Update ci uv+py311

[jeromekelleher]

Drop Python 3.10 and migrate to using a single uv lockfile to fully pin dependencies on CI/CD. This should make maintenance easier because running uv lock periodically should do the trick and it should prevent CI from breaking due to transitive dependencies.

Closes #3383
Closes #3368

[codecov]

Codecov Report

❌ Patch coverage is 36.73469% with 31 lines in your changes missing coverage. Please review.
✅ Project coverage is 33.44%. Comparing base (5dbfdce) to head (63d89ab).

Files with missing lines	Patch %	Lines
python/tskit/trees.py	15.38%	11 Missing ⚠️
python/tskit/drawing.py	9.09%	10 Missing ⚠️
python/tskit/text_formats.py	0.00%	5 Missing ⚠️
python/tskit/tables.py	60.00%	2 Missing ⚠️
python/tskit/genotypes.py	0.00%	1 Missing ⚠️
python/tskit/metadata.py	80.00%	1 Missing ⚠️
python/tskit/util.py	0.00%	1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (5dbfdce) and HEAD (63d89ab). Click for more details.

HEAD has 10 uploads less than BASE

Flag	BASE (5dbfdce)	HEAD (63d89ab)
c-tests	1	0
python-tests-numpy1	1	0
lwt-tests	1	0
python-c-tests	1	0
python-tests	6	0

Additional details and impacted files

@@             Coverage Diff             @@
##             main    #3390       +/-   ##
===========================================
- Coverage   89.76%   33.44%   -56.32%     
===========================================
  Files          29       18       -11     
  Lines       31285     8231    -23054     
  Branches     5738     1359     -4379     
===========================================
- Hits        28082     2753    -25329     
- Misses       1794     5403     +3609     
+ Partials     1409       75     -1334     

Flag	Coverage Δ
c-tests	?
lwt-tests	?
python-c-tests	?
python-tests	?
python-tests-no-jit	33.44% <36.73%> (-0.03%)	⬇️
python-tests-numpy1	?

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

Files with missing lines	Coverage Δ
python/tskit/cli.py	0.00% <ø> (-96.67%)	⬇️
python/tskit/combinatorics.py	21.99% <ø> (-77.38%)	⬇️
python/tskit/exceptions.py	100.00% <100.00%> (ø)
python/tskit/intervals.py	25.00% <ø> (-75.00%)	⬇️
python/tskit/jit/numba.py	97.90% <100.00%> (ø)
python/tskit/provenance.py	62.50% <ø> (-37.50%)	⬇️
python/tskit/stats.py	33.33% <ø> (-66.67%)	⬇️
python/tskit/vcf.py	7.59% <ø> (-89.88%)	⬇️
python/tskit/genotypes.py	34.71% <0.00%> (-64.47%)	⬇️
python/tskit/metadata.py	47.51% <80.00%> (-51.38%)	⬇️
... and 5 more

... and 11 files with indirect coverage changes

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[jeromekelleher]

Mostly working OK. Sticking points:

• Docs - this is quite complicated
• circleCI. Would be nice if we could port this all over to GitHub actions
• Something weird on windows 3.14.
• 3.14 is generally much too slow because of (I think) pins on Zarr < 3.

I'm going to switch to tszip now as it's a simpler project and generally a blocker on progress now.

[jeromekelleher]

Merging this - it's noisy, but there's nothing of any real consequence (beyond the systemic changes to follow the new tskit-dev infrastructure).