Template for starting a new scientific project, specifically designed to allow keeping track of things with git and GitHub (or other online git repos).
See individual subfolders for more complete description of what you should and should not do, but in general:
The writing folder is really just a copy of ScienceMarkdown. It is meant for writing (yes, really!). Write a paper, or anything else here. Don't do analysis here!
Analysis is for analysis of raw data. Don't put actual raw data here! Write scripts that pull raw data from your hard-drive and do something with it. You can maybe save some very simple intermediate result (like a .csv file or something) if it saves time. You should typically find Notebooks here.
Contains everything that does not fit in the other categories. Probably just a mess. But sometimes a mess is useful.
This project folder comes with its own Python environment in the form of pyproject.toml, which can be installed using poetry: just run poetry install. The supplied pyproject.toml file should cover most use cases, but you can always add a missing dependency using poetry add [package].
If you discover that you are building an awful lot of functions in your analysis folder and would want a custom package, you can just make it (use the poetry new command), push it to GitHub, and add it to the Python environment using: poetry add --editable git+https://github.com/WetenSchaap/PACKAGE.git. If you make changes, push to GitHub and import by running poetry update. Alternatively, you can also point directly to the relevant folder if you are really changing it all the time: poetry add --editable ./my-package/. But long term the git way is easier.