@dzhechkov/p-replicator 1.5.16 → 1.5.18

package/templates/.claude/skills/goap-research-ed25519/scripts/risk_statement.py

@@ -0,0 +1,289 @@
+#!/usr/bin/env python3
+"""
+Relative risk never travels alone.
+
+    "21× higher risk of heart attack"   is   1 excess case per 1394 people.
+    "the risk doubles"                  is   4 per 1000 over 25 years.
+
+Both sentences are true. Only one of each pair is interpretable, and the
+uninterpretable one is the one that gets quoted. This module makes the
+interpretable half STRUCTURALLY non-optional: `RiskStatement(relative, absolute)`
+has two required positional arguments, and `absolute` is either a real
+`AbsoluteEffect` or an explicit `UnknownBaseline(reason=…)`. A caller with no
+baseline data cannot omit the absolute half — it must SAY the baseline is unknown,
+and that sentence is printed in the slot where the number would have been:
+
+    BASELINE RISK NOT ESTABLISHED
+
+WHAT THIS MODULE DOES NOT CLAIM (D-19, ADR-002 §3)
+    It cannot stop an agent from writing «в 21 раз выше» in its own free prose. The
+    typed path here is the guarantee (`test_risk_absolute.py::
+    test_relative_risk_cannot_be_emitted_by_any_path`); the report-gate scan in
+    `check_report_evidence.py` is a BELT over prose the constructor never sees, it
+    matches FORMATS not meaning, and it may never be cited as evidence that the
+    property holds.
+
+Stdlib only. Pure: no I/O, no network, no global state.
+"""
+
+from __future__ import annotations
+
+import math
+from dataclasses import dataclass
+from typing import Any, Optional, Union
+
+# Grammar: the shapes a source may report an effect in. A new study reports a new
+# NUMBER, not a new shape — so this list is grammar, not content.
+RELATIVE_KINDS = ("RR", "HR", "OR", "IRR", "fold-change", "percent-change")
+
+# ALLOWLIST OVER EMITTED STRUCTURE. `render_risk()` builds its output solely by
+# iterating this tuple; a field added to RiskStatement without being added here is
+# simply not printed — the safe direction.
+RISK_KEYS = ("relative", "absolute", "nnt", "horizon", "population_match")
+
+BASELINE_UNKNOWN_TEXT = "BASELINE RISK NOT ESTABLISHED"
+
+
+class RiskError(ValueError):
+    """Every refusal in this module (a ValueError subclass, so existing handlers work)."""
+
+
+@dataclass(frozen=True)
+class RelativeEffect:
+    """A RATIO of two risks — and therefore not a risk.
+
+    Deliberately has NO `__str__`, NO `__format__` and no accessor returning
+    user-facing prose. The value is reachable in output only through a
+    `RiskStatement` that already carries its absolute counterpart (ADR-002 §2).
+    """
+
+    kind: str
+    value: float
+    ci: Optional[str] = None
+
+    def __post_init__(self) -> None:
+        if self.kind not in RELATIVE_KINDS:
+            raise RiskError(f"relative kind {self.kind!r} must be one of {RELATIVE_KINDS}")
+        try:
+            value = float(self.value)
+        except (TypeError, ValueError):
+            raise RiskError(f"relative value {self.value!r} is not a number") from None
+        if not math.isfinite(value):
+            raise RiskError("relative value must be finite")
+        object.__setattr__(self, "value", value)
+
+
+@dataclass(frozen=True)
+class AbsoluteEffect:
+    """Events over a stated denominator, over a stated horizon. NOT a percentage
+    with no denominator."""
+
+    control_events: float
+    control_denominator: float
+    treated_events: Optional[float] = None
+    treated_denominator: Optional[float] = None
+    horizon: Optional[str] = None
+
+    def __post_init__(self) -> None:
+        for name in ("control_events", "control_denominator", "treated_events", "treated_denominator"):
+            value = getattr(self, name)
+            if value is None:
+                continue
+            try:
+                number = float(value)
+            except (TypeError, ValueError):
+                raise RiskError(f"{name} must be a number, got {value!r}") from None
+            if not math.isfinite(number) or number < 0:
+                raise RiskError(f"{name} must be a finite, non-negative number, got {value!r}")
+            object.__setattr__(self, name, number)
+        if self.control_denominator <= 0:
+            raise RiskError("control_denominator must be > 0 — a rate needs a denominator")
