Fix usages of deprecated features.

This MR updates the usage points of several deprecated features of our dependencies.

• 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)
• Fix MatplotlibDeprecationWarning: Auto-close()ing of figures upon backend switching is deprecated since 3.8 and will be removed two minor releases later. To suppress this warning, explicitly call plt.close('all') first. by closing all open figures before and after any notebook run

Maybe (just maybe) the closing of figures also fixes this spurious error:

FAILED tests/test_stokes_setup.ipynb::test_stokes_setup.ipynb - TypeError: Axes3D.quiver() missing 4 required positional arguments: 'Z', 'U', 'V', and 'W'

for which I still could not pin down the cause.