TypeError: The numpy boolean negative, the - operator, is not supported, use the ~ operator or the logical_not function instead.

[vinayakumarr]

python preprocess.py data/smiles_50k.h5 data/processed_50k.h5

Traceback (most recent call last):
File "preprocess.py", line 85, in
main()
File "preprocess.py", line 72, in main
apply_fn=lambda ch: np.array(map(one_hot_encoded_fn,
File "preprocess.py", line 63, in create_chunk_dataset
chunks=tuple([chunk_size]+list(dataset_shape[1:])))
File "/home/vinay/chemistrytensor/local/lib/python2.7/site-packages/h5py/_hl/group.py", line 105, in create_dataset
dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
File "/home/vinay/chemistrytensor/local/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 76, in make_new_dset
if isinstance(chunks, tuple) and (-numpy.array([ i>=j for i,j in zip(tmp_shape,chunks) if i is not None])).any():
TypeError: The numpy boolean negative, the - operator, is not supported, use the ~ operator or the logical_not function instead.

[maksak]

Hi,

I think newer h5py solve this issue as the latest h5py seems to avoid your issue.
See: https://github.com/h5py/h5py/blob/master/h5py/_hl/dataset.py#L76

[3R1K]

I can confirm @maksak answer works...pip install h5py --upgrade did the trick for me.

[chshangy]

I have the same problem, just open your file File "/home/vinay/chemistrytensor/local/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 76
change the "-" to "~".

[mukaddesau]

You can update your h5py file using this fix: h5py/h5py@973c47f
I hope it works.