CR: feat/watch-deviation-report

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Proxy of sleepypod#844 for CodeRabbit review.

Why

The goal is near-zero deviation between pod biometrics and the Apple Watch for HR, HRV, breathing rate and sleep stages. Today that deviation is only measured by the offline scripts in analysis/watch-deviation/. Agents and the UI need to check it after every algorithm, profile or ruleset change without those scripts.

Stacked on sleepypod#842, which adds reference_samples (Watch breathing rate and HRV SDNN).

What

• src/biometrics/references/watch-deviation.ts: a pure module ported from analysis/watch-deviation/pairing.ts and score_live.ts. Deviation is pod − Watch. HR pairs each Watch sample with the nearest pod reading within ±60 s, breathing within ±150 s, and HRV compares Watch SDNN with the mean pod HRV within ±5 min. Each metric reports n, watchSamples, coverage, mae, bias, nearest-rank p90 and Pearson r, and these are null rather than zero when there is no data. Stages report accuracy, kappa, recall, and pod vs Watch minutes per stage over the scored epochs. The summary pools every pair and every scored epoch across nights instead of averaging the nightly figures.
• biometrics.compareToWatch (GET /api/biometrics/watch-deviation): input is side, optional startDate/endDate (default is the last 14 days, maximum 31) and minHours (default 3). Nights come back oldest first. For each sleep record it reuses loadStageInputs, loadStageView and loadReference (now exported) from the sleepStages router, and re-runs the side's effective classifier on the stored vitals and movement. Pod vitals are read up to 5 min past the record's edges so that Watch samples near bed entry or exit can still pair. The response includes the classifier it used (source, generation, stageHash) and an hrvNote saying the pod's HRV is an IBI-variability index, not SDNN.
• MCP compare_vitals_to_watch (read-only): a thin wrapper over the procedure that adds a hint when there are no nights or no Watch data. Its description tells agents to run it before and after apply_biometric_profile or set_sleep_stage_rules. get_sleep_stage_rules' heartRateAgreement now uses the same nearestWithin and ±60 s window, so the two can't disagree. Its behaviour is unchanged, including tie-breaking.
• Demo handler with seeded fixture data: the Watch reads slightly below the pod with some scatter, and the scripted hypnogram stands in for Watch stages.
• Docs: a section in src/mcp/README.md and in docs/biometrics-reference-imports.md.

Test plan

• ./node_modules/.bin/tsc --noEmit -p .
• eslint on the changed files
• vitest run src/biometrics/references/tests/watch-deviation.test.ts: pairing windows, tie and edge handling, MAE/bias/p90/r against hand-computed values, null statistics, stage kappa and minutes, pooled vs mean-of-means
• vitest run src/server/routers/tests/biometrics.compareToWatch.test.ts: in-memory DBs with migrations. Covers night selection (side, window, minHours, oldest first), pairing across the record edge, the effective classifier, pooling, window bounds, error wrapping and the OpenAPI GET path
• vitest run src/mcp src/demo/tests src/server/tests/openapi.test.ts plus the sleepStages and biometrics router suites (35 files, 528 tests)
• Full vitest run: 7537 tests, 0 failures
• After deploy: call GET /api/biometrics/watch-deviation?side=left on the pod and check the HR/breathing figures against the score_live.ts table in analysis/watch-deviation/README.md for the same nights

🤖 Generated with Claude Code

Summary by CodeRabbit

• New Features
  • Added a read-only report comparing sleep vitals and stages with Apple Watch data, with per-night and pooled results.
  • Review heart rate, breathing rate, HRV, and sleep-stage agreement for qualifying nights, including sample coverage and deviation statistics. Pod HRV is not directly comparable to Watch SDNN.
  • Choose a date range of up to 31 days and a minimum sleep duration; defaults are 14 days and 3 hours.
• Documentation
  • Added guidance on report limits, metric matching, and interpreting results.

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📥 Commits

Reviewing files that changed from the base of the PR and between 8478bf5 and d86e64f.

📒 Files selected for processing: 4

• src/biometrics/references/tests/watch-deviation.test.ts
• src/biometrics/references/watch-deviation.ts
• src/mcp/tests/server.test.ts
• src/mcp/tools/sleep.ts

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📝 Walkthrough

This change adds a Watch deviation report that pairs pod and Apple Watch measurements, scores sleep stages, and returns per-night and pooled results. The report is available through the biometrics router and an MCP tool, with a deterministic demo implementation and supporting documentation.

