WIP: update api for python module, drop python2

[simonpintarelli]

• drop python2
• update to new SIRIUS API for most important parts
• cleanup / split py_sirius.cpp into multiple cpp files
• @toxa81 ci/cd pipeline for python module

[toxa81]

IMO we should drop this file as well and submit changes directly to the spack package of sirius

[toxa81]

The vector3d intrface is not working properly. This works but is awkward:
https://github.com/electronic-structure/SIRIUS/blob/update/python-module/examples/python/Si_dft.py#L29

This should be the intrface (https://github.com/electronic-structure/SIRIUS/blob/update/python-module/examples/python/Si_dft.py#L30), but it gives the error:

TypeError: add_atom(): incompatible function arguments. The following argument types are supported:
    1. (self: sirius.py_sirius.Unit_cell, arg0: str, arg1: geometry3d::vector3d<double>) -> None

[simonpintarelli]

The vector3d intrface is not working properly. This works but is awkward: https://github.com/electronic-structure/SIRIUS/blob/update/python-module/examples/python/Si_dft.py#L29

This should be the intrface (https://github.com/electronic-structure/SIRIUS/blob/update/python-module/examples/python/Si_dft.py#L30), but it gives the error:

TypeError: add_atom(): incompatible function arguments. The following argument types are supported:
    1. (self: sirius.py_sirius.Unit_cell, arg0: str, arg1: geometry3d::vector3d<double>) -> None

I'll have a look.

[simonpintarelli]

@toxa81 Now both variants Unit_cell.add_atom(label, [list_like]) and Unit_cell.ad_atom(label, sirius.vector3d). The former also does check the length, it will accept only python list / numpy arrays with 3 entries (pybind11 does that).

[toxa81]

This looks good to me now. Unless @simonpintarelli you really want to work on cleanup / split py_sirius.cpp into multiple cpp files, it is good to go for meging. The Python intrface is restored to a minimum that can run DFT ground state.

[simonpintarelli]

@toxa81 Let's merge it. I'll work on it later.