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Revert "fix: Update script to install packages (#25)"
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Original file line number | Diff line number | Diff line change |
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#!/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 | ||
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# 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 | ||
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# 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(); | ||
' | ||
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# 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" |
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#!/usr/bin/env python3 | ||
# Copyright (c) Jupyter Development Team. | ||
# Distributed under the terms of the Modified BSD License. | ||
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# Requirements: | ||
# - Run as the root user | ||
# - The JULIA_PKGDIR environment variable is set | ||
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import logging | ||
import os | ||
import platform | ||
import shutil | ||
import subprocess | ||
from pathlib import Path | ||
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import requests | ||
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LOGGER = logging.getLogger(__name__) | ||
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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] | ||
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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"] | ||
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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() | ||
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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"] | ||
) | ||
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# 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' | ||
) | ||
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# 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]) | ||
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if __name__ == "__main__": | ||
logging.basicConfig(level=logging.INFO) | ||
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julia_url, julia_version = get_latest_julia_url() | ||
download_julia(julia_url=julia_url) | ||
configure_julia(julia_version=julia_version) |