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Problem loading Atomic conv (ACNN) datasets

See original GitHub issue

I’ve been trying to run the ACNN examples but I’ve been hitting this error:

$ python opt_random.py 
Loading dataset from disk.
Loading dataset from disk.
Traceback (most recent call last):
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/joblib/numpy_pickle_compat.py", line 226, in load_compatibility
    obj = unpickler.load()
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/pickle.py", line 1043, in load
    dispatch[key[0]](self)
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/pickle.py", line 1185, in load_binstring
    self.append(self._decode_string(data))
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/pickle.py", line 1167, in _decode_string
    return value.decode(self.encoding, self.errors)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xdd in position 0: ordinal not in range(128)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/deepchem/utils/save.py", line 115, in load_from_disk
    return joblib.load(filename)
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/joblib/numpy_pickle.py", line 576, in load
    return load_compatibility(fobj)
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/joblib/numpy_pickle_compat.py", line 235, in load_compatibility
    raise new_exc
ValueError: You may be trying to read with python 3 a joblib pickle generated with python 2. This feature is not supported by joblib.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle_compat.py", line 226, in load_compatibility
    obj = unpickler.load()
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/pickle.py", line 1043, in load
    dispatch[key[0]](self)
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/pickle.py", line 1185, in load_binstring
    self.append(self._decode_string(data))
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/pickle.py", line 1167, in _decode_string
    return value.decode(self.encoding, self.errors)
UnicodeDecodeError: 'ascii' codec can't decode byte 0xdd in position 0: ordinal not in range(128)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "opt_random.py", line 44, in <module>
    y_train = train_dataset.y
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/deepchem/data/datasets.py", line 1004, in y
    for (_, y_b, _, _) in self.itershards():
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/deepchem/data/datasets.py", line 609, in iterate
    X = np.array(load_from_disk(os.path.join(dataset.data_dir, row['X'])))
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/deepchem/utils/save.py", line 120, in load_from_disk
    return old_joblib.load(filename)
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle.py", line 573, in load
    return load_compatibility(fobj)
  File "/Users/stanlen1/anaconda/envs/deepchem/lib/python3.5/site-packages/sklearn/externals/joblib/numpy_pickle_compat.py", line 235, in load_compatibility
    raise new_exc
ValueError: You may be trying to read with python 3 a joblib pickle generated with python 2. This feature is not supported by joblib.

I’ve run into this error on linux and mac os, despite the fact that I have no problem spinning up a ipython terminal and reading the files manually. What’s going on? Is it trying to load it using the wrong loader, or is using the wrong decoding?

cc: @joegomes