[python] Remove double open For SOMAArray reads

[nguyenv]

Issue and/or context: #3472

This finishes up #3053 [sc-54744]

Changes:

• Remove clib.SOMAArray.open in all SOMAArray derived class read calls
• Pass query arguments coords, column names, result order, value filter, and platform config that were formerly passed to clib.SOMAArray.open or clib.SOMAArray.reset instead to TableReadIter and SparseNDArrayRead
• _set_coords on the ManagedQuery rather than through SOMAArray
• _arrow_table_reader and SparseTensorReadIterBase initialize a ManagedQuery object and set the query arguments listed above; set up the read; and submit reads and return results until the query is complete

[sc-59595]

[codecov]

Codecov Report

Attention: Patch coverage is 93.58974% with 5 lines in your changes missing coverage. Please review.

Project coverage is 86.03%. Comparing base (c4fe227) to head (c469c0c).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3293      +/-   ##
==========================================
+ Coverage   85.83%   86.03%   +0.20%     
==========================================
  Files          55       55              
  Lines        6191     6174      -17     
==========================================
- Hits         5314     5312       -2     
+ Misses        877      862      -15     

Flag	Coverage Δ
python	86.03% <93.58%> (+0.20%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	86.03% <93.58%> (+0.20%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[johnkerl]

This is really really nice --a well-thought-out refactor, well executed. Just some minor mods requested. :)

[johnkerl]

🚢

[bkmartinjr]

This looks great. Two small items:

1. platform_config handling - noted inline
2. ManagedQuery GIL - the read path moves some logic up from C++ to Python -- we need to make sure the pybind entry points are all releasing GIL where appropriate. My quick skim is that it looks OK, but I suggest we benchmark after landing this to confirm.

[bkmartinjr]

A bit of cleanup needed in _read_iters.py - comments inline

[bkmartinjr]

Couple of minor pythonic / lint items, but otherwise LGTM.

[johnkerl]

🚢

Thank you @nguyenv !!!