Clean optional dependencies

[schuenke]

Currently we still list a lot of dependencies in our pyproject.toml:

[project.optional-dependencies]
test = [
    "coverage",
    "codecov",
    "pre-commit",
    "pytest",
    "pytest-cov",
    "pytest-xdist",
]
lint = ["mypy", "flake8", "isort", "pre-commit", "autopep8", "pydocstyle"]
docs = ["sphinx", "sphinx_rtd_theme", "sphinx-pyproject"]
notebook = [
    "zenodo_get",
    "ipykernel",
    "ipywidgets",
    "jupytext",
    "matplotlib",
    "pip-tools",
]

Some of these like flake8, isort etc should not be needed anymore, because we do everything with ruff now. We should remove everything that is not really needed.

[fzimmermann89]

..and add ruff? or remove the lint completely and only have pre-commit in it, which in turn depend installs mypy ruff etc.

.. and remove pre-comit from tests..