Changes: Watch Deviation Report

Layer / File(s)	Summary
Comparison and scoring engine src/biometrics/references/watch-deviation.ts, src/biometrics/references/tests/watch-deviation.test.ts	Adds shared pairing logic, per-metric deviation statistics, midpoint-based sleep-stage scoring, and per-night and pooled summaries. Unit tests cover pairing boundaries, null results, rounding, and aggregate calculations.
Router endpoint and data loading src/server/routers/biometrics.ts, src/server/routers/sleepStages.ts, src/server/routers/tests/biometrics.compareToWatch.test.ts, docs/biometrics-reference-imports.md	Adds biometrics.compareToWatch, which loads qualifying nights, applies the effective stage classifier, and returns per-night and pooled results. Tests cover date and duration filters, scoring, validation, error handling, and the GET contract. The reference-import documentation describes the endpoint and comparison rules.
MCP tool and heart-rate pairing src/mcp/tools/sleep.ts, src/mcp/tests/server.test.ts, src/mcp/README.md	Adds the read-only compare_vitals_to_watch tool and updates heartRateAgreement to use the shared nearest-reading helper. Tests and MCP documentation cover the tool inputs, report output, and empty-result hints.
Deterministic demo comparison src/demo/handlers/biometrics.ts, src/demo/tests/biometrics.compareToWatch.test.ts	Adds generated Watch comparison inputs and a demo handler that filters finished nights by date range and minimum duration. Tests check filtering, repeat-call equality, and invalid date windows.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Feature

Sequence Diagram(s)

sequenceDiagram
  participant Caller
  participant Router as biometricsRouter.compareToWatch
  participant Loader as loadDeviationNight
  participant Engine as compareNightsToWatch
  Caller->>Router: Request report for a side and date window
  Router->>Loader: Load each qualifying night's comparison inputs
  Loader-->>Router: Return pod, Watch, and classified-stage series
  Router->>Engine: Compare night inputs
  Engine-->>Router: Return per-night results and pooled summary
  Router-->>Caller: Return report with classifier metadata

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Merge Risk: ⚪ Minimal · up to d86e6

The comparison paths preserve sample ordering, and the p90 calculation is corrected. No actionable merge risk was identified.

Pre-merge checks: 4 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Docstring Coverage		Docstring coverage is 68.18% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 22 functions across 9 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

Passed checks: 4 passed

Check name	Status	Explanation
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title identifies the main change as a watch deviation report feature. It is concise and related to the pull request scope.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

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Actionable comments posted: 2

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• 🪄 Fix comments: Fix CodeRabbit comments on this PR

🤖 Prompt to fix review comments

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Inline comments:
Review comments at @src/biometrics/references/watch-deviation.ts:
- Line 118: Update the p90 index in the nearest-rank calculation to use the
zero-based index equivalent of ceil(0.9 × n) − 1, so sample counts divisible by
10 select the correct rank.

Review comments at @src/mcp/tools/sleep.ts:
- Around line 272-273: Update the date-boundary handling in the code that
constructs `startDate` and `endDate` for `compareToWatch`: treat a date-only
`endDate` as the end of that day so records from the requested final night are
included, and ensure date-only `startDate` does not shift the intended day.
Preserve explicit datetime behavior.

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• Configuration used: Organization UI
• Review profile: CHILL
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• Run ID: 2af6fe8e-de07-42fc-8d02-2456e6d5e869

📥 Commits

Reviewing files that changed from the base of the PR and between 7f0e3a3 and 8478bf5.

📒 Files selected for processing: 11

• docs/biometrics-reference-imports.md
• src/biometrics/references/tests/watch-deviation.test.ts
• src/biometrics/references/watch-deviation.ts
• src/demo/handlers/biometrics.ts
• src/demo/tests/biometrics.compareToWatch.test.ts
• src/mcp/README.md
• src/mcp/tests/server.test.ts
• src/mcp/tools/sleep.ts
• src/server/routers/biometrics.ts
• src/server/routers/sleepStages.ts
• src/server/routers/tests/biometrics.compareToWatch.test.ts

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Source PR merged - closing proxy.