Clean up several warnings
I'm seeing several warnings when running unit tests:
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PCAfold/reconstruction.py:4620: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
regressed_scalar[i] = regression_model(regression_input)
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PCAfold/utilities.py:1739: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
worst_variable_index = int(worst_variable_index)
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PCAFold/utilities.py:1779: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
min_cost_function_index = int(min_cost_function_index)