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gh-246: replace `numpy.ndarray` with `numpy.typing.NDArray` (#305)

Closes #246. Use `numpy.typing.NDArray` as the first step towards #280.
With `NDArray` we can use types, i.e. `NDArray[np.float64]`, which I'll
save for future work (#306).

I have also gone throughout and made sure anything like `ArrayLike` is
using the alias `import numpy.typing as npt`. Imports are generally in a
`if TYPE_CHECKING` block where possible.

We are using `numpy.testing` in some places. This was being aliased as
`npt`. To avoid confusion, I have removed this alias and left them as an
explicit import.

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