Consistent conversion to undirected graphs

anton-bushuiev commented 1 year ago

Reference Issues/PRs

What does this implement/fix? Explain your changes

I faced an unexpected behaviour constructing k-NN graph and converting it to PyG. After the k-NN construction, the underlying nx graph is undirected (not DiGraph). It means that if u and v are mutually nearest neighbors, I still get only one edge (e.g. (u, v)). Then, after conversion to PyG this only results in one edge, which is not what is expected since in PyG all edges are directed. So, in this PR I added the symmetrization. Probably, this is also needed for DGL (not familiar with the framework) or other formats.

What testing did you do to verify the changes in this PR?

Conversion test passes. I get an undirected graph for my case.

Pull Request Checklist

[x] Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
[x] Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
[ ] Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
[x] Ran 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/protein/test_graphs.py)
[ ] Checked for style issues by running black . and isort .

anton-bushuiev commented 1 year ago

@a-r-j BTW Can I be added to the contributors?

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage: 40.12% and project coverage change: +3.72 :tada:

Comparison is base (8123f42) 40.27% compared to head (908c10e) 43.99%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #301 +/- ## ========================================== + Coverage 40.27% 43.99% +3.72% ========================================== Files 48 113 +65 Lines 2811 7739 +4928 ========================================== + Hits 1132 3405 +2273 - Misses 1679 4334 +2655 ``` | [Impacted Files](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | Coverage Δ | | |---|---|---| | [graphein/ml/datasets/foldcomp\_dataset.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvZGF0YXNldHMvZm9sZGNvbXBfZGF0YXNldC5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/ml/diffusion.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvZGlmZnVzaW9uLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ml/metrics/\_\_init\_\_.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvbWV0cmljcy9fX2luaXRfXy5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/ml/metrics/gdt.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvbWV0cmljcy9nZHQucHk=) | `0.00% <0.00%> (ø)` | | | [graphein/ml/metrics/tm\_score.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvbWV0cmljcy90bV9zY29yZS5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/ppi/graph\_metadata.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL2dyYXBoX21ldGFkYXRhLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ppi/visualisation.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL3Zpc3VhbGlzYXRpb24ucHk=) | `0.00% <0.00%> (ø)` | | | [graphein/protein/analysis.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9hbmFseXNpcy5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/protein/features/utils.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9mZWF0dXJlcy91dGlscy5weQ==) | `27.77% <0.00%> (ø)` | | | [graphein/protein/folding\_utils.py](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9mb2xkaW5nX3V0aWxzLnB5) | `0.00% <0.00%> (ø)` | | | ... and [95 more](https://codecov.io/gh/a-r-j/graphein/pull/301?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb)

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