The BokehJS function APIs are much newer and not nearly as widely used as e.g. the Python or R bindings that use the JSON interface. You've probably just run across a bug, I'd suggest filing an issue on GitHub so it can be tracked and addressed:
Basically, with the 0.12.5, i can't plot with y_axis_type:"log" without manually defining an y_range
the 0.12.6dev6 makes it possible, but in both cases, the plotted figure is not scaled:
the axis ticks are correcly labeled, but their spacing is the same as in a continuous axis.
I must forget something very basic but I can't find what I'm doing wrong.