Add support for Python 3.14

[hugovk]

Also:

• Fix compatibility with NumPy 2.0 which removed in1d
• Remove Python 3.9 dependency
• Run pyupgrade for 3.10+
• Update pre-commit and fix B018 "Found useless Tuple expression"
• Update GitHub Actions
• Set min version as 3.10 in docs and fix typos

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.21%. Comparing base (042a0cf) to head (e37a862).
⚠️ Report is 8 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2455      +/-   ##
==========================================
- Coverage   91.22%   91.21%   -0.01%     
==========================================
  Files          20       20              
  Lines       11847    11845       -2     
  Branches     2300     2300              
==========================================
- Hits        10807    10805       -2     
  Misses        569      569              
  Partials      471      471              

Flag	Coverage Δ
C	91.21% <100.00%> (-0.01%)	⬇️
python	98.63% <100.00%> (-0.01%)	⬇️

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[hyanwong]

Great spots on the typos etc and the in1d which is causing the site builds to fail. I'll let @benjeffery check on the 3.10 stuff, but it all LGTM.

[jeromekelleher]

All LGTM - thanks @hugovk (and nice to see you again!)

[hugovk]

Hello! btw saw some nice praise in https://arxiv.org/pdf/2601.09634:

It is hard to overstate the importance of msprime in the current landscape of CWR simulators. Before its publication, it was largely accepted that large-scale simulations were only possible through approximations. msprime proved that a careful implementation of Hudson’s algorithm could, for all intents and purposes, outperform sequential approximations even on genome-scale datasets.

[benjeffery]

I'm picking this up and will get it merged.

[benjeffery]

Great work, I think you found all the spots to update!

[benjeffery]

I have updated the rules at https://github.com/tskit-dev/msprime/settings/branch_protection_rules/17687413 so this should merge now.