Directed line graph

[lbluque]

Summary

Implements constructing a directed line graph, where edges in the original graph have an edge in the line graph if the dst node of the first edge matches the src node of the second. i.e. the following directed edges x = (u,v) and y = (v,w) will have a directed edge in the line graph (x, y).

Implemented:

• create_directed_line_graph
• ensure_directed_line_graph_compatibility to be used when a graph and line graph are passed (ie when training)
• prune_edges_by_features to prune graphs according to some feature.

I had to adapt compute_theta to handle the "directed" case, bc in this case one of the bond vectors must be flipped to get the correct angle and not its complement.

Checklist

• [X] Google format doc strings added. Check with ruff.
• [X] Type annotations included. Check with mypy.
• [X] Tests added for new features/fixes.
• [X] If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[codecov[bot]]

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (13a5da2) 97.97% compared to head (e32faa7) 97.99%. Report is 1 commits behind head on main.

:exclamation: Current head e32faa7 differs from pull request most recent head 52d1e17. Consider uploading reports for the commit 52d1e17 to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #178 +/- ## ========================================== + Coverage 97.97% 97.99% +0.01% ========================================== Files 28 28 Lines 1828 1891 +63 ========================================== + Hits 1791 1853 +62 - Misses 37 38 +1 ``` | [Files](https://app.codecov.io/gh/materialsvirtuallab/matgl/pull/178?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsvirtuallab) | Coverage Δ | | |---|---|---| | [matgl/graph/compute.py](https://app.codecov.io/gh/materialsvirtuallab/matgl/pull/178?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsvirtuallab#diff-bWF0Z2wvZ3JhcGgvY29tcHV0ZS5weQ==) | `99.22% <98.63%> (-0.78%)` | :arrow_down: | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/materialsvirtuallab/matgl/pull/178/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=materialsvirtuallab)

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[shyuep]

I would actually do it by simply add a kwarg called is_directed to create_line_graph which defaults to False. It should be simple to do based on your current implementation.

[lbluque]

@shyuep made the changes you suggested, pls have a look when you can

[shyuep]

Thanks