This can be done with annotate in 2D (see documentation) but not 3D. Alternatively use "text"
ax.text(x[i], y[i], z[i] , "%s" % (str(i)), size=20, zorder=1, color = "black")
x,y,z are the location in 3-space, %s stores a string, str(i) converts "i" into a string and puts it in place of %s.
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