Thanks everyone. I recently came across same exact issue in Bokeh 0.12.4, Spyder 3.1.2/Ipython 5.1.0.
bokeh.io.reset_output() did the trick.
From 2MB+ HTML file back down to 39kb 
Thanks for making this thread & pointing this bug out.
···
On Monday, July 11, 2016 at 1:46:45 PM UTC-7, Romain Jouin wrote:
Hi,
I am using jupyter notebook to make a bokeh map.
Each time I re-do my cell, the calculation time is longer.
Here is the idea of my map : I do a four-step map :
total_times =
import time
p = figure()
n_row = 100000
output_file(“france_zdc_et_unites.html”)
d = time.time()
glyph = p.patches(source =ColumnDataSource(france_hors_zdc[:n_row]), xs = “lat”, ys = “lng”, fill_color=“white”,line_color=“white”)
p.add_tools(HoverTool(renderers=[glyph], tooltips=[(“cp”, “@cp”)], name=“hors_zdc”))
source = ColumnDataSource(nb_unite_by_cp[[‘lat’, ‘lng’,‘cp_y’, ‘unite’, ‘unites’, ‘color’]][:n_row])
glyph = p.patches(source =source, xs = “lat”, ys = “lng”, fill_color=“color”,)
p.add_tools(HoverTool(renderers=[glyph], tooltips=[(“cp”, “@cp_y”), (“nb unite”, “@unite”), (“liste unites”, “@unites”)], name=“zdc”))
source =ColumnDataSource(unite_hors_zdc[[u’unit’, u’pool’, u’X_lambert93’, u’Y_Lambert93’]][:n_row])
glyph = p.circle(source =source , x = u’X_lambert93’, y = u’Y_Lambert93’, color=“red”)
p.add_tools(HoverTool(renderers=[glyph], tooltips=[(“pool”, “@pool”), (“unite”, “@unit”)], name=“pool_units”))
source = ColumnDataSource(unite_dans_zdc[[u’unit’, u’pool’, u’X_lambert93’, u’Y_Lambert93’]][:n_row])
glyph = p.circle(source=source, x = u’X_lambert93’, y = u’Y_Lambert93’, color=“orange”)
p.add_tools(HoverTool(renderers=[glyph], tooltips=[(“pool”, “@pool”), (“unite”, “@unit”)], name=“pool_units”))
show(p)
d5 = time.time()
total_times.append(d5-d)
print total_times
``
The total time get each time bigger :
First iteration was about 10 sec, then after 3 or 4 I get : [29.3, 35.6, 42.9 ]
The size of the created html is also getting bigger and bigger : [26,7 Mo, 33,4 Mo 40,1Mo]
I tried to do a “del p” , it didn’t change anything
My activity monitor also tell me the python process is getting bigger at each iteration.
Anyone else has had the same issue ?
Is it a known issue ?
Any idea of a solution ?
Thx,
romain.