everyone assignment list extension
-RUN jupyter serverextension enable --sys-prefix nbgrader.server_extensions.assignment_list \
- && jupyter nbextension enable --sys-prefix assignment_list/main --section=tree
+RUN pip install jupyter_kernel_gateway psycopg2-binary
 
 # update permissions as root
 USER root
@@ -45,6 +23,10 @@ RUN fix-permissions /etc/jupyter/ \
  && fix-permissions "${JULIA_PKGDIR}" \
  && fix-permissions "${HOME}"
 
+RUN mv "${CONDA_DIR}/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/julia/"
+
 USER "${NB_UID}"
 
-WORKDIR "${HOME}"
+WORKDIR "${HOME}"
+
+CMD ["jupyter", "kernelgateway", "--KernelGatewayApp.ip=0.0.0.0", "--KernelGatewayApp.port=8888"]

umich-notebook/install.jl

@@ -1,41 +1,46 @@
-# This mechanism allows us to import a package list.
 # Source: https://discourse.julialang.org/t/building-a-dockerfile-with-packages/37272/2
-
 using Pkg
+pkg"add BenchmarkTools"
 pkg"add Colors"
-pkg"add Conda"
 pkg"add CSV"
 pkg"add CSVFiles"
+pkg"add Compat"
+pkg"add CoordinateTransformations"
 pkg"add DataFrames"
 pkg"add DelimitedFiles"
+pkg"add DifferentialEquations"
 pkg"add Distributions"
 pkg"add FileIO"
+pkg"add FiniteDiff"
+pkg"add ForwardDiff"
+pkg"add GeometryBasics"
 pkg"add GMT"
-pkg"add GR"
-pkg"add GtkReactive"
-pkg"add IJulia"
-pkg"add ImageFiltering"
+pkg"add Images"
 pkg"add ImageInTerminal"
+pkg"add ImageFiltering"
 pkg"add ImageFeatures"
-pkg"add Images"
-pkg"add ImageView"
 pkg"add Interact"
-pkg"add LaTeXStrings"
+pkg"add Interpolations"
+pkg"add JLD2"
 pkg"add LinearAlgebra"
+pkg"add LaTeXStrings"
+pkg"add Latexify"
+pkg"add MeshCat"
 pkg"add OSQP"
-pkg"add Plotly"
 pkg"add Plots"
+pkg"add Plotly"
+pkg"add Printf"
 pkg"add ProgressBars"
-pkg"add PyCall"
 pkg"add PyPlot"
 pkg"add Random"
+pkg"add Rotations"
 pkg"add Roots"
 pkg"add SparseArrays"
-pkg"add Statistics"
 pkg"add SymEngine"
 pkg"add Symbolics"
-pkg"add SymbolicUtils"
-pkg"add TestImages"
+pkg"add Statistics"
+pkg"add StaticArrays"
 pkg"add WebIO"
+pkg"add WGLMakie"
 pkg"add https://github.com/VMLS-book/VMLS.jl"
-pkg"add https://github.com/korsbo/Latexify.jl"
+Pkg"precompile"

umich-notebook/test/test_languages.py

@@ -13,7 +13,7 @@
     'language,version_output',
     [
         ('python', ['Python', '3.9.6\n']),
-        ('julia', ['julia', 'version', '1.6.1\n']),
+        ('julia', ['julia', 'version', '1.9.0\n']),
     ],
 )
 def test_languages(language, version_output):