[python] Mutable-X mods, and explicit shaping of SparseNDArray

[johnkerl]

Implements the spec side of the plan laid out in issue single-cell-data/TileDB-SOMA#931.

This PR addresses only explicit shaping of SparseNDArray -- explicit shaping of DataFrame will be on a separate PR.

[thetorpedodog]

The semantics look good; one formatting fix before this goes in and a few optional suggestions.

[thetorpedodog]

just a note to keep a pin in this depending upon the results of single-cell-data/TileDB-SOMA#952 (comment)

(if it does get spuriously removed here, it's not a huge problem; implementations are allowed to provide extra methods and features, and we can just re-add it)

[johnkerl]

yeah @thetorpedodog totally not gonna land this PR until that one is resolved

[johnkerl]

resolved on latest commit: see also
single-cell-data/TileDB-SOMA#952 (comment)

[johnkerl]

@bkmartinjr given
#131
and latest commit on this PR
2fa64b9
can you take another look please?

[bkmartinjr]

can you take another look please

I have not had a chance to take any look - sorry, lots of threads.

Given the confusion on the design change, I would prefer we let that settle out, then review this PR.

[johnkerl]

@bkmartinjr when you click through the links I wrote you'll see that restoration of COO is a go

Pending changes on single-cell-data/TileDB-SOMA#952 include:

• restore COO
• unit-test coverage
• some impl-repo code-factoring questions

-- none of which affect the spec

I had hoped to merge this PR but, sure, take all the time you need.

Afternote: indeed there is one more mod, good call. :)