TASK-1.3 (Core Test Stabilization)

[biofe]

Goal:

Make all CORE tests pass without touching deferred functionality.

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Context

tests/TEST_CATEGORIES.md defines:

• CORE
• OPTIONAL
• DEFERRED

Only CORE tests are in scope.

Deferred areas:

• stochastic lumping
• GPCCA
• RMSD extras
• random frame export
• pdb generation
• least moving residues

These must NOT be fixed in this task.

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Task

Run only CORE tests and stabilize them.

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Scope

Allowed:

• deterministic lumping
• deterministic kernels (T, KL, JS)
• deterministic plotting
• config loading
• linkage/Z conversion
• deterministic macrostate assignment

Not allowed:

• stochastic functionality
• GPCCA
• RMSD workflows
• random frame generation
• pdb exports

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Requirements

1. Execute only CORE tests.
2. Fix failures by:

• correcting production bugs
• fixing stale deterministic references
• fixing obsolete paths/aliases

3. Replace stale aliases:

• PDZ3_7 → PDZ3
• aSyn_rdc_200ns → aSyn

4. Fix config path assumptions:

• use input/config.yml
• do NOT introduce duplicate config files

5. If expected outputs are genuinely stale:

• regenerate only deterministic outputs
• document exactly why regeneration was necessary

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Constraints

• Do NOT touch DEFERRED tests
• Do NOT remove tests
• Do NOT skip tests
• Do NOT introduce broad refactors
• Keep changes narrowly scoped

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Latitude

Controlled

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Verification

Run only CORE tests.

Expected result:

All CORE tests pass

Provide:

• exact pytest command used
• list of fixed failures
• list of regenerated outputs (if any)

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Output format

Provide:

1. failing CORE tests found
2. root causes
3. fixes applied
4. verification results
5. remaining OPTIONAL/DEFERRED failures (if encountered accidentally)