fix(neighbors): partial pbc and imports

[lil-lon]

Summary

Closes #575, fixes a partial-pbc bug in vesin_nl, and updates import paths for current releases.

Bug fix

• Require nvalchemi-toolkit-ops >= 0.4.0 (https://github.com/NVIDIA/nvalchemi-toolkit-ops/releases/tag/v0.4.0), which fixes the naive kernel wrapping positions on non-periodic axes, and drop the workaround for non-periodic systems
  • The bump also picks up upstream DFT-D3 and electrostatics updates, and I confirmed that the existing dispersion and electrostatics tests pass with 0.4.0
  • Note: 0.4.0 deprecates the direct-output flags (compute_forces / compute_virial) used in EwaldModel and PMEModel, so their calls now emit a DeprecationWarning; this issue is left as a follow-up
• Fix vesin_nl collapsing per-axis pbc into a single bool, and require vesin >= 0.5.8 for the upstream partial-pbc fixes (https://github.com/Luthaf/vesin/releases/tag/v0.5.8)
  • 0.6.0 requires cut_off argument as a key-work argument (https://github.com/Luthaf/vesin/blob/v0.6.0/python/vesin/vesin/_neighbors.py#L73-L81), so fixed it

Import path fix and refactoring

• Support the vesin-torch 0.6 module move (vesin.torch -> vesin_torch), keeping the old path as a fallback
• Import nvalchemiops from its public path (nvalchemiops.torch.neighbors) and drop the legacy fallback

Test

• Add partial-pbc slab tests and fold the dummy-cell molecule variants into the fixture for simplicity and test efficiency
• codecov fails because no tests verify the package import behavior. If needed, I'd add corresponding tests

Checklist

Before a pull request can be merged, the following items must be checked:

• Doc strings have been added in the Google docstring format.
• Run ruff on your code.
• Tests have been added for any new functionality or bug fixes.

[CompRhys]

Thanks for the follow on PR, I am currently on holiday and will review/merge next week.

[CompRhys]

lgtm