Backward incompatibility in API functions in `0.0.8`

[szhan]

The latest updates to the API functions are affecting tskit development tests here.

tskit uses the following API functions in lshmm:

• forwards
• backwards
• viterbi
• path_ll

The positional arguments have changed, because the updated API functions now take num_alleles, which is needed to scale mutation rates based on the number of distinct alleles per site.

The keyword arguments have changed. In particular, p_mutation is now prob_mutation, and scale_mutation_based_on_n_alleles is now scale_mutation_rate.

Also, path_ll has been renamed to path_loglik.

Modifications should be made to the lshmm API functions and the tskit test suite to resolve this issue.

[jeromekelleher]

We don't need to update this repo I think, just make the necessary changes to the tskit tests.

[szhan]

The num_alleles was causing problems in the tskit tests. It is no longer an argument in the API functions (see #130). But ploidy is now a required argument in the API functions, and the reference panel is a set of reference haplotypes (not genotypes as before).

[szhan]

I'll update the tskit test suite to use 0.0.7 instead.

[szhan]

I think these issues are solved in pre-release 0.0.8. The tests for the haploid cases in the tskit test suite are now passing.