Setup
Parts taken from https://nbis-reproducible-research.readthedocs.io/en/course_2104/setup/ and https://coderefinery.github.io/installation/
There are several solutions in how to work with coding and the environments around it
You can work in the environment(s) you are used to.
Many of the teachers will use Visual Studio Code (VS code)
This is not necessary if you have other solution
Benefit:
integrate you terminal and Git work with code development
graphical user interface
available in all platforms
Follow the steps from configure git if not done already
Follow the steps from configure GitHub if not done already
Follow the steps from configure ssh-keys if not done already
Shell and Git
If you will not use VS code, follow steps below.
Terminal & git
Git and terminals are already integrated in VS Code and can be the first choice Otherwise follow the steps below!
We will use terminal to some extent.
Choose one of your choice, the built-in or another!
Chances are big that you already have git installed on your computer. You can check by running e.g.
git --version.If you don’t have git, install it following the instructions here
If you have a very old version of git you might want to update to a later version.
There are several different ways to run the course material on a Windows computer. Neither is perhaps optimal, and the material itself has not been adapted specifically for Windows. Nevertheless, in principle everything should be possible to run. A few ways you could setup:
Git-windos with a command line and Git integrated
Install Git Windows: https://gitforwindows.org/ (easiest if you want to start fast and plan to work in windows environment)
See Windows part at https://coderefinery.github.io/installation/shell-and-git/#installation
Included will be the Git Bash
Other possibilities
Use the Windows 10 PowerShell
Use the Linux Bash Shell (WSL) on Windows 10/11 (perhaps best practice if you plan to run Linux as well)
This will give you access to a full command-line bash shell based on Linux on your Windows 10/11 PC.
instructions below
For the difference between the Linux Bash Shell and the PowerShell on Windows 10, see e.g. this article.
Run as Linux through a virtual machine (and see the Linux setup above)
not shown
Install Bash on Windows 10/11 (WSL), following the instructions at e.g. 1 of these resources:
Configure git
This must be done
Follow these instructions. https://nbis-reproducible-research.readthedocs.io/en/course_2104/setup/#installing-git
GitHub
Sign up for GitHub account: https://coderefinery.github.io/installation/github/
Git/GitHub connection through ssh keys
(This may take a while to get working, but is worth it) https://coderefinery.github.io/installation/ssh/
Test:
ssh -T git@github.comOutput should be something like this:
Hi bclaremar! You've successfully authenticated, but GitHub does not provide shell access.
If not working, these are the approximate steps to be done in your terminal. It can vary between systems, so link above is more certain.
$ ssh-keygen -t ed25519 -C "<email address for your GitHub account>"
$ eval "$(ssh-agent -s)"
$ ssh-add ~/.ssh/id_ed25519
$ # Copy the SSH public key to your clipboard.
$ clip < ~/.ssh/id_ed25519.pub
Then go to your GitHub account on the web.
In the upper-right corner of any page, click your profile photo, then click Settings.
In the “Access” section of the sidebar, click SSH and GPG keys.
Click New SSH key or Add SSH key.
In the “Title” field, add a descriptive label for the new key. For example, if you’re using a personal laptop, you might call this key “Personal laptop”.
Select the type of key authentication.
In the “Key” field, paste your public key.
Click Add SSH key.
If prompted, confirm access to your account on GitHub.
Now test again in your terminal:
ssh -T git@github.comOutput should be something like this:
Hi bclaremar! You've successfully authenticated, but GitHub does not provide shell access.
If there was a problem, confer the full article Adding a new SSH key to your GitHub account.
Python
Use what you already have
If you don’t have Python there are different ways to go. We won’t use Conda during the lessons, for instance.
Bare python (recommended for the “bare metal” user)
you need to install other packages (pip)
note macOS: the system install of Python on macOS is not supported, instead:
brew install python3
Anaconda (recommended for python/R developers liking GUI:s)
includes many many packages
includes conda packager
GUI launchers, like example
jupyter notebook/lab
Spyder
RStudio
etc…
miniconda (recommended for terminal user)
less packages than Anaconda, and no GUI launcher but:
conda packager
pip
etc…
In Linux and Bash, Python should work from the command line by typing
python/python3or running a script withpython <script>/python3 <script>
In VS Code
Step 1. Install a supported version of Python on your system
note: that the system install of Python on macOS is not supported
brew install python3
Step 2. Install the Python extension for Visual Studio Code.
Step 3. Open or create a Python file and start coding!
In Git-bash (Windows)
Get it working from Git Bash
if the command
type pythongives you a path, then proceedotherwise you may have to do a new installation
or find the path
if anaconda installation you may add something like this:
echo 'export PATH="<path/to/Anaconda/root>:<path/to/anaconda/root>/Scripts:$PATH:' >> .bashrcexample:
/c/Users/bjcar425/AppData/Local/anaconda3:/c/Users/bjcar425/AppData/Local/anaconda3/Scripts
$ alias python='winpty python.exe'$ python -Vdoes it give you the python version 3-something?
Make it permanent -
$ echo "alias python='winpty python.exe'" >> ~/.bashrc
PlantUML
We will use the tool PlantUML to render UML code to graphical diagrams and flowcharts.
If you want PlantUML to render directly from a file on GitHub please install the extension PlantUML viewer to your web browser.
works for multiple browsers https://github.com/marcozaccari/markdown-diagrams-browser-extension
Restart browser after installation!
if the above does not work try
Firefox: PlantUML visualizer (is not compatible with !theme none tag)
Chrome: Pegmatite,PlantUML viewer
Microsoft Edge Markdown Diagrams
When done you should see the code below as a diagram.
@startuml
!theme superhero
title:"USECASE Diagrams"
skinparam actorStyle awesome
Lecturer -d->(Present slides on UML)
Participant-d->(learn UML from SLIDES)
@enduml