superposition still needs fixing!

[AndreaVolkamer]

          So this PR now contains two unrelated changes: one is fixes to the KLIFS subpackage by Dominique, and the other is updating the Biopython version. For the latter, I had already left a review pointing to some problems, which are not yet resolved. Also, as we discussed in our last meeting, the Biopython problem is only a part of the problem with the `superposition` subpackage.

I think the best approach is to separate these two fixes, and first apply the KLIFS fix, which is already working. Also, depending on your decision on how to proceed with separating the two subpackages, there are other updates that need to be done, but first we need to decide on our strategy.
As I mentioned earlier, the best approach in my opinion is to release a new version of the KLIFS subpackage as a standalone package on PyPI. This way the updated KLIFS part will be immediately available to downstream users. I can do this in a couple of hours if you want.

Originally posted by @AAriam in #157 (comment)

[AndreaVolkamer]

Details from PR:

in opencadd/structure/superposition/sequences.py find_gap_parameter function

Armin:
Shouldn't the gap characters be removed explicitly now that BioPython doesn't recognize them?

From BioPython Documentation:

Another case where the alphabet was used was in declaring the gap character, by default - in the various Biopython sequence and alignment parsers. If you are using a different character, you will need to pass this to the Seq object .replace() method explicitly now:

# Old style
from Bio.Alphabet import generic_dna, Gapped
from Bio.Seq import Seq

my_dna = Seq("ACGT=TT", Gapped(generic_dna, "="))
print(my_dna.ungap())

# New style
from Bio.Seq import Seq

my_dna = Seq("ACGT=TT")
print(my_dna.replace("=", ""))