Build 22.04.5, WS 2024

Build 22.04.5, WS 2024#

This file:

  • Build of dsci-lab_22.04.5_ws24, 2024-03-02

  • Basis: Xubuntu 22.04.4 LTS (Jammy Jellyfish), 64 bit

  • admin user install

previous versions:

Important: You are not requested to build the dsci-lab by yourself. Instead you are advised to download the fully configured dsci-lab as a ready-to-use virtual machine, see Download the dsci-lab OVA file.

However, if you are a lecturer or a deeply interested student you might want to learn how we set up the dsci-lab. Here are the steps.

Install VM Virtual Box 7#

Create the virtual XUbuntu machine#

Download an ISO image:

Start Oracle VM Virtual Box Manager

  • Maschine > Neu > Name: e.g. dsci-lab_22.04.5_ws24

  • Ort: z.B. /home/jb/VirtualBox VMs

  • Typ: Linux, Version: Ubuntu (64-bit)

  • Experten-Modus

  • Speichergröße: minimal 4096 MB, besser z.B. 16000 MB ;-) )

  • Platte: Festplatte erzeugen > Erzeugen

  • Dateityp der Festplatte: VDI

  • Art der Speicherung: dynamisch alloziert

  • Dateiname und Größe: hier mindestens 100 GB angeben > Erzeugen

Start machine dsci-lab_22.04.5_ws24.

  • Starten > Try or install XUbuntu

VirtualBox will start the ISO image:

  • Select language, e.g. “Deutsch” > “Install XUbuntu”

  • Tastaturbelegung: German > German

  • Aktualisierungen herunterladen

  • Installationsart: Festplatte löschen und installieren (this will clean only your newly allocated virtual hard disc, NOT the disk of your host system;-) ); > Installieren

  • Wo befinden Sie sich? > Berlin

  • “Who are You?”:

    • Name: Data Scientist

    • Name des Rechners: dsci-lab_22.04.5_ws24

    • Benutzername: dsci

    • password: dscidsci

A basic version of xubuntu will be installed.

“Die Installation ist abgeschlossen. Sie müssen jetzt den Rechner neu starten, um das System zu benutzen” > Jetzt neu starten

  • Virtualbox will become black and “freeze”. Close the Window: “X”-button > die virtuelle Maschine ausschalten

  • Start the new machine again.

  • Log in with user dsci, password dscidsci

Update Basic System#

“A new Release 24.04.1 LTS is available, upgrade?” > NO, never upgrade, we want to stick with 22.04

“Aktualisierungsverwaltung” will start automatically and ask you to update the system: “Aktualisierte Anwendungen wurden seit der Veröffentlichung von Ubuntu 22.04 herausgegeben” > “jetzt installieren”.

Alternatively you may want to start Aktualisierungsverwaltung manually:

To update your installation, regularly start “Aktualisierungsverwaltung”. As an alternative to using “Aktualisierungsverwaltung” you can keep the system current with apt:

sudo apt update; sudo apt upgrade

Try it! Your system already should be up to date.

Restart the machine afterwards. Login again.

  • “Update standard folders to current language?” > im dsci-lab wollen wir englische Ordnernamen, also “update names”

We will use the command line hereafter where possible. Get a new terminal by typing Strg-Alt-t.

VirtualBox Guest Extensions#

To install new kernel modules - i.e. Oracle VirtualBox Guest Extensions - we need (the gnu C compiler) gcc:

sudo apt install gcc make perl htop

Oracle Virtual Box > Geräte > Gasterweiterungen einlegen: A window pops up, showing the directory /media/data/VBox_GAs_6.1.42./ > rightclick on background, “Open Terminal here”, a new terminal opens. Type in:

sudo ./VBoxLinuxAdditions.run

Some new kernel modules will be built. To replace the running kernel modules with the new ones you have to reboot the VM:

2024-09-19: Machine says “VirtualBox Guest Additions: reloading kernel modules and services”: The mouse cannot be used any more. However, CTRL-T works. We shut down the machine manually:

sudo reboot

Login again. You now should be able to resize the VM window. Try it!

Activate bidirectional Copy & Paste from Windows-Host to VB etc.

