Stop using the Makefile in the CI and tools installed from Poetry dev dependencies in favor of pre-commit

• Delete dev dependencies tools from pyproject.toml: black, pylint, mypy, pre-commit?
  • Since the dependencies are duplicated in Poetry and Pre-commit virtualenvs.
• Document how to use dependencies installed into pre-commit: pre-commit run black -a.
• CI: Run tools without the make rule call
  • pytest to be merged
  • Update sphinx doc to not requires make dependency to build the doc
    • Remove make installation from image generations
• Update the Makefile in favour of pre-commit run -a (${tool}) calls
  • Readme: change make commands with poetry, pre-commit, sphinx* commands