Persistent graph

[TeunHuijben]

Updates

• Removed SolutionTracks — track-id logic (get/set track & lineage ids, from_tracks, neighbor lookups) folded into Tracks; TrackAnnotator now registers based on a non-None tracklet_key instead of an isinstance check.
• Split the graph into graph_full + graph_solution — tracks.graph is gone; graph_solution is the solution=True view, graph_full is its root (every node/edge ever known). All call sites in src/ and tests/ migrated.
• Reversible soft-delete — DeleteNode/DeleteEdge flip solution=False in graph_full and remove from the view only (remove_*_from_view); AddNode/AddEdge branch on graph_full.has_node/has_edge to revive the same id in place or add genuinely new. Topology is append-only, so delete↔undo is a true inverse across repeated/divergent cycles.
• Annotator scope split — RegionpropsAnnotator/EdgeAnnotator compute on graph_full (features persist on soft-deleted candidates, ready for re-solving); TrackAnnotator stays on graph_solution. Low-level attr get/set route through graph_full (shared attr dicts keep the view in sync).
• Depth-1 guard — Tracks.__init__ raises if graph_solution._root is itself a GraphView, and _get_new_node_ids allocates against graph_full to avoid colliding with soft-deleted ids.
• tracksdata pinned to TeunHuijben/tracksdata@040ed9f for the view-only add/remove primitives (revert once merged upstream).
• Import/export + builders updated to construct Tracks (declaring tracklet/lineage intent), preserve solution flags, and backfill Solution() on legacy saves.
• Tests — new test_soft_delete_roundtrip.py (12 cases) and test_features_on_full_graph.py; full suite green (588 passed).

Breaking changes

• SolutionTracks is removed — use Tracks (pass tracklet_attr/lineage_attr, or a FeatureDict with a tracklet_key).
• tracks.graph is removed — use tracks.graph_solution (solution view) or tracks.graph_full (full graph).

[codecov]

Codecov Report

❌ Patch coverage is 97.08333% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.89%. Comparing base (6baed08) to head (66aa352).

Files with missing lines	Patch %	Lines
src/funtracks/data_model/tracks.py	95.41%	5 Missing ⚠️
src/funtracks/import_export/geff/_export.py	75.00%	1 Missing ⚠️
...funtracks/user_actions/user_update_segmentation.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #241      +/-   ##
==========================================
+ Coverage   93.78%   93.89%   +0.10%     
==========================================
  Files          59       58       -1     
  Lines        3284     3275       -9     
==========================================
- Hits         3080     3075       -5     
+ Misses        204      200       -4     

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[TeunHuijben]

@cmalinmayor, persistent graph is ready for a first glance 😇

[cmalinmayor]

First pass, some high level comments, some low level suggestions

[cmalinmayor]

graph_full

[TeunHuijben]

graph_solution, because we can only remove edges that are in the solution, since we only do a soft-delete technically

[TeunHuijben]

Hi @cmalinmayor, here we go again, hahah (why are these PRs always so big 😂)

I implemented and answered all of your concerns. Biggest change is that:

• graph_full is now the main player, and graph_solution merely a view of it, so not the other way around.

Notes:

• we probably need a lot of extra work again once we switch to a persistent SQL graph (because of the view-out-of-sync issues), but lets park that for later
• the failing Windows benchmark is solved on tracksdata PR 310, will be merged soon

Let me know what you think 😊