Refactor SAAMR topology traversal for MDAnalysis/RDKit exporters

[joelaforet]

Summary

• Adds shared SAAMR role topology traversal helpers under mupt.interfaces._shared.
• Refactors MDAnalysis all-atom export to use the shared indexed traversal.
• The previous implementation called DFS traversal multiple times for each "role-level". Rather than run DFS more than once, we instead populate a dataclass to hold the information about node data corresponding to the different roles as we iterate. This means we only call DFS once per tree.
• Adds shared-topology tests.

Stack Position

This is PR 1 of 3 in the role-aware RDKit/SDF export stack.

Stack:

1. This PR: shared SAAMR topology traversal.
2. Add role-aware RDKit molecule export #59: role-aware RDKit Mol export.
3. Add export-only MuPT SDF writer #60: export-only mupt.muptio.sdf writer.

After This Merges

After merging this PR into main:

• Retarget Add role-aware RDKit molecule export #59 from base issue-51/shared-saamr-topology-index to base main.
• Do not rebase Add role-aware RDKit molecule export #59 unless GitHub reports conflicts.
• If conflicts appear, merge updated main into Add role-aware RDKit molecule export #59's branch, resolve, and push.

Verification

• python -m pytest mupt/tests/interfaces/test_shared_topology.py -q
• python -m pytest mupt/tests/interfaces/mdanalysis/test_exporters.py -q

[codecov]

Codecov Report

❌ Patch coverage is 90.27778% with 14 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
mupt/interfaces/_shared/topology.py	88.33%	14 Missing ⚠️

📢 Thoughts on this report? Let us know!

[joelaforet]

No comments on this one, happy to answer any questions/confusions.