refactor: clean up GraphDataset and Trainer class #255
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deeprankcore/dataset.py
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| if any(key in grp for key in ("internal_edge_index", "internal_edge_data")): | ||
| warnings.warn( | ||
| """Internal edges are not supported anymore. | ||
| You should probably prepare the hdf5 file | ||
| with a more up to date version of this software.""", DeprecationWarning) | ||
| """Internal edges are not supported anymore.\n | ||
| You should probably prepare hdf5 files with a more up to date version of this software.""", | ||
| DeprecationWarning) |
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do we still need this warning or can it go?
If it stays, I'll reword the warning.
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We can leave it for now, just in case. This warning was placed by Coos for older hdf5 files.
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@cbaakman is this warning still necessary?
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| self.complete_exporter = ConciseOutputExporter(self.output_dir) | ||
| self.neuralnet = neuralnet |
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Recall that neuralnet argument so far is a class, and here you're assigning it to an attribute without properly initializing it. I would suggest declaring here model attribute = None, and using neuralnet later on as in the original code. It's still possible to access the details of the neural network through model attribute, without messing with the class itself.
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This is not clear to me. Maybe we can sit down and you explain what you mean?
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will be taken care of in #234
closes: #152 and #194
also partially addresses: #236 (the rest will move to #234)