Prevent deprecation warning

[joaander]

Description

Manually unpack scalar quantities from numpy arrays.

Motivation and Context

This prevents the following deprecation warning:

gsd/test/test_hoomd.py: 10 warnings
  /Users/joaander/build/gsd/gsd/hoomd.py:1170: 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.)                                                            
    logged_data_dict[log][idx] = data 

How Has This Been Tested?

I executed the tests locally and no longer observe the warning:

(venv) cheme-walker:~/build/gsd ▶ pytest gsd
======================================================================= test session starts ========================================================================
platform darwin -- Python 3.11.4, pytest-7.3.2, pluggy-1.0.0
rootdir: /Users/joaander/build/gsd
plugins: anyio-3.6.2
collected 125 items                                                                                                                                                

gsd/test/test_fl.py ..............................................................................                                                           [ 62%]
gsd/test/test_hoomd.py ............................................                                                                                          [ 97%]
gsd/test/test_largefile.py sss                                                                                                                               [100%]

================================================================== 122 passed, 3 skipped in 2.00s ==================================================================
(venv) cheme-walker:~/build/gsd ▶

Checklist:

• I have reviewed the Contributor Guidelines.
• I agree with the terms of the GSD Contributor Agreement.
• My name is on the list of contributors (doc/credits.rst) in the pull request source branch.
• I have added a change log entry to CHANGELOG.rst.

[janbridley]

Looks good to me