What is this?

This is a collection of instructions to install and configure the tools I use for development/data science/physics ... I use WSL on Windows 11 to use things like Python, Latex, Git, C++, ... Most of this comes from the Pep Toolbox-Workshop (https://toolbox.pep-dortmund.org/) other things come from personal experience. This collection is mainly for myself, so that I have everything I need at one place, but I guess it could be useful for other people too. And most of it should work on native Ubuntu or Linux too.

Installation Instructions (mainly on Windows 11 + WSL)

Preferably use Windows Terminal and Visual Studio Code for everything.

WSL and Ubuntu

• Open Windows Terminal (PowerShell) as an Administrator
• enter wsl --update
• enter wsl --install -d Ubuntu
• after successfull completion, restart your computer
• enter a username and password for the Ubuntu login
• Update the packages via sudo apt update && sudo apt upgrade
• Optional: Set Ubuntu as the default shell in Windows Terminal

For more info: https://docs.microsoft.com/de-de/windows/wsl/install If you are having Connection issues and using Avast: MicrosoftDocs/WSL#481

Useful/Essential Linux Tools

Install each via sudo apt install <Name>

-> sudo apt install git make curl

• make
• curl
• git

Visual Studio Code

Download VSCode from here: https://code.visualstudio.com/ Or if you are worried about privacy, open source, tracking... use VSCodium from here: https://vscodium.com/ And then install it.

It's best to always open VS Code via the Ubuntu shell: code <Path> (or codium <Path>) -> this will run VS Code with "Remote for WSL" and it will use WSL for Python etc.

Recommended Settings (in VSCode->File->Preferences->Settings):

• English as Language
• Word Wrap as "always"

Recommended VS Code Extensions:

• Remote - WSL
• Rainbow CSV
• PDF preview (or vscode-pdf)
• Python
• C/C++
• LaTeX Workshop (disable auto compile!)
  • in VSCode->File->Preferences->Settings:
  • search for "latex auto build clean and retry" and remove the checkmark
  • search for "latex auto build run" and set it to "never"
• Visual Studio Live Share

Python (Scientific Python via Miniconda with Mamba, recommended)

• Download the Installer: wget -O ~/Miniconda-Installer.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

• Install Miniconda via bash ~/Miniconda-Installer.sh -b -p ~/.local/miniconda3

  • -b is for batch-mode so that the ~/.bashrc does not get cluttered
  • -p is to specify where Anaconda should be installed to

• Remove the Installer: rm ~/Miniconda-Installer.sh

• To automatically activate conda (i.e. Python) add the following lines at the end of you ~/.bashrc or ~/.zshrc file:

  # Python/Anaconda:
  . "$HOME/.local/miniconda3/etc/profile.d/conda.sh"
  conda activate
  

  • You could for example open it with code ~/.bashrc

• Install Mamba: while conda is active do conda install mamba -n base -c conda-forge

• Create a new environment with many useful packages: mamba create -n anaconda anaconda

  Python (Scientific Python via Anaconda, not recommended!)

  The installation using Miniconda is more clean and offers faster updates and installations using mamba.

• Go to https://www.anaconda.com/products/individual

• Copy the link adress of the Linux(!) "64-Bit (x86) Installer"

• Download the Installer: wget -O ~/Anaconda-Installer.sh <Copied-Link-Adress>

  • For example: wget -O ~/Anaconda-Installer.sh https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh

• Install Anaconda via bash ~/Anaconda-Installer.sh -b -p ~/.local/anaconda3

  • -b is for batch-mode so that the ~/.bashrc does not get cluttered
  • -p is to specify where Anaconda should be installed to

• Remove the Installer: rm ~/Anaconda-Installer.sh

• To automatically activate Anaconda (i.e. Python) add the following lines at the end of you ~/.bashrc file:

  # Python/Anaconda:
  . "$HOME/.local/anaconda3/etc/profile.d/conda.sh"
  conda activate
  

  • You could for example open it with code ~/.bashrc

Useful Python Packages not in Anaconda

• Uncertainties: pip install uncertainties

Latex (with TexLive)

• Warning: This installation takes a long time because TexLive is a large package (~5GB)
• Download and extract the TexLive Installer: cd ~ && curl -L http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz | tar xz
• Install TexLive: TEXLIVE_INSTALL_PREFIX=$HOME/.local/texlive ~/install-tl-*/install-tl
  • Start the Installation using the option I
• Remove the installer: rm -rf ~/install-tl-*
• Add the following to your ~/.bashrc file:

