Refactoring memmapped dataset classes #256
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RaulPPelaez
reviewed
Jan 24, 2024
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That is really cool! Thanks! |
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Lets see if tests pass and then merge |
tests/test_dataset_comp6.py::test_dataset_s66x8 FAILED
______________________________ test_dataset_s66x8 ______________________________
def test_dataset_s66x8():
with TemporaryDirectory() as root:
> data_set = S66X8(root)
tests/test_dataset_comp6.py:15:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/share/miniconda3/envs/torchmd-net/lib/python3.11/site-packages/torchmdnet/datasets/comp6.py:41: in __init__
super().__init__(
/usr/share/miniconda3/envs/torchmd-net/lib/python3.11/site-packages/torchmdnet/datasets/memdataset.py:47: in __init__
super().__init__(root, transform, pre_transform, pre_filter)
/usr/share/miniconda3/envs/torchmd-net/lib/python3.11/site-packages/torch_geometric/data/dataset.py:102: in __init__
self._process()
/usr/share/miniconda3/envs/torchmd-net/lib/python3.11/site-packages/torch_geometric/data/dataset.py:228: in _process
if files_exist(self.processed_paths): # pragma: no cover
/usr/share/miniconda3/envs/torchmd-net/lib/python3.11/site-packages/torch_geometric/data/dataset.py:187: in processed_paths
files = self.processed_file_names
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <[AttributeError("'S66X8' object has no attribute 'idx_mm'") raised in repr()] S66X8 object at 0x7f16715fe310>
@property
def processed_file_names(self) -> Union[str, List[str], Tuple]:
r"""The name of the files in the :obj:`self.processed_dir` folder that
must be present in order to skip processing."""
> raise NotImplementedError
E NotImplementedError
/usr/share/miniconda3/envs/torchmd-net/lib/python3.11/site-packages/torch_geometric/data/dataset.py:58: NotImplementedError |
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Cool! |
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I see, there is a bit of a chicken-egg issue with the processed_file_names. I'll fix it |
… since the processed_file_names needs to be available before the process function
RaulPPelaez
approved these changes
Jan 24, 2024
|
You got it, shall we merge then? |
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I refactored all memmaped datasets into a separate class to reduce code duplication