modernize python code base, part 2

[nim65s]

Hi,

This follow #2367 by enabling additional opt-in features of ruff, and implementing those either manually or through auto-fix.

Commit history was rewritten to ease review, but things can be squashed once agreed.

[github-actions]

👋 Hi,
This is a reminder message to assign an extra build label to this Pull Request if needed.
By default, this PR will be build with minimal build options (URDF support and Python bindings)
The possible extra labels are:

• build_collision (build Pinocchio with coal support)
• build_casadi (build Pinocchio with CasADi support)
• build_autodiff (build Pinocchio with CppAD support)
• build_codegen (build Pinocchio with CppADCodeGen support)
• build_extra (build Pinocchio with extra algorithms)
• build_mpfr (build Pinocchio with Boost.Multiprecision support)
• build_sdf (build Pinocchio with SDF parser)
• build_accelerate (build Pinocchio with APPLE Accelerate framework support)
• build_all (build Pinocchio with ALL the options stated above)

Thanks.
The Pinocchio development team.

[ManifoldFR]

Great work again @nim65s :)

[jcarpent]

Thanks @nim65s for the cleanage of the code.
Could you squeeze everything into a single commit?

[nim65s]

done

[nim65s]

macos CI is consistently failing with:

CMake Error at CMakeLists.txt:324 (message):
  Your version of Eigen is too low.  Should be at least 3.4.90.  Current
  version is 3.4.0.

windows CI is failing with

C:\Miniconda\envs\pinocchio\Library\include\cppad/cg/cg.hpp(217): error C2143: syntax error: missing ';' before '<'
C:\Miniconda\envs\pinocchio\Library\include\cppad/cg/cg.hpp(217): error C2433: 'CppAD::cg::NearEqual': 'friend' not permitted on data declarations
C:\Miniconda\envs\pinocchio\Library\include\cppad/cg/cg.hpp(217): error C2365: 'CppAD::cg::NearEqual': redefinition; previous definition was 'function'

In both cases, this is not related to this PR.

[jcarpent]

macos CI is consistently failing with:

CMake Error at CMakeLists.txt:324 (message):
  Your version of Eigen is too low.  Should be at least 3.4.90.  Current
  version is 3.4.0.

For this issue, I've removed the support Apple Accelerate for build_all