Problem running test_sbm.py

[rougier]

Output is:

Using TensorFlow backend.
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: compiletime version 3.6 of module 'tensorflow.python.framework.fast_tensor_util' does not match runtime version 3.7
  return f(*args, **kwds)
Traceback (most recent call last):
  File "test_sbm.py", line 34, in <module>
    G = nx.read_gpickle(file_prefix)
  File "<decorator-gen-404>", line 2, in read_gpickle
  File "/usr/local/lib/python3.7/site-packages/networkx/utils/decorators.py", line 205, in _open_file
    fobj = _dispatch_dict[ext](path, mode=mode)
FileNotFoundError: [Errno 2] No such file or directory: 'sbm.gpickle'

[palash1992]

I have now created a "tests" folder with required files. The issue should now be resolved

[rougier]

Just updated, now I get (OSX / Python 3.7):

Using TensorFlow backend.
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: compiletime version 3.6 of module 'tensorflow.python.framework.fast_tensor_util' does not match runtime version 3.7
  return f(*args, **kwds)
Traceback (most recent call last):
  File "test_sbm.py", line 34, in <module>
    open('data/sbm_node_labels.pickle', 'rb')
UnicodeDecodeError: 'ascii' codec can't decode byte 0x80 in position 512: ordinal not in range(128)

[palash1992]

This was caused due to Pickle incompatibility between Python 2 and 3. I have fixed the issue.

[rougier]

Now I get:

Using TensorFlow backend.
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: compiletime version 3.6 of module 'tensorflow.python.framework.fast_tensor_util' does not match runtime version 3.7
  return f(*args, **kwds)
Traceback (most recent call last):
  File "test_sbm.py", line 35, in <module>
    open('data/sbm_node_labels.pickle', 'rb')
FileNotFoundError: [Errno 2] No such file or directory: 'data/sbm_node_labels.pickle'

[palash1992]

Should be fixed now. Had renamed the sbm_node_labels for testing the Pickle incompatibility

[rougier]

Another error now (see below). I think you should test your software starting from a more neutral environment (for example using a virtual environment and cloning your own repo as a "standard" user). This would hep spotting simple errors. I'm leaving on conference for one week and won't be able to test it during that time. You thus have plenty of time to test it more thoroughly.

Using TensorFlow backend.
/usr/local/Cellar/python/3.7.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: compiletime version 3.6 of module 'tensorflow.python.framework.fast_tensor_util' does not match runtime version 3.7
  return f(*args, **kwds)
Traceback (most recent call last):
  File "test_sbm.py", line 57, in <module>
    print ('Num nodes: %d, num edges: %d' % (G.number_of_nodes(), G.number_of_edges()))
  File "/usr/local/lib/python3.7/site-packages/networkx/classes/graph.py", line 780, in number_of_nodes
    return len(self._node)
AttributeError: 'DiGraph' object has no attribute '_node'

[palash1992]

The above error is due to Networkx version incompatibility. You need to install a Networkx version < 2. In the setup, I have modified the networkx version to 1.11. I hope this clears all the issues.

I will clone the repository on some systems to find possible incompatibilities.