fix NumPy warnings on null vector instantiation (NaN as value for int array); updates to match newer Numba deprecations; new simpler clock() impl; NUMBA_OPT for CI; Python 3.11 on CI

[bhiogade]

No description provided.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (7eec9a7) 91.79% compared to head (161b5e9) 92.02%.
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #416      +/-   ##
==========================================
+ Coverage   91.79%   92.02%   +0.23%     
==========================================
  Files          30       30              
  Lines        1475     1468       -7     
==========================================
- Hits         1354     1351       -3     
+ Misses        121      117       -4     

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[slayoo]

OK, first here's an explanation why the problem has not been earlier caught on CI: it only show up on newer NumPy.
After bumping to newer Numpy (1.26.2), the same error can be observed on Github Actions:

Traceback (most recent call last):
  File "/home/runner/work/PyMPDATA/PyMPDATA/readme.py", line 60, in <module>
    stepper = Stepper(options=options, n_dims=2)
  File "/home/runner/work/PyMPDATA/PyMPDATA/PyMPDATA/stepper.py", line 67, in __init__
    self.__call, self.traversals = make_step_impl(
  File "/home/runner/work/PyMPDATA/PyMPDATA/PyMPDATA/stepper.py", line 116, in make_step_impl
    traversals = Traversals(
  File "/home/runner/work/PyMPDATA/PyMPDATA/PyMPDATA/impl/traversals.py", line 45, in __init__
    null_vector_field=VectorField.make_null(self.n_dims, self).impl,
  File "/home/runner/work/PyMPDATA/PyMPDATA/PyMPDATA/vector_field.py", line 104, in make_null
    VectorField(
  File "/home/runner/work/PyMPDATA/PyMPDATA/PyMPDATA/vector_field.py", line 47, in __init__
    self.data = tuple(
  File "/home/runner/work/PyMPDATA/PyMPDATA/PyMPDATA/vector_field.py", line 48, in <genexpr>
    np.full(shape_with_halo[dim], INVALID_INIT_VALUE, dtype=self.dtype)
  File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/numpy/core/numeric.py", line 330, in full
    multiarray.copyto(a, fill_value, casting='unsafe')
RuntimeWarning: invalid value encountered in cast

(https://github.com/open-atmos/PyMPDATA/actions/runs/7378420709/job/20073521039?pr=418)

Hence, bumping Numpy (and Numba) requirements in this PR