Unit test failed
See original GitHub issue_________________________________________ test_get_molnet_bbbp_dataset_with_smiles _________________________________________
@pytest.mark.slow
def test_get_molnet_bbbp_dataset_with_smiles():
# test default behavior
pp = AtomicNumberPreprocessor()
datasets = molnet.get_molnet_dataset('bbbp', preprocessor=pp,
return_smiles=True)
assert 'smiles' in datasets.keys()
assert 'dataset' in datasets.keys()
smileses = datasets['smiles']
datasets = datasets['dataset']
assert len(smileses) == 3
assert len(datasets) == 3
# Test each train, valid and test dataset
for i, dataset in enumerate(datasets):
# --- Test dataset is correctly obtained ---
index = np.random.choice(len(dataset), None)
atoms, label = dataset[index]
assert atoms.ndim == 1 # (atom, )
assert atoms.dtype == np.int32
# (atom from, atom to) or (edge_type, atom from, atom to) assert label.ndim == 1
assert label.shape[0] == 1
assert label.dtype == np.int32
> assert len(dataset) == expect_bbbp_lengths[i]
E assert 1630 == 1631
E + where 1630 = len(<chainer_chemistry.datasets.numpy_tuple_dataset.NumpyTupleDataset object at 0x2b5c61c03d30>)
datasets_tests/molnet_tests/test_molnet.py:81: AssertionError
Issue Analytics
- State:
- Created 5 years ago
- Comments:11 (9 by maintainers)
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Good news. When we add the option here, too. The error disappears. https://github.com/pfnet-research/chainer-chemistry/blob/a54b464dc2ec90b6dfce7326bfd981024cd91d8b/chainer_chemistry/dataset/preprocessors/mol_preprocessor.py#L33
So, we can identify the cause was https://github.com/rdkit/rdkit/issues/1679 , which has been included in rdkit 2018.03.1
This problem is solved by #237 When you encounter same problem, please re-open issue.