resolve merge conflicts; debugged compose_emcoinc

I hope this fixes all the merge conflicts. There are still lint errors, but these are just from currently unused variables (path_to_output_CBC and UL50) which we haven't figured out what to with yet.

@jean-gregoire.ducoin I think you should clean up your branch by resetting it before you accept this merge request. You already have several overlapping commits in your __init__.py and this would add even more confusion. Don't worry about losing your commits, because my branch still has the full commit history.