Optimize: Update transitive closure algorithm

[hneiva]

The previous implementation scanned all edges on every iteration of a fixed-point loop, resulting in O(depth * edges) complexity. For deep dependency chains this is catastrophic - a 5000-node chain required 5000 full passes over all edges.

Replace with a standard Breadth-First Search using an adjacency list built once upfront, reducing complexity to O(vertices + edges). Benchmarks on large graphs show 22x-1333x speedups depending on graph shape, with identical results verified against the original algorithm.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.18%. Comparing base (01028b2) to head (f19b24b).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #920      +/-   ##
==========================================
+ Coverage   77.14%   77.18%   +0.04%     
==========================================
  Files         130      130              
  Lines       11868    11883      +15     
  Branches     1458     1462       +4     
==========================================
+ Hits         9155     9172      +17     
+ Misses       2331     2330       -1     
+ Partials      382      381       -1     

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[bhearsum]

If you haven't already, testing this with Gecko would be a good additional sanity check (eg: that it produces identical graphs, no exceptions, etc.).

[hneiva]

If you haven't already, testing this with Gecko would be a good additional sanity check (eg: that it produces identical graphs, no exceptions, etc.).

I have tested this against gecko and found no diffs on the generated graphs.

[bhearsum]

I'm -0 on this...it adds complexity for no real world win. As long as it doesn't hurt perf in our real world cases I guess it's fine to take.

[ahal]

Seems fine to me. It's a few more lines of code, but I can't really say it's much more complex than the old algorithm

[codspeed-hq]

Merging this PR will improve performance by ×3.3

⚠️ Different runtime environments detected

Some benchmarks with significant performance changes were compared across different runtime environments,
which may affect the accuracy of the results.

Open the report in CodSpeed to investigate

⚡ 3 improved benchmarks
❌ 1 regressed benchmark
✅ 20 untouched benchmarks

Warning

Please fix the performance issues or acknowledge them on CodSpeed.

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
❌	test_transitive_closure[fan]	881.2 µs	2,056.4 µs	-57.15%
⚡	test_transitive_closure[linear]	196.9 ms	2.3 ms	×87
⚡	test_transitive_closure[diamond]	390 ms	133.9 ms	×2.9
⚡	test_transform_sequence	6.9 ms	6.1 ms	+12.43%

Tip

Investigate this regression by commenting @codspeedbot fix this regression on this PR, or directly use the CodSpeed MCP with your agent.

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_{Comparing hneiva/transitive-closure (1cee94b) with main (81f3b38)}