Reinstall Julia - You don't need to prove this

A couple of days ago, I found that I could not install and compile ArbNumerics.jl. The only options is to reinstall Julia. Fortunately, this is quite easy.

To be extra cautious, I started with a backup of the whole ~/.julia. Start a terminal by typing

cp -r ~/.julia/ ~/Downloads/

Then I removed ~/.julia without mercy 👿.

rm -rf ~/.julia/

This means all my previously installed Julia packages are now gone, but Julia itself (the binary and core packages) are still there.

Most of my project has its own environment. In other words, there are two files Project.toml and Manifest.tomal in the directory containing an environment. For example, to play with Weave.jl, I have an environment in ~/Work/weave. The content of Project.toml is quite simple, which just indicates that this environment needs three dependencies DSP, Plots and Weave.

[deps]
DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Weave = "44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9"

The content of Manifest.toml is a bit more complicated. The first few lines of it are like this.

# This file is machine-generated - editing it directly is not advised

[[AbstractFFTs]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "051c95d6836228d120f5f4b984dd5aba1624f716"
uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
version = "0.5.0"

[[Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

What it does, is to indicate what exact packages are installed the last time I modified the environment.

These two files allow me to install all the packages needed to run this environment. I can simply to launch Julia REPL in the directly where the environment is, active the environment, and run the command instantiate.

(@v1.4) pkg> activate . # press ] to get the pkg prompt
 Activating environment at `~/Work/weave/Project.toml`

(weave) pkg> st
Status `~/Work/weave/Project.toml`
→ [717857b8] DSP v0.6.6
  [91a5bcdd] Plots v1.2.4
→ [44d3d7a6] Weave v0.9.4
┌ Warning: Some packages (indicated with a red arrow) are not downloaded, use `instantiate` to instantiate the current environment
└ @ Pkg.Display /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Display.jl:238

(weave) pkg> instantiate
   Updating registry at `~/.julia/registries/General`
   Updating git-repo `https://github.com/JuliaRegistries/General.git`
  Installed AbstractFFTs ──────────────── v0.5.0
  Installed Parsers ───────────────────── v1.0.3
  Installed Tables ────────────────────── v1.0.4
  Installed SpecialFunctions ──────────── v0.10.0
  Installed Weave ─────────────────────── v0.9.4
  Installed DataStructures ────────────── v0.17.15
  Installed Plots ─────────────────────── v1.2.4
  Installed DSP ───────────────────────── v0.6.6
  Installed IteratorInterfaceExtensions ─ v1.0.0
  Installed TableTraits ───────────────── v1.0.0
  Installed PlotUtils ─────────────────── v1.0.2
  Installed Mustache ──────────────────── v1.0.2
  Installed DataValueInterfaces ───────── v1.0.0
  Installed FFTW ──────────────────────── v1.2.1
  Installed IntelOpenMP_jll ───────────── v2018.0.3+0
  Installed Polynomials ───────────────── v0.8.0
  Installed IterTools ─────────────────── v1.3.0
  Installed FFTW_jll ──────────────────── v3.3.9+5
  Installed MKL_jll ───────────────────── v2019.0.117+2
  Installed YAML ──────────────────────── v0.4.0
   Building Plots → `~/.julia/packages/Plots/zOV0T/deps/build.log`
   Building FFTW ─→ `~/.julia/packages/FFTW/5DZuu/deps/build.log`
Downloading artifact: IntelOpenMP
######################################################################## 100.0%##O=#  #                               Downloading artifact: FFTW
######################################################################## 100.0%##O=#  #

To test, I load Weave into the REPL.

julia> using Weave
[ Info: Precompiling Weave [44d3d7a6-8a23-5bf8-98c5-b353f8df5ec9]

Everything seems to be fine. 😄

Now if you check, you will see a ~/.julia has been recreated.

shell> ls ~/.julia # Press ; to get shell prompt
artifacts  compiled  conda  environments  logs  packages  prefs  registries

So one last thing is to do is to restore my config folder by.

shell> cp -r ~/Downloads/.julia/config/ ~/.julia

and remove the backup

shell> rm -rf ~/Downloads/.julia/config/