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hddm-devs / hddm

HDDM is a python module that implements Hierarchical Bayesian parameter estimation of Drift Diffusion Models (via PyMC).
http://ski.clps.brown.edu/hddm_docs/
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Having problems running demo code on v 0.5.5 on a Mac #37

Open rdhyee opened 8 years ago

rdhyee commented 8 years ago

Here's a Jupyter notebook showing the problem:

https://gist.github.com/rdhyee/50926afc4d6e591e51dd

The conda environment I'm running is:

# packages in environment at /Users/raymondyee/anaconda/envs/hddm_test:
#
appnope                   0.1.0                    py27_0  
backports.ssl-match-hostname 3.4.0.2                   <pip>
certifi                   2015.9.6.2               py27_0  
decorator                 4.0.4                    py27_0  
freetype                  2.5.5                         0  
gdal                      1.11.2                    <pip>
hddm                      0.5.5                np19py27_0  
ipykernel                 4.1.1                    py27_0  
ipython                   4.0.0                    py27_1  
ipython-genutils          0.1.0                     <pip>
ipython_genutils          0.1.0                    py27_0  
ipywidgets                4.1.0                    py27_0  
jinja2                    2.8                      py27_0  
jsonschema                2.4.0                    py27_0  
jupyter                   1.0.0                    py27_0  
jupyter-client            4.1.1                     <pip>
jupyter-console           4.0.3                     <pip>
jupyter-core              4.0.6                     <pip>
jupyter_client            4.1.1                    py27_0  
jupyter_console           4.0.3                    py27_0  
jupyter_core              4.0.6                    py27_0  
kabuki                    0.5.3                np19py27_0  
libpng                    1.6.17                        0  
markupsafe                0.23                     py27_0  
matplotlib                1.4.3                np19py27_3  
mistune                   0.7.1                    py27_0  
mock                      1.0.1                     <pip>
nbconvert                 4.0.0                    py27_0  
nbformat                  4.0.1                    py27_0  
notebook                  4.0.6                    py27_0  
numpy                     1.9.3                    py27_0  
openssl                   1.0.2d                        0  
pandas                    0.16.2               np19py27_0  
path.py                   8.1.2                    py27_0  
patsy                     0.4.0                np19py27_0  
pexpect                   3.3                      py27_0  
pickleshare               0.5                      py27_0  
pip                       7.1.2                    py27_0  
ptyprocess                0.5                      py27_0  
pygments                  2.0.2                    py27_0  
pygobject                 3.16.2                    <pip>
pymc                      2.3.5                np19py27_0  
pyparsing                 2.0.3                    py27_0  
pyqt                      4.11.4                   py27_0  
python                    2.7.10                        2  
python-dateutil           2.4.2                    py27_0  
python.app                1.2                      py27_4  
pytz                      2015.6                   py27_0  
pyzmq                     14.7.0                   py27_1  
qt                        4.8.7                         1  
qtconsole                 4.1.0                    py27_0  
readline                  6.2                           2  
scipy                     0.16.0               np19py27_1  
setuptools                18.4                     py27_0  
simplegeneric             0.8.1                    py27_0  
sip                       4.16.9                   py27_0  
six                       1.10.0                   py27_0  
sqlite                    3.8.4.1                       1  
ssl_match_hostname        3.4.0.2                  py27_0  
terminado                 0.5                      py27_1  
tk                        8.5.18                        0  
tornado                   4.2.1                    py27_0  
traitlets                 4.0.0                    py27_0  
wheel                     0.26.0                   py27_1  
zeromq                    4.1.3                         0  
zlib                      1.2.8                         0

I'm running Python 2.7.10 on OS X 10.9.5.

twiecki commented 8 years ago

This should be fixed in the most recent pymc: https://github.com/pymc-devs/pymc/pull/60 Unfortunately there's no conda package yet.

rdhyee commented 8 years ago

@twiecki Thanks for your quick reply. Doing

pip install -U pymc

to upgrade to 2.3.6 (latest version of pymc) fixed the problem for me.