Test suite to use new msprime calling convention

[hyanwong]

Ideally we should switch to the new msprime for testing, since it has discrete genome coords, individuals, metadata, etc. This switches the tree sequences used for testing to new format versions

[hyanwong]

Oh damn, requires tskit 0.4. Will wait, I guess.

[hyanwong]

Lots of this seems to be "TypeError: 'PopulationTable' object does not support item assignment". Is this post-tskit 0.4.0?

[codecov]

Codecov Report

Merging #614 (0e2b25c) into main (b6662b3) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #614   +/-   ##
=======================================
  Coverage   93.08%   93.08%           
=======================================
  Files          17       17           
  Lines        5136     5136           
  Branches      954      954           
=======================================
  Hits         4781     4781           
  Misses        235      235           
  Partials      120      120           

Flag	Coverage Δ
C	93.08% <ø> (ø)
python	96.31% <ø> (ø)

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[hyanwong]

I think this is entirely uncontroversial, and gets CI working again, so other PRs can start going through. Looks like the requirements conflict needs a tiny tweak before merging, so that we are using tskit 0.4.1, but after that it presumably can be merged. Do you think you might have time to do that @benjeffery or @jeromekelleher ? I'm not sure how to do it.

[jeromekelleher]

I'll take a look now.

[hyanwong]

Thanks Jerome. That's much appreciated.

[jeromekelleher]

That should do it, thanks for sorting this out @hyanwong!

[hyanwong]

Hooray, thanks @jeromekelleher. Merge away

[jeromekelleher]

Looks like a random number problem on Windows, can you take a look please?