Geräte > Gemeinsame Zwischenablage > bidirektional

After updating virtualbox on the host you might want to update the guest extensions on the guest. Simply repeat the steps above. Donn’t forget to reboot your guest engine.

Firefox Privacy#

Start firefox. Hit the “ALT”-button to show the menu.

Edit > Settings (Bearbeiten > Einstellungen):

  • Home > New Windows and Tabs (Startseite und neue Fenster): point default to https://www.startpage.com/

    • Inhalte des Firefox-Startbildschirms: privacy! … but do not deactivate these widges (don’t close your eyes), but go to

  • Datenschutz und Sicherheit > Benuzerdefiniert > Cookies und Website-Daten

    • Cookies und Website-Daten beim Beenden von Firefox löschen: Check!

    • Hauptpasswort verwenden: Enter a save password!

    • Chronik: Firefox wird eine Chronik > nach benutzerdefinierten Einstellungen anlegen

      • “Die Chronik löschen, wenn Firefox geschlossen wird”: Check!

    • Datenerhebung durch Firefox und deren Verwendung

      • (de-)select whatever you want

Extras > Add-Ons und Themes > Erweiterungen

  • Ghostery – datenschutzorientierter Werbeblocker

    • optionally configure Ghostery: “ausführen in privaten Fenstern erlauben”

document this installation properly#

To document subsequent personal installations of your VM you might wish to update this very file you are reading currently.

  • In Firefox push the .md-Button in the upper right corner of the page and save the file to Downloads/build.md.

  • Alternatively you might want to download the markdown-source of this file locally:

cd ~/Downloads
wget http://jbusse.de/dsci-lab/_sources/build.md
cd

Edit the file build.md e.g. with Mousepad. Alternatively you want to use your favourite programming editor.

VS Code#

As of 2024 we recommend Microsoft Visual Studio Code (aka VS Code) https://code.visualstudio.com/docs/python/python-tutorial:

snap install code --classic

From File > Preferences > Settings, search for telemetry, and set the Telemetry: Telemetry Level setting to off. This will silence all telemetry events including crash reporting from VS Code. You will need to restart VS Code for the setting change to take effect. https://code.visualstudio.com/docs/supporting/FAQ#_how-to-disable-crash-reporting

Optionally also get MyST-Marksown Syntax extension for VS Code: https://marketplace.visualstudio.com/items?itemName=ExecutableBookProject.myst-highlight

vim, emacs#

Only if you are over 50 years old ;-) you still want to stick to vim or emacs:

sudo apt install vim emacs

More basic Packages#

At this stage you have a clean, brand new virtual XUbuntu machine, with VirtualBox Guest extensions enabled.

To get our dsci-lab version you have to install some more packages. You can do so by simply copying the following commands into a terminal (open a new terminal e.g. by typing Strg-Alt-t):

freeplane#

Mindmap (incl. Java):

sudo apt install freeplane

LaTeX#

https://jupyterbook.org/en/stable/advanced/pdf.html recommends using the texlive distribution.

We have found that in combination with jupyterbook (see below) the following packes are actually required, with a total size about 2 GB (!):

sudo apt install imagemagick\
     	 	 texlive-latex-recommended texlive-latex-extra \
                 texlive-fonts-recommended texlive-fonts-extra \
                 texlive-xetex latexmk texlive-lang-german\
		 xindy biber texlive-science

GitHub Desktop#

GitHub Desktop - The Linux Fork: shiftkey/desktop

wget -qO - https://apt.packages.shiftkey.dev/gpg.key | gpg --dearmor | sudo tee /usr/share/keyrings/shiftkey-packages.gpg > /dev/null
sudo sh -c 'echo "deb [arch=amd64 signed-by=/usr/share/keyrings/shiftkey-packages.gpg] https://apt.packages.shiftkey.dev/ubuntu/ any main" > /etc/apt/sources.list.d/shiftkey-packages.list'
sudo apt update && sudo apt install github-desktop

ca 300 MB (!)

(Mini-)Conda#

Important: Install Conda not with sudo. Install it with the role of a normal user instead. Every user and every virtual conda environment are completely independent from each other. There is no system-wide installation.

