PySMO: fix warnings

[OOAmusat]

Fixes

#1403, #1363

Summary/Motivation:

Recent changes to the numpy backend have resulted in a large number of deprecation warnings (>7500) being raised in PySMO. This PR makes changes to address these warnings.

Changes proposed in this PR:

• Fix all numpy deprecation warnings, primarily arising from assigning scalar values to arrays, e.g., y[i, 0] = x. This is resolved in this PR by either extracting the specific elements of the scalar (y[i, 0] = x[0]) or using the item method (y[i, 0] = x.item())
• Replacing warnings.warn with the idaes logger warnings, and fix tests to use caplog to reflect this change
• Adding @pytest.mark.filterwarnings to specific tests to ignore runtime warnings around np.log

Legal Acknowledgement

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1. I agree my contributions are submitted under the license terms described in the LICENSE.txt file at the top level of this directory.
2. I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 95.83333% with 1 line in your changes missing coverage. Please review.

Project coverage is 76.36%. Comparing base (575953b) to head (8577f4e).
Report is 25 commits behind head on main.

Files with missing lines	Patch %	Lines
...daes/core/surrogate/pysmo/polynomial_regression.py	85.71%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1472      +/-   ##
==========================================
- Coverage   76.36%   76.36%   -0.01%     
==========================================
  Files         394      394              
  Lines       65130    65136       +6     
  Branches    14429    14429              
==========================================
+ Hits        49737    49740       +3     
- Misses      12831    12835       +4     
+ Partials     2562     2561       -1     

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• Flaky Tests Detection - Detect and resolve failed and flaky tests

[lbianchi-lbl]

Thanks a lot @OOAmusat. From a quick look through the pytest job output log, I believe this resolves all of the unanticipated warnings from the PySMO submodules (i.e., I wasn't able to spot any).

The only one that looks like it might be related is the following:

However, if you feel this belongs outside of PySMO's "jurisdiction", then feel free to disregard and we can address it at a later time.

[andrewlee94]

This looks good to me. My only questions is just to confirm that the warnings about invalid values in logs is not a sign of underlying issues.