Audited the in-progress move from data/src to src/ve2e/data_pipeline and from data/config to package-local configuration.
Inspected imports, config and secret resolution, root and pipeline Pixi manifests, lockfiles, Docker assembly, CI targets, documentation, and ignore rules.
Reported required fixes to the implementing agent. The highest-risk items were the stale data/.env.secrets path in ISUP inference, the root lockfile update required by frozen installs, preservation of the externally used pixi run generate command, and newly exposing pipeline code to root mypy.
Flagged package-data verification for YAML, the missing direct nibabel declaration, and runtime-version drift from the former isolated Transformers/PEFT environment.
Did not edit the ve2e worktree.
Lessons Learned: Pitfalls
The knowledge base has no clinical workstream although the agent startup instructions list it. Infrastructure was the closest available workstream for this packaging and Docker audit.
The repository was being edited concurrently, so an initial inventory became stale during the audit. Re-reading git status and the unstaged diff was necessary before reporting findings.
The local machine cannot execute the repository’s Linux-only Pixi environments, so the exact mypy command could not be validated locally. Static inspection still showed that the move expands the CI type-check scope.
Lessons Learned: Improvements
A project-level consolidation checklist would help: preserve CLI contracts, relocate secret/config paths, declare package data, merge direct dependencies and version constraints, regenerate frozen lockfiles, update container bootstrap layers, and compare CI scope before and after a source-tree move.
Document the Data Platform’s exact command contract for repository pipelines. This would make it clear whether deleting a nested Pixi task is a breaking production change.