Installing on Linux:

cd
cd Downloads
chmod +x

Miniconda Installer: https://docs.conda.io/projects/miniconda/en/latest/ > Quick command line install:

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm ~/miniconda3/miniconda.sh
~/miniconda3/bin/conda init bash

==> For changes to take effect, close and re-open your current shell. <==

Why close and open? In an earlier step you have installed conda. Conda puts an extra virtual environment layer over the standard Python installation, so we can work with multiple Python configurations in parallel. To learn more about virtual environments:

Your termial command line now should start with (base), which is the name of your current virtual environment:

(base) dsci@dsci-lab-ss24:~$

Keep conda current:

conda update --all

(Note:Instead of installing miniconda you instead want to install anaconda (https://www.anaconda.com/products/individual). Anaconda is much more complete than miniconda, but IMHO fo “fat”. In our dsci-lab we prefer a lightweight system. This allows you to look more easily “under the hood”, to understand what’s going on, and to maintain the whole system - the dependencies in our setup are complex enough anyhow.)

Install python packages into the virtual conda environment base#

As said: Conda is minimalistic. Tus we have to install some modules by ourselfes.

Some important ones are:

pip install pandas numpy matplotlib scikit-learn seaborn \
   rdflib owlrl markdownify lxml markdown python-slugify \
   jupyter jupyter-book jupytext

Notes:

  • We do install these packages into the virtual conda environment base. If we decide to create another virtual conda environment, it will be empty again, and we have to populate it with libraries again. This is the reason (a) why we prefer lightweight environments, and (b) why we want to learn how to install libraries by ourselfes.

Jupyterbook#

Test the jupyterbook installation: Build the book according to https://jupyterbook.org/start/build.html

mkdir -p ~/c
cd ~/c
jb create jupyterbook-test

build html:

jb build jupyterbook-test
firefox jupyterbook-test/_build/html/index.html &

build pdf via LaTeX:

jb build jupyterbook-test --builder pdflatex
atril jupyterbook-test/_build/latex/book.pdf &

Start Jupyter. Jupyter will launch firefox. Stop Jupyter again:

jupyter notebook &
jupyter notebook stop

system login screen image#

Download desired image to /Downloads.

cp this image with sudo rights into folder /usr/share/xfce4/backdrops/:

cd  /usr/share/xfce4/backdrops/
sudo mv /tmp/IMG_2247.JPG .
sudo chmod 655 IMG_2247.JPG

“Bildschirmhintergrund des Nutzers verwenden, falls verfügbar”: NO

Open Whisker-Menue > Settings > LightDM GTK+ Greeter

  • select image in folder backdrops

  • enter install password

  • select background image

customize user install background image#

copy private background image into folder Documents.

right click on background > desktop settings > folder Documents > select image

Zotero#

https://www.jbusse.de/dsci-lab/h_zotero.html

Export OVA#

Maschine aktualisieren, Gasterweiterungen installieren, Shared Folder deaktivieren, Medium auswerfen, Maschine ‘runterfahren, USB auf 1.0 umstellen, dann Export OVA:

  • /home/jb/v/dsci-lab_22.04.5_ws24.ova

  • “alle Netzwerkadressen mit einbeziehen”

  • Hersteller-URL: jbusse.de/dsci-lab

SHA und Größe der Datei feststellen:

ls -ls v/dsci-lab_22.04.5_ws24.ova
# 11558000 -rw------- 1 jb jb 11835387904 Sep 30 09:20 v/dsci-lab_22.04.5_ws24.ova

sha256sum v/dsci-lab_22.04.5_ws24.ova
# XXXXXf810530ff34b1a52d6b79f96cb313b8935ccfebd8dcbf56e7868e232cf5fb0a4  v/dsci-lab_22.04.5_ws24.ova

Auf den Server hochladen, auch dort sha256sum berechnen, kontrollieren, erst dann in Download the dsci-lab OVA file eintragen.

Admin#

Aktualisieren:

sudo apt update; sudo apt upgrade
sudo snap refresh

next steps#

http://jbusse.de/dsci-lab/h_shared-folders.html

http://jbusse.de/dsci-lab/h_customizing.html

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