Is the hover tool for patch different than other glyphs? The plot can see the index for circle but not for patch.
output_file("patch.html")
TOOLTIPS = [
("index", "$index"),
]
p = figure(plot_width=400, plot_height=400, tooltips=TOOLTIPS, tools='hover,help')
# add a patch renderer with an alpha an line width
p.patch([1, 2, 3, 4, 5], [6, 7, 8, 7, 3], alpha=0.5, line_width=2)
p.circle([2], [4],size=20, line_width=2)
show(p)