Issues with using sqlite backend for pymc

[jhamrick]

I'm not sure whether to report this to kabuki or HDDM, but the error occurred in a file from kabuki, so I figured I'd report this here...

Saving traces into a sqlite backend seems to cause issues. First, I see warnings like this:

WARNING: Will not save custom link functions.
WARNING: Custom link functions will not be loaded.

and then when I try to concatenate my models, I get the following error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-16-21a90b2e13a0> in <module>()
      1 #m1 = kabuki.utils.concat_models(models_1)
----> 2 m2 = kabuki.utils.concat_models(models_2)

/Users/jhamrick/miniconda3/envs/hddm/lib/python2.7/site-packages/kabuki/utils.pyc in concat_models(models, concat_traces)
    160             assert node.__name__ == target_node.__name__, "Node names do not match. You have to pass identical models."
    161             if concat_traces:
--> 162                 target_node.trace._trace[0] = np.concatenate([target_node.trace[:], node.trace[:]])
    163             else:
    164                 target_node.trace._trace[i+1] = node.trace[:]

AttributeError: 'Trace' object has no attribute '_trace'

It seems to possibly be the same issue as this one: pymc-devs/pymc#790

[twiecki]

Thanks for the report @jhamrick.

The warning is unrelated to the backend and just says that if you provide a custom link function it will not save that with the model.

The error is probably related to the backend. Maybe the sqlite backend does not provide a ._trace attribute? The issue you pointed to is pymc3, HDDM uses pymc2. I guess I'm not sure what that could be.