Code clean-up, increased modularity and more tests. #63
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to work with newer setuptools versions.
with test agains rdkit Tanomoto sims.
graphs and molecules to make dependencies a bit more modular.
adaptable, added tests.
to make it more modular and extendable. Added more unit tests.
Added type hints to data transform function.
to avoid having PyTorch Geometric as a dependency.
feaurisations/kernels.
graph kernels that allow node/ edge label checking.
grakel graph kernel.
inputs to allow usage of graphs with rdkit attributes.
graph kernel formulation.
to see if kernels work in eval mode.
Accidentally uploaded test notebook.
Ryan-Rhys
reviewed
Dec 3, 2023
| @@ -55,11 +56,7 @@ def main( | |||
| n_trials: Number of random train/test splits for the datasets. Default is 20 | |||
| test_set_size: Size of the test set for evaluation. Default is 0.2 | |||
| dataset_name: Benchmark dataset to use. One of ['Photoswitch', 'ESOL', 'FreeSolv', 'Lipophilicity'] | |||
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Nice, this makes things easier!
Ryan-Rhys
approved these changes
Dec 3, 2023
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Reference Issues/PRs
Fixes the following issues: #42 #61 #4 #62 #52
What does this implement/fix? Explain your changes
This PR fixes a range of issues and makes the code base more modular, adaptable and easier to use. In particular, this PR:
What testing did you do to verify the changes in this PR?
I added extensive unit tests for the changes I made, as well as existing parts of the code base, bringing the total number of unit tests to >200. The only breaking change that this PR introduces is a slight simplification of the data loader call when using the benchmark datasets which will need to be adjusted in the notebooks.
Pull Request Checklist
./CHANGELOG.mdfile (if applicable)./gauche/tests/*directories (if applicable)./notebooks/(if applicable)python -m py.test tests/and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g.,python -m py.test tests/kernels/test_graph_kernels.py)black .andisort .