Bump development tools: mypy, codespell, isort, ...

Move all tools configuration in pyproject.toml.

Remove no longer needed mypy overrides.

packaging.version.parse is dedicated to parse Python package version
numbers but crate versions do not necessarily respect Python version
number conventions and thus some crate versions cannot be parsed.

Prefer to use looseversion.LooseVersion2 instead which in a drop-in
replacement for deprecated distutils.version.LooseVersion and enables
to parse all kind of version numbers.

This fixes python 3.7 support due to poetry, a dependency of isort, that
removed support for that Python version in a recent release.

- pre-commit from 4.1.0 to 4.3.0,
- codespell from 2.2.1 to 2.2.2,
- black from 22.3.0 to 22.10.0 and
- flake8 from 4.0.1 to 5.0.4. Also freeze flake8 dependencies.

Also change flake8's repo config to github (the gitlab mirror
being outdated).

That hook can be frustrating as it can discard a long commit message
if it finds a typo in it so better removing it.

black is considered stable since release 22.1.0 and the version
we are currently using is quite outdated and not compatible with
click 8.1.0, so it is time to bump it to its latest stable release.

Please note that E501 pycodestyle warning related to line length
is replaced by B950 one from flake8-bugbear as recommended by black.
https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#line-length

Related to T3922

The Crates lister retrieves crates package for Rust lang.

It basically fetches https://github.com/rust-lang/crates.io-index.git
to a temp directory and then walks through each file to get the
crate's info.

To install the new hook:

  $ pre-commit install -t commit-msg

Related to T2610

flake8 hook has been removed from https://github.com/pre-commit/pre-commit-hooks
so now use the one from https://gitlab.com/pycqa/flake8

- blackify all the python files,
- enable black in pre-commit,
- add a black tox environment.