[python] Dataframe read path

[nguyenv]

Issue and/or context:

Running Changes:

• When opening a DataFrame in read-mode, use DataFrameWrapper which wraps around clib.SOMADataFrame. Otherwise, DataFrame should use the already existing write-path with ArrayWrapper which wraps around a TileDB-Py Array
• Corrections to C++ unit tests where SOMADataFrame needs to use sparse array
• SOMADataFrame::count needs to use nnz
• C++ API create needs to set soma_object_type and exists needs to check soma_object_type
• Get full nonempty domains for SOMADataFrame
• Add getters and methods to DataFrameWrapper and ArrayWrapper (i.e nonempty domain, attr names, dim names, etc)
• Support query conditions for SOMADataFrame
• _query_condition.py no longer has dependency on TileDB-Py and uses Pyarrow schema instead of TileDB ArraySchema and SOMAError instead of TileDBError
• Reorganize Pybind11 code to place util functions and PyQueryCondition (note: should refactor QueryCondition to completely remove PyQueryCondition usage) into common.h
• SOMAArray now resides in its own soma_array.cc file
• pytiledbsoma.cc is now the top-level file that contains stats bindings and loads modules from query_condition.cc, soma_array.cc, soma_dataframe.cc
• Support enumerations / dictionaries for SOMADataFrame
• Support all enumeration values in ArrowAdapter::to_arrow
• read Pybind11 function now uses correct Arrow schema to convert dictionary arrays when importing from C to Python
• SOMAObject::schema returns ArrowSchema which calls from SOMAArray::arrow_schema
• Create C++ factory unique_ptr<SOMAObject> SOMAObject::open and bind in Pybind11 as clib.SOMAObject.open which returns the correct Python SOMA class
• Fix for [python] Errors raised as RuntimeError should raise SOMAError #783

[codecov-commenter]

Codecov Report

Merging #1793 (53cca7e) into main (08931d3) will decrease coverage by 1.55%.
The diff coverage is 66.01%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1793      +/-   ##
==========================================
- Coverage   77.59%   76.05%   -1.55%     
==========================================
  Files          87      136      +49     
  Lines        7784    10552    +2768     
  Branches        0      206     +206     
==========================================
+ Hits         6040     8025    +1985     
- Misses       1744     2433     +689     
- Partials        0       94      +94     

Flag	Coverage Δ
libtiledbsoma	67.69% <26.31%> (?)
python	91.40% <84.36%> (+2.31%)	⬆️
r	67.72% <100.00%> (ø)

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

Components	Coverage Δ
python_api	91.40% <84.36%> (+2.31%)	⬆️
libtiledbsoma	50.61% <14.28%> (∅)

[thetorpedodog]

(the usual disclaimer that I’m mostly looking at the Python side for style etc. and didn’t look at the C++ code in detail)

[thetorpedodog]

(the usual disclaimer that I’m mostly looking at the Python side for style etc. and didn’t look at the C++ code in detail)

I should add that I like the way the open-and-select-the-right-wrapper thing works now. It’s very well structured and understandable.

[johnkerl]

Nothing huge to sugggest -- some spelling changes etc

[nguyenv]

@beroy I have now merged your changes into my PR. The only change I did was move your reindexer unit tests to reside within the apis/python/tests directory. This is a part of changes within this PR where I've moved all Python unit tests from libtilesoma/tests into the Python API directory as to not have them split between two directories. Because this PR is already large enough as is, I have decided to leave the reindexer bindings within pytiledbsoma.cc for now but will be opening a subsequent PR where this gets separated out into its own reindexer.cc.