AttributeError while using topographica

[kalok87]

OS: Ubuntu 12.04 Version of topographica: 0.9.8 Error massage: kalok@kalok:~$ topographica -a -c "generate_example('gcal_10000.typ')"`` Found examples in /home/kalok/.local/share/topographica/examples /usr/local/bin/topographica /home/kalok/.local/share/topographica/examples/gcal.ty -c "topo.sim.run(10000)" -c " from topo.command.analysis import measure_or_pref; from topo.command.pylabplot import measure_position_pref,measure_cog,measure_or_tuning_fullfield; measure_or_pref(); #measure_position_pref(); measure_cog(); #measure_or_tuning_fullfield() " -c "from topo.command import save_snapshot ; save_snapshot('gcal_10000.typ')" In file included from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0, from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from /home/kalok/.python27_compiled/sc_b373d0df23bd7e002602a012c820e1440.cpp:22: /usr/local/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] Traceback (most recent call last): File "/usr/local/bin/topographica", line 18, in process_argv(argv[1:]) File "/home/kalok/.local/lib/python2.7/site-packages/topo/misc/commandline.py", line 549, in process_argv execfile(filename,main.dict) File "/home/kalok/.local/share/topographica/examples/gcal.ty", line 157, in nominal_bounds_template=sheet.BoundingBox(radius=0.25)) File "/home/kalok/.local/lib/python2.7/site-packages/topo/base/simulation.py", line 1500, in connect conn = connection_type(src=self[src],dest=self[dest],*_conn_params) File "/home/kalok/.local/lib/python2.7/site-packages/topo/projection/init.py", line 143, in init self._create_cfs() File "/home/kalok/.local/lib/python2.7/site-packages/topo/base/cf.py", line 617, in _create_cfs self.cfs = vectorized_create_cf(_self._generate_coords()) File "/home/kalok/.local/lib/python2.7/site-packages/topo/base/cf.py", line 610, in _generate_coords return vectorized_coord_mapper(X,Y) File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 1573, in call return self._vectorize_call(func=func, args=vargs) File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 1633, in _vectorize_call ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args) File "/usr/local/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 1586, in _get_ufunc_and_otypes if func is self.pyfunc and self._ufunc is not None: AttributeError: 'vectorize' object has no attribute '_ufunc' OpenMP: Using 3 threads on a machine with 4 detected CPUs

[jbednar]

Thanks for the report! This issue was fixed in commit 663b4. Unfortunately, we have not had time to make a new PyPi/pip release of Topographica, but in the meantime you can either apply that patch to your copy, or can install the current version from github (See Cloning Topographica at https://github.com/ioam/topographica). Sorry about the trouble!

[kalok87]

Dear Bednar,

Actually the version of my numpy is 1.8.1, and I also replace the cf.py with the new one from commit 663b4, but it does not work.

[jbednar]

I've tried the new Ubuntu 14.04 release, which has numpy 1.8.1 and doesn't show the above error when I use the github version of Topographica. However, it shows a new error that I think is entirely unrelated, having to do with saving snapshots: "ImportError: No module named _winreg". We don't use winreg for anything, so I'm trying to figure out where this error would come from...