Refactoring various `requirements.txt` into ` setup.py` extras

[FelixBenning]

• Uses extras_require= in the setup.py to achieve the amount of custom installation variants currently achieved with many different requirements.txt e.g.

  pip install -e .[dev]
  

• Update the Makefile (create virtual environment)
• pip -e now works with a pyproject.toml move black configuration into pyproject.toml