BUG: fix graph kernel builder when kernel returns zero

[martinfleis]

When the kernel function returns zeros, the conversion of sparse to arrays drops observations causing a mismatch in the shape of Graph.sparse and original input.

We simply cannot use taper. If there is a good use case for calling eliminate_zeros(), we may revise that but with a smarter implementation to avoid this issue. See the test for reproducible example.

[martinfleis]

covecov messed up :) codecov/codecov-action#1089

including fix here to make CI run

[ljwolf]

While I think we should jettison the eliminate_zeros() call right now, I do think we need to provide for a separate taper() implementation eventually that correctly induces a sparse data structure. Could we set taper=False for now and raise NotImplementedError() when taper==True?

[martinfleis]

Yup, can do that.

[codecov]

Codecov Report

Merging #569 (d3aa1eb) into main (d7b458d) will increase coverage by 0.1%.
The diff coverage is 96.0%.

@@           Coverage Diff           @@
##            main    #569     +/-   ##
=======================================
+ Coverage   81.6%   81.6%   +0.1%     
=======================================
  Files        127     128      +1     
  Lines      14933   14937      +4     
=======================================
+ Hits       12183   12195     +12     
+ Misses      2750    2742      -8     

Files Changed	Coverage Δ
libpysal/graph/_kernel.py	71.3% <0.0%> (-0.9%)	⬇️
libpysal/graph/_triangulation.py	98.0% <ø> (ø)
libpysal/graph/_utils.py	92.5% <100.0%> (+0.8%)	⬆️
libpysal/graph/base.py	95.6% <100.0%> (-0.2%)	⬇️
libpysal/graph/tests/test_kernel.py	100.0% <100.0%> (ø)

... and 1 file with indirect coverage changes

[jGaboardi]

Failures seem to be simple connection errors.

[knaaptime]

what about setting a temporary sentinel value, elim zeros, then replace sentinel with 0?

edit: sorry, scratch that. I see by that time we're already in sparse land, so replacement is hard

[martinfleis]

I'll merge this now. We have the NotImplementedError there so easy to pick it up later.