create new HDF5 close() method and call at the end of run().

[rburghol]

To my mind, this is NOT OK to merge @PaulDudaRESPEC -- it seems to function, and the old commits still fail the more complex tests, so I think we should wait to sort out the tests with value errors. This solves some of the problems that seemed to just appear over the last week traced to pandas. It:

• Adds a close() method to the custom local HDF5 class
• Invokes this method a the end of the run() function to insure that the hdf5 is handled cleanly -- will at last eliminate a warning.
  • This eliminates the pytest error: ValueError: The file '/opt/model/HSPsquared/tests/test10/HSPFresults/test10.h5' is already opened, but not in read-only mode (as requested). in pandas >= 3.0.0
• Integrates the changes to utilities.py and main.py from a brief comment to trigger git #207

What remains unsolved are the (follow these at #209 ):

• The value comparison problems in python < 3.11
• and the pandas.errors.IndexingError: Unalignable boolean Series provided as indexer (index of the boolean Series and of the indexed object do not match)

These arose when retesting runs that passed testing a week or more ago, so, likely reflect the need for a more restrictive dependency versions, or, adaptation of existing model (or maybe test_regression) code to meet new requirements in pandas and/or other dependencies.