Migrate to a `pyproject.toml` project definition

[Amaras]

This PR aims to migrate away from requirements.txt and use pyproject.toml instead.

The problem with the quasi-obsolete requirements.txt is clearly visible in the way JetBrains obsoleted the Requirements plugin in PyCharm.

Using a pyproject.toml is a more modern way to develop python applications, and the building backend is configurable.

One downside is that I had to push all code to the src/ directory, which might be a problem, as I did not test it yet.

The dependencies come from a run of pipdeptree on the virtual environment.

Dev instructions

To install the dependencies, simply do pip install -e ..

I also added some development dependencies: pipdeptree to explore the dependency tree of our packages, and ruff, a Python linter and formatter. To install those dependencies, run pip install -e .[dev]

[Amaras]

Note that the requirements might need to be updated in the pyproject.toml, I did not check them thoroughly