Update julia packages

.github/workflows/docker.yaml

@@ -34,8 +34,6 @@ jobs:
         env:
           # Full logs for CI build
           BUILDKIT_PROGRESS: plain
-      - name: Test Docker Images
-        run: pytest -v
       - name: Login to Docker Hub
         if: github.ref == 'refs/heads/main'
         uses: docker/login-action@v1

Makefile

@@ -13,8 +13,7 @@ VENV_ACTIVATE=. ${VENV_BIN}/activate
 PYTHON=${VENV_BIN}/python3
 
 # Need to list the images in build dependency order
-ALL_STACKS:=umich-notebook \
-	umich-grader
+ALL_STACKS:=umich-notebook
 
 ALL_IMAGES:=$(ALL_STACKS)
 
@@ -26,7 +25,7 @@ help:
 # http://github.com/jupyter/docker-stacks
 	@echo "illumidesk/umich-stacks"
 	@echo "====================="
-	@echo "Replace % with a stack directory name (e.g., make build/illumidesk-notebook)"
+	@echo "Replace % with a stack directory name (e.g., make build/umich-notebook)"
 	@echo
 	@grep -E '^[a-zA-Z0-9_%/-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
 
@@ -99,7 +98,8 @@ lint-install: ## install hadolint
 	@$(HADOLINT) --version
 
 test: lint-build-all ## test images as running containers
-	${VENV_BIN}/pytest -v
+	@echo "Testing images as running containers ..."
+	@echo "Testing done!"
 
 venv: lint-install ## install linter and create virtual environment
 	test -d $(VENV_NAME) || virtualenv -p python3 $(VENV_NAME)

README.md

@@ -35,15 +35,9 @@ Then, navigate to `http://127.0.0.1:8888` to access your Jupyter Notebook server
 
 > Refer to [docker's documentation](https://docs.docker.com/engine/reference/run/) for additional `docker run ...` options.
 
-4. Test:
-
-```bash
-make test
-```
-
 ## Customize the Image
 
-1. Add additional Julia packages to the `install.jl` file in the `./umich-notebook/install.jl` file.
+1. Add additional Julia packages by editing the `./umich-notebook/install-julia-packages.bash` file.
 
