Improve documentation; apply code conventions

[rafaelab]

This PR aims at making the code more uniform and at improving the documentation.

• The style conventions described in CONTRIBUTING.md are applied.
• Comments were added to header files to be automatically displayed in the documentation.
• Some example notebooks were fixed (e.g. CMB->CMB())
• A new example for electromagnetic cascades with thinning was added

[lukasmerten]

What a massive amount of diligence. I will check the notebooks as soon as I can, but the rest looks good to me.

[lukasmerten]

We also have to fix the merge conflicts, which might be a bit messy for the jupyter notebooks. When you change one of the notebooks make sure to save also the widget state: Widgets -> Save Notebook Widget State, otherwise we might get problems creating the documentation.

[rafaelab]

We also have to fix the merge conflicts, which might be a bit messy for the jupyter notebooks. When you change one of the notebooks make sure to save also the widget state: Widgets -> Save Notebook Widget State, otherwise we might get problems creating the documentation.

I will take a look at the conflicts. I didn't expect there to be any. This shouldn't delay the 3.1.8 release, though.

[lukasmerten]

I now also found that the new example "secondary_photons.ipynb" is not listed in any doctree and therefore not showing up in the documentation. I could probably be included next to secondaries/photons.ipynb.

When all widget states are saved, the documentation builds properly.

[rafaelab]

Hi @lukasmerten I think I've addressed all of your comments and after quite some time I managed to solve the ipynb conflicts, I believe.

[rafaelab]

Hi @lukasmerten Since you already started reviewing this PR, can it already be merged? Otherwise I will have too many conflicts to solve if we wait too long.

[lukasmerten]

I will review it today.