first rework of project setup chapter

[nehamoopen]

Hi! I've made a first attempt at updating the Project Setup chapter. There's still some things to be cleaned up, both in the chapter and the slides. I'm happy to get feedback before I get to the second round of edits.

[chStaiger]

I am not so sure about that. Data is usually updated, extended or even fully revised (e.g. an experiment that did not go well).
I like the distinction between human-writeable and project-generated. Although I would also rename the latter to "output files" or "generated files" ...

[nehamoopen]

I think it's more about the principle, in that there are some folders that may only be read-only? It doesn't necessarily have to be the data directory. It can be another one. Or perhaps the raw data directory.

[chStaiger]

Suggested change

	In R, you can further ensure a consistent working directory by using an R Project File (.Rproj), which automatically sets the working directory to the project root.
	Let's inspect the following example file structure and some best parctices for R, Matlab and python.
	```sh
	my_project/
	│
	├ data/
	│ file.csv
	│
	└ script.py

Python

Open the folder my_project in your Development environment (IDE), e.g. Jupyter Notebooks or PyCharm (see some suggestions below.). You can address the csv file like this:

import pandas as pd

df = pd.read_csv("data/file.csv")

Since the working directory of your IDE is your project folder, the compiler will find the data automatically.

R

In R you can use RStudio as IDE, simply create File → New Project → New Directory

data <- read.csv("data/file.csv")

Matlab

Similar as in R you can set up a project folder in Matlab and use:

data = readtable("data/file.csv");

In general IDEs help you to make use of relative paths:

Language	Beginner IDE	Feature
Python	Visual Studio Code	workspace folder
R	RStudio	built-in projects
MATLAB	MATLAB	current folder

[chStaiger]

Suggested change

[chStaiger]

I am not sure whether this chapter fits here or better in book/chapters/reusability.qmd

[nehamoopen]

I revisited the reusability chapter and I think we could keep the stuff about paths here, so people can focus on the concept of functionalizing/modularizing code in that section. But you can let me know if you think otherwise!

[chStaiger]

Many thanks this looks good.

I gave some inspiration to extend the relative paths section a bit and I think this section can be moved or at least referenced in the resuability section of the book.
I would be fine either way. Doing the deep dive here and mentioning it in the resuability section; or the other way around.

[nehamoopen]

@chStaiger, I made some changes and did a quick update of the slides! Could you do a final review? And we can merge after the workshop, don't want to break something 😅

[chStaiger]

The video needs to be removed

[chStaiger]

Pun intended ;)

[chStaiger]

I fixed the layout for the slide that only show code blocks.
Thank you for adjusting the contents. Approved by me.