Compile on numpy2

[jeromekelleher]

Part of supporting numpy >= 2. Following the ABI advice from numpy, we should be able to compile against numpy version >= 2, and also have a runtime dependency < 2. Hopefully this is all we need to do initially to ship compatible wheels and conda packages (which are also broken)

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 89.62%. Comparing base (f467db6) to head (bb137ff).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #2964 +/- ## ======================================= Coverage 89.62% 89.62% ======================================= Files 29 29 Lines 30170 30170 Branches 5867 5867 ======================================= Hits 27041 27041 Misses 1790 1790 Partials 1339 1339 ``` | [Flag](https://app.codecov.io/gh/tskit-dev/tskit/pull/2964/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | Coverage Δ | | |---|---|---| | [c-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2964/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `86.20% <ø> (ø)` | | | [lwt-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2964/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `80.78% <ø> (ø)` | | | [python-c-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2964/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `88.72% <ø> (ø)` | | | [python-tests](https://app.codecov.io/gh/tskit-dev/tskit/pull/2964/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `99.01% <100.00%> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/tskit-dev/tskit/pull/2964?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | Coverage Δ | | |---|---|---| | [python/tskit/formats.py](https://app.codecov.io/gh/tskit-dev/tskit/pull/2964?src=pr&el=tree&filepath=python%2Ftskit%2Fformats.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev#diff-cHl0aG9uL3Rza2l0L2Zvcm1hdHMucHk=) | `99.46% <100.00%> (ø)` | |

[jeromekelleher]

Looks like this is mostly working now. Outstanding issues:

• Some tests are failing on most recent numpy 1.x version and also on numpy 2.x.
• We need numpy 2.x compatible kastore distributions, so parking this until that's ready.

[jeromekelleher]

Shall I pick this up or is it simpler to start again @benjeffery? The kastore conda-forge packages should be built and available in the next few hours, so that should unblock us here.

[benjeffery]

Shall I pick this up

I'm working on this now!

[benjeffery]

All seems to be working - I'll squash and merge.

[benjeffery]

Realised we were doing wheels for 3.12, but not testing on it. Fixing that now

[benjeffery]

LGTM! What's the strategy for pushing an updated release - cherry pick this back onto last release tag?

Seems the simplest approach.