Revert "Update script to install packages"

Makefile

@@ -23,9 +23,9 @@ HADOLINT="${HOME}/hadolint"
 help:
 # http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html
 # http://github.com/jupyter/docker-stacks
-	@echo "illumidesk/illumidesk-stacks"
+	@echo "illumidesk/umich-stacks"
 	@echo "====================="
-	@echo "Replace % with a stack directory name (e.g., make build/python-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}'
 

README.md

@@ -1,9 +1,9 @@
-[![Test Docker Image Status](https://github.com/illumidesk/illumidesk-stacks/workflows/Test%20and%20Push/badge.svg)](https://github.com/illumidesk/illumidesk-stacks/actions?query=branch%3Amain+workflow%3A%22Test+and+Push%22)
+[![Test Docker Image Status](https://github.com/illumidesk/umich-stacks/workflows/Test%20and%20Push/badge.svg)](https://github.com/illumidesk/umich-stacks/actions?query=branch%3Amain+workflow%3A%22Test+and+Push%22)
 
 
-# IllumiDesk Docker Stacks
+# IllumiDesk Docker Stacks for the University of Michigan
 
-This repo is used to manage IllumiDesk's standard docker images for the IllumiDesk learning environment to power Jupyter Server backends.
+This repo is used to manage University of Michigan's docker images for the IllumiDesk learning environment integrated with the Canvas LMS.
 
 ## Pre Requisits
 
@@ -28,7 +28,7 @@ make build-all
 Running the image standalone is helpful for testing:
 
 ```bash
-docker run -p 8888:8888 illumidesk/python-notebook:latest
+docker run -p 8888:8888 illumidesk/umich-notebook:latest
 ```
 
 Then, navigate to `http://127.0.0.1:8888` to access your Jupyter Notebook server.
@@ -37,24 +37,19 @@ Then, navigate to `http://127.0.0.1:8888` to access your Jupyter Notebook server
 
 ## Customize the Image
 
-1. Add additional Python packages by editing the `./python-notebook/requirements.txt` 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`.
 
-3. Push images to AWS ECR
-
-- [You must first authenticate](https://docs.aws.amazon.com/AmazonECR/latest/userguide/registry_auth.html) to push to AWS ECR repos using `docker` coomands.
-- Run `docker push <repo>` where `<repo>` represents the full path to your AWS ECR repository.
-
-1. (Optional) Push images to DockerHub
+3. (Optional) Push images to DockerHub
 
 This step requires creating an Organization account in DockerHub or other docker image compatible registry. The `docker push ...` command will push the image to the DockerHub registry by default. Please refer to the official Docker documentation if you would like to push another registry.
 
-For example, assuming the DockerHub organization is `illumidesk`, the source files are in the `python-notebook` folder, and the tag is `latest`, then the full namespace for the image would be `illumidesk/python-notebook:latest`. Assuming the image has been built, push the image to DockerHub or any other docker registry with the `docker push <image-namespace>:<image-tag>` command:
+For example, assuming the DockerHub organization is `illumidesk`, the source files are in the `umich-notebook` folder, and the tag is `latest`, then the full namespace for the image would be `illumidesk/umich-notebook:latest`. Assuming the image has been built, push the image to DockerHub or any other docker registry with the `docker push <image-namespace>:<image-tag>` command:
 
 ```bash
 docker login
-docker push illumidesk/python-notebook:latest
+docker push illumidesk/umich-notebook:latest
 ```
 
 ## Development and Testing

python-notebook/Dockerfile → umich-notebook/Dockerfile

@@ -2,21 +2,30 @@
 # https://github.com/jupyter/docker-stacks/blob/main/images/julia-notebook
 ARG REGISTRY=quay.io
 ARG OWNER=jupyter
-ARG BASE_CONTAINER=$REGISTRY/$OWNER/datascience-notebook
-FROM ${BASE_CONTAINER}
+ARG BASE_CONTAINER=$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
+
+# 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
-COPY --chown=${NB_UID}:${NB_GID} requirements.txt "${HOME}/requirements.txt"
-WORKDIR "${HOME}"
-RUN pip install -r requirements.txt
+RUN /opt/setup-scripts/setup-julia-packages.bash
 
