Variant copy for lowlevel python

[benjeffery]

Stacked on #2157
Adds restricted_copy to the low-level python. I think I've covered all the lifecycle stuff here, but a close review would be appriciated.

[benjeffery]

Note to self - run the stress test for leaks.

[codecov]

Codecov Report

Merging #2169 (a2c01fa) into main (fecad52) will decrease coverage by 0.01%.
The diff coverage is 71.42%.

@@            Coverage Diff             @@
##             main    #2169      +/-   ##
==========================================
- Coverage   93.29%   93.28%   -0.02%     
==========================================
  Files          27       27              
  Lines       26039    26059      +20     
  Branches     1163     1163              
==========================================
+ Hits        24294    24308      +14     
- Misses       1715     1721       +6     
  Partials       30       30              

Flag	Coverage Δ
c-tests	92.20% <ø> (ø)
lwt-tests	89.05% <ø> (ø)
python-c-tests	72.27% <71.42%> (-0.01%)	⬇️
python-tests	98.89% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
python/_tskitmodule.c	90.94% <71.42%> (-0.07%)	⬇️

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[benjeffery]

Looks like the linter has broken deps, will investigate.

[benjeffery]

@Mergifyio rebase

[mergify]

rebase

❌ Base branch update has failed

Git reported the following error:

Rebasing (1/2)
Auto-merging python/_tskitmodule.c
CONFLICT (content): Merge conflict in python/_tskitmodule.c
Auto-merging python/tests/test_lowlevel.py
CONFLICT (content): Merge conflict in python/tests/test_lowlevel.py
error: could not apply 28a4394... Add initial lowlevel Variant class
hint: Resolve all conflicts manually, mark them as resolved with
hint: "git add/rm <conflicted_files>", then run "git rebase --continue".
hint: You can instead skip this commit: run "git rebase --skip".
hint: To abort and get back to the state before "git rebase", run "git rebase --abort".
Could not apply 28a4394... Add initial lowlevel Variant class

err-code: F4A65

[jeromekelleher]

I can take a look at this once it's rebased @benjeffery

[jeromekelleher]

Looks right to me, but I'd run some serious stress tests on this sort of thing to reassure myself as it's very subtle.

[benjeffery]

Looks right to me, but I'd run some serious stress tests on this sort of thing to reassure myself as it's very subtle.

Stress test is fine, max iter is at 100 after 1000 runs. I've also gone over the code again to try and satisfy myself.

[jeromekelleher]

I'd usually run in a loop in a standalone script as well, as the stress script is quite slow and noisy when checking specific changes like this. Problems usually show up very quickly.

[benjeffery]

I modified the stress script to only run the Variant tests. I'll also run a tight loop before merging though.