+        if (self.treated_events is None) != (self.treated_denominator is None):
+            raise RiskError(
+                "treated_events and treated_denominator must be supplied together — half a treated "
+                "arm cannot produce an absolute risk difference"
+            )
+        if self.treated_denominator is not None and self.treated_denominator <= 0:
+            raise RiskError("treated_denominator must be > 0")
+
+    def control_rate(self) -> float:
+        return self.control_events / self.control_denominator
+
+    def treated_rate(self) -> Optional[float]:
+        if self.treated_events is None or self.treated_denominator is None:
+            return None
+        return self.treated_events / self.treated_denominator
+
+    def render(self) -> str:
+        if self.treated_rate() is None:
+            body = f"{_num(self.control_events)} per {_num(self.control_denominator)}"
+        else:
+            body = (f"{_num(self.control_events)} per {_num(self.control_denominator)} (control) vs "
+                    f"{_num(self.treated_events)} per {_num(self.treated_denominator)} (treated)")
+        return body + (f" over {self.horizon}" if self.horizon else "")
+
+
+@dataclass(frozen=True)
+class UnknownBaseline:
+    """The source reports no control-arm event rate — AND WE SAY SO, with a reason.
+
+    `reason=""` raises. A degradation whose cause is not recorded is
+    indistinguishable from a bug (the same rule as `create_listing_fact(reason=…)`).
+    """
+
+    reason: str
+
+    def __post_init__(self) -> None:
+        if not isinstance(self.reason, str) or not self.reason.strip():
+            raise RiskError(
+                "UnknownBaseline requires a non-empty reason — 'how many times' is known, "
+                "'how many people' is not, and the reader must be told which"
+            )
+
+    def render(self) -> str:
+        return f"{BASELINE_UNKNOWN_TEXT} — {self.reason.strip()}"
+
+
+@dataclass(frozen=True)
+class NNT:
+    """Number Needed to Treat/Harm. Exactly one of `value` / `not_applicable_reason`."""
+
+    value: Optional[float] = None
+    not_applicable_reason: Optional[str] = None
+    horizon: Optional[str] = None
+
+    def __post_init__(self) -> None:
+        has_value = self.value is not None
+        has_reason = self.not_applicable_reason is not None and str(self.not_applicable_reason).strip() != ""
+        if has_value == has_reason:
+            raise RiskError(
+                "NNT carries exactly one of value / not_applicable_reason — "
+                "an unnamed missing NNT is the thing this class exists to prevent"
+            )
+        if has_value:
+            try:
+                number = float(self.value)
+            except (TypeError, ValueError):
+                raise RiskError(f"NNT value {self.value!r} is not a number") from None
+            if not math.isfinite(number) or number <= 0:
+                raise RiskError(
+                    f"NNT value must be finite and > 0, got {self.value!r}. An infinite NNT is a "
+                    f"NAMED not_applicable_reason, never a number"
+                )
+            object.__setattr__(self, "value", number)
+
+    def render(self) -> str:
+        if self.value is None:
+            return f"n/a — {str(self.not_applicable_reason).strip()}"
+        text = _num(self.value)
+        return text + (f" over {self.horizon}" if self.horizon else "")
+
+
+AbsoluteHalf = Union[AbsoluteEffect, UnknownBaseline]
+
+
+@dataclass(frozen=True)
+class RiskStatement:
+    """`relative` and `absolute` are REQUIRED POSITIONAL arguments. There is no
+    default, and no `None` path (ADR-002 §1, D-11)."""
+
+    relative: RelativeEffect
+    absolute: AbsoluteHalf
+    intervention: bool = False
+    nnt: Optional[NNT] = None
+    horizon: Optional[str] = None
+    population_match: Optional[str] = None
+
+    def __post_init__(self) -> None:
+        if not isinstance(self.relative, RelativeEffect):
+            raise TypeError(f"relative must be a RelativeEffect, got {type(self.relative).__name__}")
+        if not isinstance(self.absolute, (AbsoluteEffect, UnknownBaseline)):
+            raise TypeError(
+                f"absolute must be an AbsoluteEffect or an explicit UnknownBaseline(reason=…), got "
+                f"{type(self.absolute).__name__}. A relative effect may not travel alone (DC-2)."