  # LaTeX/TexLive:
  export PATH="$HOME/.local/texlive/2021/bin/x86_64-linux:$PATH"
  

  • You may need to adjust the path (i.e. the year)
• restart your terminal (or use source ~/.bashrc)
• adjust the config: tlmgr option autobackup -- -1 and tlmgr option repository http://mirror.ctan.org/systems/texlive/tlnet

C++

• see: https://code.visualstudio.com/docs/cpp/config-wsl

• or better use a Makefile

• to install Eigen:

  • sudo apt install libeigen3-dev
  • now it could be included with #include <eigen3/Eigen/Dense>
  • if you want to include it with #include <Eigen/Dense> you need to create a symbolical link: sudo ln -s /usr/include/eigen3/Eigen /usr/include/Eigen

Git configuration (for GitHub)

• Git has to be installed: sudo apt install git
• recommended configuration (as commands):

  git config --global user.name "Max Mustermann"
  git config --global user.email "[email protected]"
  git config --global rebase.stat true
  git config --global merge.conflictstyle diff3
  

• You need to use a SSH key for GitHub (https://docs.github.com/en/github/authenticating-to-github/connecting-to-github-with-ssh):
  • Create SSH-Key: ssh-keygen -t ed25519 -C "[email protected]"
  • Use the default path
  • Enter the password you want to use (optional)
  • Copy the public key: cat ~/.ssh/id_ed25519.pub | clip.exe
  • Go to GitHub (https://github.com/settings/keys) and add the key (the title is not important)
  • now you can clone the GitHub repositories using the SSH URLs (for example git clone [email protected]:NicoJG/WSL_Instructions.git)

Useful Windows Configurations

in the Windows Explorer, configure:

• show file extensions
• show hidden files/folders

WSL Bug fixes / workarounds

Graphical Interfaces don't work (for example matplotlib)

Should not be necessary for Windows 11 but on Windows 10 it was necessary. You need a XServer.

• Install VcXsrv (https://sourceforge.net/projects/vcxsrv/)
• in Windows search for XLaunch and choose the following configurations:
  • Multiple Windows, Start no client, all extra settings, save configuration
  • You may (or must perhaps) reject the firewall permissions that should pop up
• mkdir /tmp/vcxsrv
• Add the following to your ~/.bashrc:

  # XServer/VcXsrv:
  export DISPLAY="$(route.exe print | grep 0.0.0.0 | head -1 | awk '{print $4}'):0.0"
  export XDG_RUNTIME_DIR="/tmp/vcxsrv"
  export LIBGL_ALWAYS_INDIRECT=1
  

  • if this does not work try export DISPLAY='grep -oP "(?<=nameserver ).+" /etc/resolv.conf':0.0 or export DISPLAY=localhost:0.0

  • Optional: to be able to start the XServer from the command line check_xsrv, add the following to your ~/.bashrc:

  # open vcxsrv if it is not running
  open_vcxsrv() {
      if ! cmd.exe /c tasklist | grep --quiet vcxsrv; then
          cmd.exe /c "C:\Users\Nico\Documents\config.xlaunch"
      fi
  }
  alias check_xsrv=open_vcxsrv
  

GDB fix for Ubuntu 22

microsoft/WSL#8356

Jupyter Lab/Jupyter Notebook on WSL

At the moment Jupyter is buggy and won't open right. For more information: https://stackoverflow.com/a/65133953 For Jupyter Notebook just replace every "Lab" with a "Notebook"

• Generate the config file jupyter server --generate-config
• Add the following line to ~/.jupyter/jupyter_server_config.py: c.ServerApp.use_redirect_file = False
  • if this does not work, try the following (see jupyterlab/jupyterlab#10413):
  • Generate the config file jupyter lab --generate-config
  • Add the following line to ~/.jupyter/jupyter_lab_config.py: c.LabApp.open_browser = False

Terminal Customizations

The default terminal (Windows Terminal + Bash) is fine, but you can do so much more. I like to use zsh with oh-my-zsh (https://github.com/ohmyzsh/ohmyzsh). Once it is configured properly it looks amazing and has man convenient tools.

