Update packaging and installation

[lfarv]

This updated the packaging and installation setup with two main changes:

Upgrade setuptools:

The main motivation is to ease the compilation of AT with MPI. To allow the modification of the build requirements depending on the context, setuptools now provides in-tree backends: _custom_build/backend.py here. The command for compilation with MPI is now:

MPI=1 pip install ".[mpi]".  # from the local clone
MPI=1 pip install --no-binary accelerator-toolbox "accelerator-toolbox[mpi]"  # from the PyPI repository

Note both the [mpi] option to add mpi4py to the installation requirements, and the MPI=1 environment variable which will add mpi4py to the build requirements and select the mpicc compiler.

As a side effect, most of the configuration moves from setup.cfg to pyproject.toml. Completely removing setup.cfg works but is still considered as beta. So for the time being, we keep a minimal setup.cfg.

Also, setuptools >= 62 cannot be installed on python 3.6. Removing support for python 3.6 also removes some complexity in at/__init__.py.

Move to project to the root of the repository:

1. This is a common practice to have the project definition at the top-level
2. This simplifies a lot the installation process: the source code of integrators (atintegrators directory) is now part of the project, so we do not need any more to make copy into pyat/integrator-src. setup.py is simpler and only deals with the definition of extensions.
3. The idea was also to have a single machine_data package for both Matlab and python by having the top-level machine_data also part of the project. This still does not work because of restrictions in the way setuptools looks for packages. It looks impossible to have package search at two levels, top-level for ./machine_data and pyat/at for the at package. So we still have 2 machine_data repositories.

The difference for users is that pip install must now be run from the top-level instead of from the pyat directory. The documentation is updated.

[lfarv]

In addition to the syntax for compiling with MPI involving an environment variable, there is now another syntax:

pip install --config-settings mpi=1 ".[mpi]".  # from the local clone
pip install --no-binary accelerator-toolbox --config-settings mpi=1 "accelerator-toolbox[mpi]"   # from the PyPI repository

This uses recent features of PEP 517. However it's only cosmetic, since the environment variable is still used internally to communicate with setup.py.

This is also valid for compilation with OpenMP:

pip install --config-settings openmp=1  .  # from the local clone
pip install --no-binary accelerator-toolbox --config-settings openmp=1 accelerator-toolbox   # from the PyPI repository

[lfarv]

Rebased on master,

[swhite2401]

Very nice, could you improve the doc page with these informations? I could not find any modifications related to MPI

[lfarv]

@swhite2401 : right, I'll do that.

[swhite2401]

Ok after help is updated

[lfarv]

@swhite2401: I'd like to have your feedback on the updated documentation that you can preview here.

[swhite2401]

@swhite2401: I'd like to have your feedback on the updated documentation that you can preview here.

This looks fine to me, at some point we will provide examples but for now we are still working on the multibunch/beamloading devs