Fix counting of mutations in genome.mutate

[HenrikMettler]

This PR fixes the mutation counter by explicitly comparing the number of differences in dna before and after mutations

fixes #156

[jakobj]

thanks for the update ✨ unfortunately travis is unhappy with the new changes, could you please have a look and fix the issues?

[mschmidt87]

Looks good, thanks for fixing this, I just have some small suggestions.

Actually, don't we need to adapt the parameters set in the examples with this change, @jakobj ?

[jakobj]

regarding the example: the mutation rate was chosen accordingly to the CGP literature, assuming the implementation is correct, so it should be fine. seems like they all still work, don't they?

[mschmidt87]

regarding the example: the mutation rate was chosen accordingly to the CGP literature, assuming the implementation is correct, so it should be fine. seems like they all still work, don't they?

I haven't tested the examples. The CI only checks if they crash, not if they convert.

[mschmidt87]

I think that CI is failing because of flake8 issues. I would recommend to install pre-commit hooks for git to catch such errors locally, @HenrikMettler .

[jakobj]

regarding the example: the mutation rate was chosen accordingly to the CGP literature, assuming the implementation is correct, so it should be fine. seems like they all still work, don't they?

I haven't tested the examples. The CI only checks if they crash, not if they convert.

good point! @HenrikMettler please also manually test the examples and check whether they converge properly.

[HenrikMettler]

For the examples:

• all of them stop prior to the max number of generations with values ~ -1e-15 (to -1e-30) -> that this is convergence I assume?
• example_evo_regression.py: The first only converges after 950 of (max) 1000 generations. Should I increase the max number of allowed generations?

[jakobj]

no, i think it's fine, no need to change it as long as it converges within the given number of generations. thanks for checking this :)

[edit]
i think as soon as you've reintroduce the "long loop" in the test i'm fine. travis is also fine, it's just showing an error due to a communication issue between travis and github. before we merge please squash your commits.
[/edit]

[HenrikMettler]

the latest commit should clear all the issues. I can't squash though (I think) since i don't have the rights to squash and merge (if I understand this: https://cloudfour.com/thinks/squashing-your-pull-requests/ correctly)

[mschmidt87]

LGTM, thanks for catching this bug and fixing it right away.

[mschmidt87]

Before we merge, one more (minor) thing: could you make the commit message a bit nicer, i.e., remove the "some more changes" lines etc., and stick to imperative tense and capitalized beginning?