My current terminal:

Customize your terminal (Windows Terminal)

To look good, you first have to customize Windows Terminal

• Choose a color scheme from https://windowsterminalthemes.dev/
  • I like "Solarized Dark Higher Contrast" (https://windowsterminalthemes.dev/?theme=Solarized%20Dark%20Higher%20Contrast)
  • click on "Get Theme"
  • in Windows Terminal->Settings click "Open JSON file"
  • paste the color scheme after "schemes": [ and add a , after the closing } (then save)
    • potentially change "background" to black (#000000)
  • make the chosen color scheme the default for Ubuntu (in Settings->Ubuntu->Appearance)
• choose a background image and make it ~30% opaque (in Settings->Ubuntu->Appearance) (for example https://en.wikipedia.org/wiki/Helix_Nebula#/media/File:NGC7293_(2004).jpg)
• Change the "Bell notification style" to not audible (in Settings->Ubuntu->Advanced)
• Install a "Nerd Font" from https://www.nerdfonts.com/font-downloads
  • I like "DejaVuSansMono NF" (DejaVu Sans Mono Nerd Font Complete Windows Compatible.ttf)
  • Set the Font for the Ubuntu profile (in Settings->Ubuntu->Appearance)

Installing Oh My Zsh

• Install Zsh: sudo apt install zsh
• Make Zsh your default shell: chsh -s $(which zsh)
  • If you dont have the permission for chsh put the commands at the end of this section into your ~/.bashrc
• Install OhMyZsh: sh -c "$(wget -O- https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)"
• restart the shell (by using exec zsh)
• you need to copy all customizations you did to the ~/.bashrc to ~/.zshrc! Because the bashrc won't be run anymore.

For a few tips and tricks on using Zsh: https://www.twilio.com/blog/zsh-tricks-to-blow-your-mind

if [ -z "${NOZSH}" ] && [ $TERM = "xterm" -o $TERM = "xterm-256color" -o $TERM = "screen" ] && type zsh &> /dev/null
then
    export SHELL=$(which zsh)
    if [[ -o login ]]
    then
        exec zsh -l
    else
        exec zsh
    fi
fi

Styling Zsh with Powerlevel10k

Powerlevel10k is not necessary, you could choose a theme shipped with Oh My Zsh (agnoster or look at https://github.com/ohmyzsh/ohmyzsh/wiki/Themes) But I really like Powerlevel10k.

• Install Powerlevel10k:
  • git clone --depth=1 https://github.com/romkatv/powerlevel10k.git ${ZSH_CUSTOM:-$HOME/.oh-my-zsh/custom}/themes/powerlevel10k
  • Set ZSH_THEME="powerlevel10k/powerlevel10k" in ~/.zshrc
  • exec zsh
  • Follow the configuration wizard (p10k configure) which should show up (You should have already installed a Nerd Font!)
  • (https://github.com/romkatv/powerlevel10k#oh-my-zsh)
• Powerlevel10k is fully customizable (look into ~/.p10k.zsh)
  • a few suggestions to look into:

    POWERLEVEL9K_SHORTEN_DIR_LENGTH
    POWERLEVEL9K_LEFT_PROMPT_ELEMENTS
    POWERLEVEL9K_RIGHT_PROMPT_ELEMENTS
    POWERLEVEL9K_TIME_FORMAT
    

• Choose plugins for Zsh (in ~/.zshrc)
  • https://github.com/ohmyzsh/ohmyzsh/wiki/Plugins or somewhere else via google
  • a few suggestions to look into:

    git
    colorize (with alias cat="ccat")
    command-not-found 
    vscode
    lol
    zsh-interactive-cd
    

  • recommended plugins that are not included in Oh My Zsh (don't forget so change the ~/.zshrc):
    • zsh-autosuggestions: git clone https://github.com/zsh-users/zsh-autosuggestions.git $ZSH_CUSTOM/plugins/zsh-autosuggestions
    • zsh-syntax-highlighting: git clone https://github.com/zsh-users/zsh-syntax-highlighting.git $ZSH_CUSTOM/plugins/zsh-syntax-highlighting
    • conda-zsh-completion
• Oh My Zsh also has many customizations (look into ~/.zshrc)

Updating

• WSL-Kernel(in PowerShell): wsl --update
• most of it: sudo apt update && sudo apt upgrade
• Anaconda: conda update anaconda
• TexLive: tlmgr update --self --all --reinstall-forcibly-removed
• Oh My Zsh: omz update
• Powerlevel10k: git -C ${ZSH_CUSTOM:-$HOME/.oh-my-zsh/custom}/themes/powerlevel10k pull