search

tskit-dev / msprime

Simulate genealogical trees and genomic sequence data using population genetic models
GNU General Public License v3.0
170 stars 84 forks source link

Support numpy >= 2, drop Python 3.8 #2286

Open jeromekelleher opened 1 week ago

jeromekelleher commented 1 week ago

Also add support for Python 3.12

codecov[bot] commented 1 week ago

Codecov Report

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

Project coverage is 91.09%. Comparing base (cbb5db3) to head (28bae68).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #2286 +/- ## ========================================== - Coverage 98.70% 91.09% -7.62% ========================================== Files 11 20 +9 Lines 4029 11918 +7889 Branches 908 2433 +1525 ========================================== + Hits 3977 10857 +6880 - Misses 28 581 +553 - Partials 24 480 +456 ``` | [Flag](https://app.codecov.io/gh/tskit-dev/msprime/pull/2286/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](https://app.codecov.io/gh/tskit-dev/msprime/pull/2286/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `91.09% <ø> (?)` | | | [python](https://app.codecov.io/gh/tskit-dev/msprime/pull/2286/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `98.70% <ø> (-0.01%)` | :arrow_down: | 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.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

jeromekelleher commented 1 week ago

OK, looks like this mostly just works. We're successfully compiling against numpy 2.0, and running tests against numpy 1.x. We can't really test against numpy 2.0 at runtime until there's a tskit package.

Note the last commit isn't doing what it should here because we're pulling in multiple versions of numpy, and a 1.x version is coming from pip for some reason. I think we should try to reduce the number of packages coming from pip here, hopefully most of what we need is on conda-forge now.

Going to park this until a tskit package is available.