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[Sad Catapella B8][Scientific identity] Changing notebook output directory retains and can overwrite the wrong confirmed experiment design #98
run() lines 2223–2242 passes the oldself.design while writing to the newoutput_folder. run_experiment() contract reconciles that supplied design and publishes it as experiment_design.csv. An existing design in the new output is not loaded.
Create experiment with confirmed, independently saved output-A design control=ctrl and output-B design control=drug, both with valid matching folders. Load notebook pointing at A, confirm labels and roles, then change only output widget to B and click run. The UI retains A's confirmed design and can publish it to B, overriding B's user-approved controls/repeat grouping. A change to a completely new output also shows misleading saved state from A.
Impact
Loss of confirmed experimental pairing/control provenance and potential overwriting of an existing valid design in another workspace. The current run revalidates axis and source data, but it cannot detect that the wrong design object was provided.
Fix/acceptance
Bind design state to canonical output folder identity. On output change, invalidate confirmed design state, inspect/load destination design with existing refusal-on-unreadable semantics, and require explicit confirmation before run. Do not silently copy the previous output's design to a new destination. If user explicitly chooses Copy my design to new output, make that an explicit audited action. Add A→B→A, missing destination, unreadable design, changed controls/groups and save-failure integration tests. No Numba opportunity.
Activity
Changing the notebook's output folder reads that folder's design (#98)
Test that an answer for a locked new output folder is not saved (#98)
Merge pull request #130 from CellMigrationLab/claude/fix-design-counts
Merge origin/main (#129, #130) into claude/pp-12-staging-resume