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 "max.mustermann@email-provider.com"
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 "max.mustermann@email-provider.com"
- 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 git@github.com: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

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What is this?

Installation Instructions (mainly on Windows 11 + WSL)

WSL and Ubuntu

Useful/Essential Linux Tools

Visual Studio Code

Python (Scientific Python via Miniconda with Mamba, recommended)

Python (Scientific Python via Anaconda, not recommended!)

Useful Python Packages not in Anaconda

Latex (with TexLive)

C++

Git configuration (for GitHub)

Useful Windows Configurations

WSL Bug fixes / workarounds

Graphical Interfaces don't work (for example matplotlib)

GDB fix for Ubuntu 22

Jupyter Lab/Jupyter Notebook on WSL

Terminal Customizations

Customize your terminal (Windows Terminal)

Installing Oh My Zsh

Styling Zsh with Powerlevel10k

Updating

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README.md

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What is this?

Installation Instructions (mainly on Windows 11 + WSL)

WSL and Ubuntu

Useful/Essential Linux Tools

Visual Studio Code

Python (Scientific Python via Miniconda with Mamba, recommended)

Python (Scientific Python via Anaconda, not recommended!)

Useful Python Packages not in Anaconda

Latex (with TexLive)

C++

Git configuration (for GitHub)

Useful Windows Configurations

WSL Bug fixes / workarounds

Graphical Interfaces don't work (for example matplotlib)

GDB fix for Ubuntu 22

Jupyter Lab/Jupyter Notebook on WSL

Terminal Customizations

Customize your terminal (Windows Terminal)

Installing Oh My Zsh

Styling Zsh with Powerlevel10k

Updating

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