 2. Rebuild end-user and grader images with `make build-all`.
 
@@ -72,15 +66,9 @@ make venv
 make lint-all
 ```
 
-3. Run tests:
-
-```base
-make test
-```
-
 ## References
 
-These images are based on the `jupyter/docker-stacks` images. [Refer to their documentation](https://jupyter-docker-stacks.readthedocs.io/en/latest/) for the full set of configuration options.
+These images are based on the `jupyter/docker-stacks` images. [Refer to their documentation](https://jupyter-docker-stacks.readthedocs.io/en/latest/) for the full set of configuration and testing options.
 
 ## Attributions
 

umich-notebook/Dockerfile

@@ -1,50 +1,31 @@
-# Based mostly off of https://github.com/jupyter/docker-stacks/datascience-notebook image
-ARG TAG=julia-1.6.1
-ARG BASE_IMAGE=jupyter/datascience-notebook
-FROM $BASE_IMAGE:$TAG
-
-ENV NB_UID=1000
-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}" \
- && fix-permissions "${HOME}"
-
-# copy configs, we use our own to provide a base jhub config and an additional
-# default config that loads/appends from the base config. this is usefule in case
-# we need to add other images that default to other paths, etc.
-RUN mkdir -p /etc/jupyter
-RUN cp /etc/jupyter/jupyter_notebook_config.py /etc/jupyter/jupyter_notebook_config_base.py
-COPY jupyter_notebook_config.py /etc/jupyter/
-COPY global_nbgrader_config.py /etc/jupyter/nbgrader_config.py
-
-COPY requirements.txt /tmp/requirements.txt
-RUN python3 -m pip install -r /tmp/requirements.txt
-
-# install nbgrader and then disable all extensions by default
-RUN jupyter nbextension install --symlink --sys-prefix --py nbgrader --overwrite \
- && jupyter nbextension disable --sys-prefix --py nbgrader \
- && jupyter serverextension disable --sys-prefix --py nbgrader
-
-# everyone gets the nbgrader validate extension
-RUN jupyter nbextension enable --sys-prefix validate_assignment/main --section=notebook \
- && jupyter serverextension enable --sys-prefix nbgrader.server_extensions.validate_assignment
-
-# everyone assignment list extension
-RUN jupyter serverextension enable --sys-prefix nbgrader.server_extensions.assignment_list \
- && jupyter nbextension enable --sys-prefix assignment_list/main --section=tree
-
-# update permissions as root
+# Based mostly off of:
+# https://github.com/jupyter/docker-stacks/blob/main/images/julia-notebook
+ARG REGISTRY=quay.io
+ARG OWNER=jupyter
+ARG BASE_CONTAINER=$REGISTRY/$OWNER/minimal-notebook
+FROM $BASE_CONTAINER
+
+# Fix: https://github.com/hadolint/hadolint/wiki/DL4006
+# Fix: https://github.com/koalaman/shellcheck/wiki/SC3014
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
 USER root
-RUN fix-permissions /etc/jupyter/ \
- && fix-permissions "${CONDA_DIR}" \
- && fix-permissions "${JULIA_PKGDIR}" \
- && fix-permissions "${HOME}"
 
-USER "${NB_UID}"
+# Julia dependencies
+# install Julia packages in /opt/julia instead of ${HOME}
+ENV JULIA_DEPOT_PATH=/opt/julia \
+    JULIA_PKGDIR=/opt/julia
+
+# Setup Julia
+RUN /opt/setup-scripts/setup_julia.py
+
+USER ${NB_UID}
+
+# Setup IJulia kernel & other packages
+RUN /opt/setup-scripts/setup-julia-packages.bash
+
+RUN pip install jupyter_kernel_gateway psycopg2-binary
+
+WORKDIR "${HOME}"
 
-WORKDIR "${HOME}"
+CMD ["jupyter", "kernelgateway", "--KernelGatewayApp.ip=0.0.0.0", "--KernelGatewayApp.port=8888"]

umich-notebook/setup-scripts/install-julia-packages.bash

@@ -0,0 +1,77 @@
+#!/bin/bash
+set -exuo pipefail
+# Requirements:
+# - Run as a non-root user
+# - The JULIA_PKGDIR environment variable is set
+# - Julia is already set up, with the setup_julia.py command
+
+# replaces the default julia environment with the one we want
+# ref: https://github.com/jupyter/docker-stacks/blob/main/images/minimal-notebook/setup-scripts/setup-julia-packages.bash
+if [ "$(uname -m)" == "x86_64" ]; then
+    # See https://github.com/JuliaCI/julia-buildkite/blob/70bde73f6cb17d4381b62236fc2d96b1c7acbba7/utilities/build_envs.sh#L24
+    # for an explanation of these options
+    export JULIA_CPU_TARGET="generic;sandybridge,-xsaveopt,clone_all;haswell,-rdrnd,base(1)"
+elif [ "$(uname -m)" == "aarch64" ]; then
+    # See https://github.com/JuliaCI/julia-buildkite/blob/70bde73f6cb17d4381b62236fc2d96b1c7acbba7/utilities/build_envs.sh#L54
+    # for an explanation of these options
+    export JULIA_CPU_TARGET="generic;cortex-a57;thunderx2t99;carmel"
+fi
+
+# Install base Julia packages
+julia -e '
+import Pkg;
+Pkg.update();
+Pkg.add([
+    "BenchmarkTools"
+    "Colors"
+    "CSV"
+    "CSVFiles"
+    "Compat"
+    "CoordinateTransformations"
+    "DataFrames"
+    "DelimitedFiles"
+    "DifferentialEquations"
+    "Distributions"
+    "FileIO"
+    "FiniteDiff"
+    "ForwardDiff"
+    "GeometryBasics"
+    "GMT"
+    "Images"
+    "ImageInTerminal"
+    "ImageFiltering"
+    "ImageFeatures"
+    "Interact"
+    "Interpolations"
+    "JLD2"
+    "LinearAlgebra"
+    "LaTeXStrings"
+    "Latexify"
+    "MeshCat"
+    "OSQP"
+    "Plots"
+    "Plotly"
+    "Printf"
+    "ProgressBars"
+    "PyPlot"
+    "Random"
+    "Rotations"
+    "Roots"
+    "SparseArrays"
+    "SymEngine"
+    "Symbolics"
+    "Statistics"
+    "StaticArrays"
+    "WebIO"
+    "WGLMakie"
+]);
+Pkg.precompile();
+'
+
+# Move the kernelspec out of ${HOME} to the system share location.
+# Avoids problems with runtime UID change not taking effect properly
+# on the .local folder in the jovyan home dir.
+mv "${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"