fix(binaryfile): avoid numpy deprecation warnings

[wpbonelli]

In the future, numpy will stop treating arrays with 1 element and dimension >0 as scalars. Use .item() to access the single element.

This may need to be fixed elsewhere in the codebase, this is the only place I have seen warnings from recently.

[codecov]

Codecov Report

Merging #1868 (57f6dba) into develop (a84d885) will not change coverage.
The diff coverage is 100.0%.

@@           Coverage Diff           @@
##           develop   #1868   +/-   ##
=======================================
  Coverage     72.2%   72.2%           
=======================================
  Files          257     257           
  Lines        56226   56226           
=======================================
  Hits         40621   40621           
  Misses       15605   15605           

Impacted Files	Coverage Δ
flopy/utils/binaryfile.py	80.0% <100.0%> (ø)
flopy/utils/gridutil.py	98.4% <100.0%> (ø)

[wpbonelli]

I took a brief look through the repo and the warnings raised by autotests and don't see this anywhere else. Will keep an eye out for more though

[mwtoews]

Thanks, I was considering addressing this new warning, you beat me to it! And agree that using .item() is a good approach. Also, keep in mind that new NumPy releases only support Python 3.9 or later, so new deprecation warnings are not visible with Python 3.8 runs.

Missed one from a different package, however:

test_gridutil.py: 7442 warnings
/home/runner/work/flopy/flopy/flopy/utils/gridutil.py:91: 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.)
top[n] = tp

[wpbonelli]

Thanks @mwtoews I did not realize this

new NumPy releases only support Python 3.9 or later, so new deprecation warnings are not visible with Python 3.8 runs

Fixed the one in gridutil and added type hints to the ndarray params in the get_disu_kwargs() signature