+            )
+        if self.nnt is not None and not isinstance(self.nnt, NNT):
+            raise TypeError(f"nnt must be an NNT, got {type(self.nnt).__name__}")
+        if self.intervention and self.nnt is None:
+            raise RiskError(
+                "intervention=True requires an NNT — computed from the absolute figures, or a "
+                "named not_applicable_reason (D-13)"
+            )
+
+
+def _num(value: float) -> str:
+    number = float(value)
+    if abs(number - round(number)) < 1e-9:
+        return str(int(round(number)))
+    return f"{number:.4g}"
+
+
+def nnt_from_excess(excess_events: float, denominator: float, horizon: Optional[str] = None) -> NNT:
+    """`NNT = M / N` from an "N excess cases per M people" figure (FR-7, FR-8).
+
+    "1 excess case per 1394" → 1394.  "4 per 1000 over 25 years" → 250 over 25 years.
+    Never raises for an unusable input, never returns Infinity or 0: an NNT that
+    cannot be computed comes back as a NAMED reason (D-15).
+    """
+    try:
+        excess = float(excess_events)
+        total = float(denominator)
+    except (TypeError, ValueError):
+        return NNT(not_applicable_reason=f"non-numeric input ({excess_events!r} per {denominator!r})",
+                   horizon=horizon)
+    if not math.isfinite(excess) or not math.isfinite(total):
+        return NNT(not_applicable_reason="non-finite input", horizon=horizon)
+    if total <= 0:
+        return NNT(not_applicable_reason="denominator is not positive — no population to count over",
+                   horizon=horizon)
+    if excess == 0:
+        return NNT(not_applicable_reason="no excess cases reported — the absolute difference is zero, "
+                                         "so no finite NNT exists", horizon=horizon)
+    return NNT(value=abs(total / excess), horizon=horizon)
+
+
+def nnt_from_absolute(absolute: AbsoluteHalf, horizon: Optional[str] = None) -> NNT:
+    """`NNT = 1 / |ARC − ART|` — COMPUTED from the two arms, never supplied as prose (D-14)."""
+    if isinstance(absolute, UnknownBaseline):
+        return NNT(not_applicable_reason=f"cannot be computed without a baseline — {absolute.reason.strip()}",
+                   horizon=horizon)
+    if not isinstance(absolute, AbsoluteEffect):
+        raise TypeError(f"nnt_from_absolute needs an AbsoluteEffect or UnknownBaseline, got "
+                        f"{type(absolute).__name__}")
+    treated = absolute.treated_rate()
+    if treated is None:
+        return NNT(not_applicable_reason="observational association, no intervention arm compared",
+                   horizon=horizon or absolute.horizon)
+    difference = abs(absolute.control_rate() - treated)
+    if difference == 0:
+        return NNT(not_applicable_reason="the two arms have the same event rate — no finite NNT exists",
+                   horizon=horizon or absolute.horizon)
+    return NNT(value=1.0 / difference, horizon=horizon or absolute.horizon)
+
+
+def render_risk(statement: RiskStatement) -> str:
+    """THE ONLY exit. Builds output solely by iterating RISK_KEYS; there is no
+    `__str__`, no `format()`, and no accessor on RelativeEffect returning prose."""
+    if not isinstance(statement, RiskStatement):
+        raise TypeError(f"render_risk needs a RiskStatement, got {type(statement).__name__}")
+    slots = {key: getattr(statement, key, None) for key in RISK_KEYS}
+    relative = slots["relative"]
+    lines = [f"risk: {relative.kind} {_num(relative.value)} (relative)"
+             + (f", CI {relative.ci}" if relative.ci else "")]
+    lines.append(f"  absolute: {slots['absolute'].render()}")
+    if slots["nnt"] is not None:
+        lines.append(f"  NNT: {slots['nnt'].render()}")
+    elif statement.intervention:  # unreachable: __post_init__ requires nnt (D-13)
+        lines.append("  NNT: n/a — not supplied")
+    if slots["horizon"]:
+        lines.append(f"  horizon: {slots['horizon']}")
+    if slots["population_match"]:
+        lines.append(f"  {slots['population_match']}")
+    return "\n".join(lines)
+
+
+__all__ = [
+    "RELATIVE_KINDS", "RISK_KEYS", "BASELINE_UNKNOWN_TEXT", "RiskError",
+    "RelativeEffect", "AbsoluteEffect", "UnknownBaseline", "NNT", "RiskStatement",
+    "nnt_from_excess", "nnt_from_absolute", "render_risk",
+]

