remove np alias types

[jamesmkrieger]

These are deprecated and get removed in numpy 1.24, so now we can hopefully support it as requested in #1594

[jamesmkrieger]

Not sure what is happening with atom numbers in selections in Python 3.11

[jamesmkrieger]

There are also updates to scipy with deprecation now:

prody/tests/atomic/test_select.py:471: 270 warnings
  /home/runner/work/ProDy/ProDy/prody/tests/atomic/test_select.py:471: DeprecationWarning: the np.testing.dec decorators are included for nose support, and are deprecated since NumPy v1.21. Use the nose2 or pytest frameworks instead.
    def func(self, pdb=case, test=test, type_=type_, **kwargs):

prody/utilities/eigtools.py:43
prody/utilities/eigtools.py:43
prody/utilities/eigtools.py:43
prody/utilities/eigtools.py:43
prody/utilities/eigtools.py:43
prody/tests/dynamics/test_enms.py::TestRTB::testCalcModes
  /home/runner/work/ProDy/ProDy/prody/utilities/eigtools.py:43: DeprecationWarning: Keyword argument 'eigvals' is deprecated in favour of 'subset_by_index' keyword instead and will be removed in SciPy 1.12.0.
    values, vectors = linalg.eigh(M, turbo=turbo, eigvals=eigvals)

prody/utilities/eigtools.py:43
prody/utilities/eigtools.py:43
prody/utilities/eigtools.py:43
prody/utilities/eigtools.py:43
  /home/runner/work/ProDy/ProDy/prody/utilities/eigtools.py:43: DeprecationWarning: Keyword argument 'turbo' is deprecated in favour of 'driver=gvd' keyword instead and will be removed in SciPy 1.12.0.
    values, vectors = linalg.eigh(M, turbo=turbo, eigvals=eigvals)

prody/sequence/sequence.py:52: 107 warnings
prody/tests/ensemble/test_functions.py: 9 warnings
prody/tests/ensemble/test_pdbensemble.py: 25 warnings
prody/tests/sequence/test_analysis.py: 2 warnings
prody/tests/sequence/test_msa.py: 25 warnings
prody/tests/sequence/test_msafile.py: 100 warnings
prody/tests/sequence/test_sequence.py: 1 warning
  /home/runner/work/ProDy/ProDy/prody/sequence/sequence.py:52: DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
    return self._array.tostring().decode()****

[jamesmkrieger]

It seems like scipy 1.12.0 still has turbo and eigvals, so we have a bit more time