Update outdated dependencies (SPEC-0)#556
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Expose surface cluster IDs through atoms.surface_clusters and document the new topology attribute. Extend cluster handling so extra cluster groups can use per-group cutoffs/density thresholds, retain a configurable number of majority clusters, and report the DBSCAN min_samples value. Also make automatic DBSCAN density thresholding reproducible and raise a clear error when the selected cluster group is empty.
The Profile pbservable now can compute intrinsic distances from user-provided upper and lower surface AtomGroups, instead of always using the interface layers. This is useful when the reference surfaces are selected or filtered separately.
Add reduced-unit profiles for simulations with changing box size. Also make profile sampling handle failed interpolation points more clearly. Use freud for periodic Voronoi calculations when available, while keeping the slower SciPy implementation as a fallback.
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