[DEMO] pre-commit and pre-commit-ci

[aucampia]

Add pre-commit and pre-commit-ci with the following hooks:

• pycln for cleaning up unused imports.
• isort for sorinting imports.
• black for formatting code.
• check-yaml for validating yaml files.

For more info see docs/developers.rst.

Also:

• Changed tox config:
  • Added environments for pre-commit.
  • Removed some redudant options.
  • Created a covreport environment for reporting coverage for all
    environments.
  • Make it possible to run a custom command instead of pytest.
  • Make it possible to run an extra command
  • Make it possible to change the mypy command
  • Use extras instead of using requirements files.
• Update setup.py
  • Remove berkleydb and networkx from tests_require and tests extra
    group as they are not always needed for tests.
  • Added seperate extra groups for berkleydb and networkx
  • Added a dev extras group with dev tools.
• Update github actions
  • Use tox to run tests.
  • Run flake8 only once.
  • Change docs job to rather be more generic for potential future tox
    environments.

[aucampia]

pre-commit.ci run

[aucampia]

pre-commit.ci autofix