Two-way two-locus statistics (python proto)

This PR implements two-way LD statistics, specified between sample sets.
During the development of this functionality, a number of issues with
the designation of state_dims/result_dims were discovered. These have
been resolved, testing clean for existing code and providing the proper
behavior for this new code.

The mechanism by which users will specify a multi-population (or
two-way) statistic is by providing the `index` argument. This helps us
avoid creating another `ld_matrix` method for the TreeSequence object.

In other words, for a one-way statistic, a user would specify:
```python
ts.ld_matrix(stat="D2", sample_sets=[[ss1, ss2]])
```
Which would output a 3D ndarray containing one LD matrix per sample set.

```python
ts.ld_matrix(stat="D2", sample_sets=[[ss1, ss2]], indexes=[(0, 1)])
```
Which would output a 2D ndarray containing one LD matrix for the index
pair. This would use our `D2_ij_summary_func`, instead of the
`D2_summary_func`. Finally, if a user provided
```python
ts.ld_matrix(stat="D2", sample_sets=[[ss1, ss2]], indexes=[(0, 1), (1, 1)])
```
We would output a 3D ndarray containing one LD matrix _per_ index pair
provided.

Since these are two-way statistics, the indexes must be length 2. We
plan on enabling users to implement k-way via a "general_stat" api. We did
not implement anything more than two-way statistics here because of the
combinatoric explosion of logic required for indexes > 2.

I added some basic tests to demonstrate that things were working
properly. If we compute two-way statistics on identical sample sets,
they should be equal to the one-way statistics. Unfortunately, this does
not apply to unbiased statistics, which I've validated manually.

I've also cleaned up the docstrings a bit and fixed a bug with the
D_prime statistic, which should not be weighted by haplotype frequency.

Author: lkirk

c/tskit/trees.c

@@ -4231,7 +4231,7 @@ tsk_treeseq_D_prime(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
 {
     options |= TSK_STAT_POLARISED; // TODO: allow user to pick?
     return tsk_treeseq_two_locus_count_stat(self, num_sample_sets, sample_set_sizes,
-        sample_sets, num_sample_sets, NULL, D_prime_summary_func, norm_hap_weighted,
+        sample_sets, num_sample_sets, NULL, D_prime_summary_func, norm_total_weighted,
         num_rows, row_sites, row_positions, num_cols, col_sites, col_positions, options,
         result);
 }