Fix usages of deprecated features.

 - Scipy subnamespaces `ndimage.filters` and `ndimage.morphology` have been deprecated for a while
 - `np.trapz` is replaced by `np.trapezoid` in numpy 2.0 (https://numpy.org/doc/stable/numpy_2_0_migration_guide.html#main-namespace)
 - Path-like arguments in pytest have been switched to `pathlib` a long time ago
   (https://docs.pytest.org/en/latest/deprecations.html#fspath-argument-for-node-constructors-replaced-with-pathlib-path
    and
    https://docs.pytest.org/en/latest/deprecations.html#py-path-local-arguments-for-hooks-replaced-with-pathlib-path)