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Migrate to uv#799

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caprilesport wants to merge 11 commits intogeem-lab:mainfrom
caprilesport:migrate-to-uv
Open

Migrate to uv#799
caprilesport wants to merge 11 commits intogeem-lab:mainfrom
caprilesport:migrate-to-uv

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Migrate the package manager to uv.

Closes #771.

Some notes regarding the transition:

  • It was performed using the migrate-to-uv project.
  • jaxlib required a bump, so both jax and jaxlib were updated to the latest version.
  • numpy was updated along with it, as well as scipy.
  • The minimal python version was also updated along with it.

The above was mainly done because there was some issue with jaxlib the version jaxlib overreact was using, and uv could not synchronize the dependencies.

Beyond that, I've also added thermo and rich as dev dependencies, so when developing all tests have their dependency installed. This would also require adding jax and jaxlib as test dependencies though, so if you're against this I can change it back.

Test changes

These bumps made some ~50 tests fail, these were mainly related to four items:

To account for the new constant values in scipy the values that depended on it were updated.

Regarding the eigenvector instability, it seems that numpy delegates this to LAPACK, and different CPU architectures could give different results, so I think it's good to remove these tests.

Even though we're not strictly testing those, we're still testing moments of inertia values, orthogonality of the axes matrix, count of symmetry elements and the final point group, so I think the relevant behaviour is still well tested.

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