Simplify the smck OOA verification and refactor smck verifications fix 2462, 2463

[hossam26644]

fixes #2462
Now it takes: real 1m51.020s on my PC.
@jeromekelleher let me know if the time is still too long

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.21%. Comparing base (8b6acb5) to head (c536518).
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##             main    #2468   +/-   ##
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  Coverage   91.21%   91.21%           
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  Files          20       20           
  Lines       11845    11845           
  Branches     2300     2300           
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  Hits        10805    10805           
  Misses        569      569           
  Partials      471      471           

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[hossam26644]

I added the fix for #2463 here so that you won't have to deal with merge conflict

[jeromekelleher]

That's still quite long. I'd rather do a smaller simulation with more replicates here. Why does it need to take so much time?

[jeromekelleher]

Can drop this to 1 diploid sample each, see if that brings the time down.

[hossam26644]

This is how it looks if dropped to one sample and do 20 replicates instead of 10 (takes ~30 seconds). We can also reduce the recombination rate by one order of magnitude and keep the large number of samples.

It is slow because the sampling algorithm takes a lot of time.

[hossam26644]

since you mentioned it, test_smc_k_num_trees and test_smc_k_oldest_time take long as well. But I think the plots are more informative with the long time vs when I simplify the parameters. I will followup with how the figures look simplified and non simplified

[hossam26644]

For the test_smc_k_oldest_time:
num_loci = np.linspace(100, 10**4, 10).astype(int)
num_loci = np.linspace(100, 10**5, 10).astype(int)

[hossam26644]

Variance plots for test_smc_k_num_trees:
L = np.linspace(100, 10**4, 10).astype(int)

L = np.linspace(100, 10**5, 10).astype(int)

[jeromekelleher]

OK looks good. But the basic point is that more replicates of a smaller simulation is more useful here, so let's optimise for that. I know some of the other tests are a bit slow but they need to be because you need lots of replicates to get variance. This doesn't need to have lots of replicates, or to be a big simulation.

[hossam26644]

check now @jeromekelleher