search

hudon / spike

Brain Simulator Parallelization
http://nengo.ca/
1 stars 1 forks source link

add test_writeout.py to the test suite #79

Closed gretac closed 10 years ago

gretac commented 10 years ago

Closes #72

I was able to find and install hdf5io related libraries. Here is the page with detailed install instructions http://pythonhosted.org/neo/install.html Specifically, I think these are the things that we are missing now to make it work:

$ apt-get install libhdf5-serial-dev python-numexpr cython
$ pip install tables

The python-neo repo (in case more details are needed): https://github.com/NeuralEnsemble/python-neo

TODO: probes with spikes are not yet implemented, so the probe using them was commented out for this test

RobertElder commented 10 years ago

I tried to install it using the link provided, but when I get the the step for installing pip install tables it complains:

robert@robert-ubuntu:~/spike$ sudo pip install tables Downloading/unpacking tables Downloading tables-3.0.0.tar.gz (6.2Mb): 6.2Mb downloaded Running setup.py egg_info for package tables * Using Python 2.7.3 (default, Aug 1 2012, 05:14:39) * Found numpy 1.6.1 package installed. .. ERROR:: You need numexpr 2.0.0 or greater to run PyTables! Complete output from command python setup.py egg_info: * Using Python 2.7.3 (default, Aug 1 2012, 05:14:39)

.. ERROR:: You need numexpr 2.0.0 or greater to run PyTables!

I'm sure I can figure out how to fix this if I try, but it might not be worth the effort to merge into mainline. You already did all the hard work of proving that our stuff works with this library, which should be enough if the researchers use this in the future. If we integrate to be an actual unit test, we should probably fix it on travis, (it is currently failing, but the test passes, because theirs fails to import too, so the inputs are identical and this is a pass (we should probably update this, because we don't have any unit tests that require an expected failure to pass)). Getting dependencies to work on Travis is usually a pain, and if we don't bring it in we save Artem from getting all these extra dependencies installed in whatever crazy place he runs his setup. My two cents.

gretac commented 10 years ago

ok agreed, this extra effort is not necessary at the moment. I will include this ported test in master, it will be commented out from the test harness with a note that it requires extra libraries.