Update `pedigree_kinship` API to match `hybrid_relationship`

[timothymillar]

This only concerns the founder_kinship parameter. This is an optional sub-matrix which is used to initialize the estimate. Currently this is expected to have different dimensions to the output matrix (samples * samples). This should probably be updated to follow the hybrid_relationship API in which a full-sized NaN-padded matrix is used.

[timothymillar]

We could do this by deprecating the old API, rather than an immediate breaking change.

Old API:

• founder_kinship is a matrix of shape founders * founders (where founders < samples)
• founder_indices is an array of length founders specifying the index of each founder within the samples dimension.

• New API:

• founder_kinship is a matrix of shape samples * sample and the founders are automatically detected using the parent matrix.

So

• founder_kinship has shape samples * sample and founder_indices is None --> new API
• founder_kinship does not have shape samples * sample and founder_indices is None --> raise error
• founder_indices is not None --> old API with deprecation warning