+RUN pip install jupyter_kernel_gateway psycopg2-binary
 
 WORKDIR "${HOME}"
 
-CMD ["jupyter", "kernelgateway", "--KernelGatewayApp.ip=0.0.0.0", "--KernelGatewayApp.port=8888"]
+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"

umich-notebook/setup-scripts/setup_julia.py

@@ -0,0 +1,97 @@
+#!/usr/bin/env python3
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+# Requirements:
+# - Run as the root user
+# - The JULIA_PKGDIR environment variable is set
+
+import logging
+import os
+import platform
+import shutil
+import subprocess
+from pathlib import Path
+
+import requests
+
+LOGGER = logging.getLogger(__name__)
+
+
+def unify_aarch64(platform: str) -> str:
+    """
+    Renames arm64->aarch64 to support local builds on on aarch64 Macs
+    """
+    return {
+        "aarch64": "aarch64",
+        "arm64": "aarch64",
+        "x86_64": "x86_64",
+    }[platform]
+
+
+def get_latest_julia_url() -> tuple[str, str]:
+    """
+    Get the last stable version of Julia
+    Based on: https://github.com/JuliaLang/www.julialang.org/issues/878#issuecomment-749234813
+    """
+    LOGGER.info("Downloading Julia versions information")
+    versions = requests.get(
+        "https://julialang-s3.julialang.org/bin/versions.json"
+    ).json()
+    stable_versions = {k: v for k, v in versions.items() if v["stable"]}
+    # Compare versions semantically
+    latest_stable_version = max(
+        stable_versions, key=lambda ver: [int(sub_ver) for sub_ver in ver.split(".")]
+    )
+    latest_version_files = stable_versions[latest_stable_version]["files"]
+    triplet = unify_aarch64(platform.machine()) + "-linux-gnu"
+    file_info = [vf for vf in latest_version_files if vf["triplet"] == triplet][0]
+    LOGGER.info(f"Latest version: {file_info['version']} url: {file_info['url']}")
+    return file_info["url"], file_info["version"]
+
+
+def download_julia(julia_url: str) -> None:
+    """
+    Downloads and unpacks julia
+    The resulting julia directory is "/opt/julia-VERSION/"
+    """
+    LOGGER.info("Downloading and unpacking Julia")
+    tmp_file = Path("/tmp/julia.tar.gz")
+    subprocess.check_call(
+        ["curl", "--progress-bar", "--location", "--output", tmp_file, julia_url]
+    )
+    shutil.unpack_archive(tmp_file, "/opt/")
+    tmp_file.unlink()
+
+
+def configure_julia(julia_version: str) -> None:
+    """
+    Creates /usr/local/bin/julia symlink
+    Make Julia aware of conda libraries
+    Creates a directory for Julia user libraries
+    """
+    LOGGER.info("Configuring Julia")
+    # Link Julia installed version to /usr/local/bin, so julia launches it
+    subprocess.check_call(
+        ["ln", "-fs", f"/opt/julia-{julia_version}/bin/julia", "/usr/local/bin/julia"]
+    )
+
+    # Tell Julia where conda libraries are
+    Path("/etc/julia").mkdir()
+    Path("/etc/julia/juliarc.jl").write_text(
+        f'push!(Libdl.DL_LOAD_PATH, "{os.environ["CONDA_DIR"]}/lib")\n'
+    )
+
+    # Create JULIA_PKGDIR, where user libraries are installed
+    JULIA_PKGDIR = Path(os.environ["JULIA_PKGDIR"])
+    JULIA_PKGDIR.mkdir()
+    subprocess.check_call(["chown", os.environ["NB_USER"], JULIA_PKGDIR])
+    subprocess.check_call(["fix-permissions", JULIA_PKGDIR])
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level=logging.INFO)
+
+    julia_url, julia_version = get_latest_julia_url()
+    download_julia(julia_url=julia_url)
+    configure_julia(julia_version=julia_version)