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gdiff: copied subnodes aren't renamed/recolored after parent copy #70

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gdiff: copied subnodes aren't renamed/recolored after parent copy#70

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@wshlavacek
wshlavacek
opened on May 9, 2026

Location:bionetgen/core/tools/gdiff.py:714

Original marker:

# TODO: Need to get in there and rename and recolor each
# node under the one we just copied

When gdiff copies a node into a derived graph (e.g. when a node exists in one model but not the other), the parent node gets a fresh ID via _set_node_id and the rename map is updated, but the loop below only walks the immediate copy's properties — it does not recurse into the children to rename and recolor them. The result is a graphml output where the copied subtree carries duplicated IDs from the original subtree, which can break downstream graph consumers.

What would unblock this: decide whether the children should:

  1. Get fresh IDs derived from the parent's new ID (current rename-map convention), and
  2. Get the parent's color or retain their original colors.

If "fresh IDs + parent color," thread _set_node_id and _set_node_color calls into the existing child-walking loop. If colors should be preserved per-child, only IDs need rewriting.

Discovered during: non-Atomizer TODO/FIXME triage sweep, 2026-05-08.

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