compute mutation parents on text input

[petrelharp]

Over in #2729 we saw a bug due to not computing mutation parents on text input. This isn't really a bug, as the text input is not part of the public API, but I could easily imagine us making the same error in test code.

(More generally we ought to think about doing this as part of tree sequence instantiation; I seem to recall us having a reason not to do it, but I don't remember specifically what it was?)

[petrelharp]

Closes #2729.

[benjeffery]

@Mergifyio rebase

[petrelharp]

Whoops; looks like I've made some silly mistake.

[petrelharp]

Okay - I got this to work; I had to rearrange the tables in one of the tests.

HOWEVER, I'm worried that putting in compute_mutation_parents might not be the right way to go here. This is because there may be some operations we want to do without having indexes or mutation parents, so I am nervous putting these into all our examples.

[codecov]

Codecov Report

Merging #2730 (a1f89a2) into main (23d35ac) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #2730   +/-   ##
=======================================
  Coverage   94.08%   94.08%           
=======================================
  Files          29       29           
  Lines       28516    28516           
  Branches     1609     1609           
=======================================
  Hits        26828    26828           
  Misses       1653     1653           
  Partials       35       35           

Flag	Coverage Δ
c-tests	92.36% <ø> (ø)
lwt-tests	89.05% <ø> (ø)
python-c-tests	70.89% <ø> (ø)
python-tests	99.05% <ø> (ø)

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[jeromekelleher]

HOWEVER, I'm worried that putting in compute_mutation_parents might not be the right way to go here. This is because there may be some operations we want to do without having indexes or mutation parents, so I am nervous putting these into all our examples.

I'm tending to agree actually. These functions are just for creating test examples, and it'll be easy to forget that any mutation parents you specify will be nuked by this call.

Maybe we should either leave it as it is, or only compute mutation parents when that column is missing from the input?

[mergify]

rebase

✅ Branch has been successfully rebased

[petrelharp]

Maybe we add a flag to the function, that if true does indexes and computes mutation parents, and if false then does not? That'd make it real hard to miss the fact that the function does or doesn't do it.