figure out sparse vs dense scipy matrix stuff

[ctb]

As of v0.3.2, we now have the command pairwise_to_compare, which seems to work ok. (but, you know, tests needed! #24).

This is implemented in hokey code,

sourmash_plugin_betterplot/src/sourmash_plugin_betterplot.py

Line 423 in 59b870d

class Command_PairwiseToCompare(CommandLinePlugin):

and there is broken sparse-matrix loading code here,

sourmash_plugin_betterplot/src/sourmash_plugin_betterplot.py

Line 557 in 59b870d

def create_sparse_dissimilarity_matrix(tuples, num_objects):

and it feels like the mds2 command

sourmash_plugin_betterplot/src/sourmash_plugin_betterplot.py

Line 489 in 59b870d

class Command_MDS2(CommandLinePlugin):

should be able to operate entirely on sparse matrix representations,

but I find the scipy sparse matrix stuff https://docs.scipy.org/doc/scipy/reference/sparse.html difficult to interpret, and I keep on running into "this operation not allowed".

To the extent that I have any understanding at all, it's that we should be looking at COO arrays, maybe?

pls send help. kthxbye.