libpysal items for deprecation

Deprecations identified in the 2022-10-28 Sprint

[ ] keep everything in distance & contiguity, but reorganize the voronoi, delaunay, gabriel, and relative neighborhood into a triangulations.py
[ ] move wsp out of spint
[ ] move spint weights into spint itself, since no one else has used it since then
[ ] move perimeter-weighted contiguity into contiguity
[ ] move some stuff from momepy
[ ] deprecate adjtools.py

[ ] migrate da2W/da2WSP into W.from_da() methods instead, so deprecate the functions.

[ ] WSP2W gets deprecated in favour of WSP.to_w()
[ ] full2W gets deprecated in favour of a W.from_dense()
[ ] full() gets deprecated in favour of a W.to_dense()
[ ] fill_diagonal() is retained
[ ] keep higher_order, shimbel gets re-written to use csgraph.floydwarshall
[ ] comb, remap_ids, get_ids, get_points_array_from_shapefile gets deprecated
[ ] consolidate higher_order, order, and heigher_order_sp to one function
[ ] min_threshold_distance move to cg
[ ] lat2SW, hexlat2W moves to same module as lat2W
[ ] min_threshold_dist, build_lattice_shapefile, spw_from_gal, w_local_cluster, spw_from_gal deprecated
[ ] attach_islands, nonplanar, fuzzy is kept
[ ] neighbor_equality should be enhanced, made to recognize the difference between "equality" and "isomorphism"
- [ ] two weights are equal when their matrix representations are the same (i.e. they're ordered the same)
- [ ] two weights are isomorphic when the ids are equal, links are present in both, and weights are equal.
[ ] the rest of weights should be kept (w_sets, lag_spatila/categorical ,etc. )

[ ] all of sphere will be deprecated
[ ] all of shapes will get deprecated
[ ] all of standalone will get deprecated
[ ] locators are already deprecated and should be removed
[ ] kdtree should be deprecated, point users to BallTree with haversine metric as an alternative to Arc_KDTree
[ ] deprecate ops
[ ] deprecate shapely_ext
[ ] deprecate segmentLocator

[ ] deprecate all io functionality not reading weights
[ ] keep weights readers, wrap into a W.from_file() method that works kind of like the existing implementation

[ ] to/from_file should stay
[ ] to_wsp() stays, build from_wsp()
[ ] to/from_networkx() stays
[ ] make _build_sparse() public as to_sparse, add a from_sparse, and keep .sparse
[ ] keep n_components, all the math/stats on the graph
[ ] rename islands to isolates to match networkx
[ ] deprecate id2i, from_shapefile, __set/get_id_order, id_order, id_order set, neighbor_offsets,
[ ] turn get/set_transform() and transform itself into a single transform method that returns a copy() (at new geograph module)
[ ] re-write iter to remove _id_order and instead just use dictionary iteration
[ ] keep remap_ids
[ ] keep asymmetry
[ ] keep symmetrize, but fix the docstring
[ ] deprecate full, move to to/from_dense and a .dense attribute
[ ] deprecate set_shapefile()
[x] merge plot with splot's weights plotter... keep W.plot()'s flexibility, but adapt to splot's performance

Oct 28 '22 17:10 sjsrey

xref #477 #427

Oct 28 '22 17:10 jGaboardi

We might think about moving some of these into individual tickets (maybe by module) to facilitate collaboration.

Oct 28 '22 17:10 sjsrey