Scaffold schema v2 - #5
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Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
- pyproject.toml + uv.lock (Python 3.11, ruff/pyright/pytest configured) - src/fmharness/schema/ pydantic models: Patient, Sample, DrugAssay, BaselineExpression, Prediction, Tranche, LeakageProfile, EnvironmentSnapshot (all frozen, extra=forbid) - src/fmharness/utils/determinism.py with fix_seeds(seed) - tests/test_schema.py: hypothesis property tests, round-trip + bounds - .pre-commit-config.yaml, .github/workflows/ci.yml - containers/fmharness.def, .env.example - docs/environment.md (container/secrets/determinism contract) Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]>
Co-Authored-By: Claude Opus 4.7 (1M context) [email protected]
…ace. fix by definining protected_namespace parameter as (). Suggested fix by copilot PR review.
graceakatsu
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May 20, 2026
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Apologies for the delay - this looks great, I like the super clear documentation! I do wonder if maybe the plan ([docs/fm-pdo-evaluator-plan.md]) could be excluded from being committed to the greenelab github - but I think it could go either way! maybe I doesn't need to live there long-term?
Also, with other PRs (mine and others'), we sometimes request a review from Github Copilot, which often catches small things that are easy to miss. Just an option~
Otherwise, approving to merge!
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Good call. I removed the 3 week plan from tracking. Thanks! |
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This PR sets up the scaffold for the evaluation harness and plans for future model/data additions:
pyproject.toml + uv.lock (Python 3.11, ruff/pyright/pytest configured)
src/fmharness/schema/ pydantic models: Patient, Sample, DrugAssay, BaselineExpression, Prediction, Tranche, LeakageProfile, EnvironmentSnapshot (all frozen, extra=forbid)
src/fmharness/utils/determinism.py with fix_seeds(seed)
tests/test_schema.py: hypothesis property tests, round-trip + bounds
.pre-commit-config.yaml, .github/workflows/ci.yml
containers/fmharness.def, .env.example
docs/environment.md (container/secrets/determinism contract)
docs/adapter_contract.md (model and control ingest settings)