items for deprecation

[sjsrey]

Deprecations identified in the 2022-10-28 Sprint

by module

weights

• 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

raster

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

util & user

• 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. )

cg

• 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

io

• 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

examples (see #485)

• keep the module
• allow for get_path() to list remote paths, too
• enhance to only download the requested data

by class

W see #493

• 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()
• merge plot with splot's weights plotter... keep W.plot()'s flexibility, but adapt to splot's performance

[jGaboardi]

xref #477 #427

[sjsrey]

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

[jGaboardi]

The last libysal version that contains native geometries will be the max pin for spaghetti at the conclusion of sunset.

xref: pysal/spaghetti#780