Completed the non-training vxData ISUP benchmark implementation and full-cohort validation using the canonical model, preprocessing, forward, and classification-metric paths.
Kept benchmark policy in scripts/benchmarking/benchmark_isup.py, including unbiased study eligibility, separate biopsy/RPE QWK, PHI-safe reporting, and private JSON output.
Refactored the 419-line src/ve2e/inference.py monolith into focused checkpoint and classification modules under src/ve2e/inference/.
Split the temporary legacy checkpoint adapter into checkpoint, config, and DinoFlex mapping modules under src/ve2e/inference/legacy/.
Used calldiff trees and reachability reports to verify that the benchmark reaches the new checkpoint loader and canonical classification iterator.
Removed the unrelated legacy csPCa Hydra workflow and its orphan configs/inference.yaml after confirming that preserving it obscured the ISUP-focused package boundary.
Kept every inference package file below 250 lines and every function at cyclomatic complexity 8 or lower.
Validated locally with Ruff, formatting, compilation, mocked benchmark orchestration, legacy-config mapping, secure JSON checks, and git diff --check. The Linux-only Pixi environment could not run on the macOS host.
Appended and normally pushed commit 36a6db51 to feat/isup-inference. No PR was created.
Lessons Learned: Pitfalls
Mechanically preserving the old csPCa Hydra entrypoint created code unrelated to the ISUP goal. It also made the new package look like another end-to-end inference application rather than reusable primitives.
A correctness-only review reported no regression but did not question whether the preserved workflow belonged in scope. Boundary reviews must check product intent, not only behavior parity.
The project Pixi environments are Linux-only, so macOS validation is limited to host tooling and dependency-mocked tests.
Lessons Learned: Improvements
For focused inference refactors, first classify old code as required primitive, required caller, or obsolete workflow. Delete obsolete workflows instead of preserving them by default.
State the intended package API before moving code. For this package it is checkpoint loading, inference datamodule construction, classification iteration, and isolated legacy checkpoint translation only.
Add a documented Linux-independent static validation command for contributors on macOS.