package/templates/.claude/skills/goap-research-ed25519/scripts/test_ed25519_verifier.py

@@ -1,12 +1,46 @@
 #!/usr/bin/env python3
-"""Load-bearing security tests for ed25519_verifier.py."""
+"""Load-bearing security tests for ed25519_verifier.py.
+
+RUN COMMAND (ADR-006 / D-21) — this module, like every other `test_*.py` beside it,
+is collected by the ONE canonical command, never by a hand-kept enumeration:
+
+    cd .../goap-research-ed25519/scripts && python3 -m unittest discover -s . -p 'test_*.py' -v
+
+That is not a formatting preference. Before slice C this file — the security suite of
+the very module the slice edits — was named by NO run command anywhere, so a "full
+suite green" claim could have been true of the command and false of the code
+(AM-14). `test_suite_completeness.py` now asserts the collected set equals `ls
+test_*.py`, so a module that stops being collected fails BY NAME.
+"""
 
 import copy
+import sys
+
+# Import NOTHING local before this line: a stray __pycache__ inside this vendored
+# skill reads as canonical drift and turns an unrelated repo test red.
+sys.dont_write_bytecode = True
+
 import unittest
 
 import ed25519_verifier as ev
 
 
+def _pop():
+    """A minimal VALID study population (FR-1 / D-1 made it mandatory, no default).
+
+    These four call sites are the reason AM-14 is a P0: they are the security suite of
+    the module being edited, and they were in no run command, so this migration could
+    have silently broken them while every report still said "green".
+    """
+    return {
+        "description": "adults enrolled in the cited cohort",
+        "criteria": {
+            "age": {"op": "range", "value": [18, 80], "kind": "eligibility",
+                    "verbatim": "adults aged 18-80", "locator": "[Methods]"},
+        },
+    }
+
+
 @unittest.skipIf(ev.CRYPTO_BACKEND is None, "No Ed25519 backend installed")
 class Ed25519VerifierSecurityTests(unittest.TestCase):
     def make_pinned_pair(self):
@@ -30,6 +64,7 @@ class Ed25519VerifierSecurityTests(unittest.TestCase):
             source_url="https://nature.com/articles/example",
             source_content="attacker-controlled content",
             issuer="nature.com",
+            study_population=_pop(),
         )
 
         result = verifier.verify_fact(fact)
@@ -39,6 +74,20 @@ class Ed25519VerifierSecurityTests(unittest.TestCase):
         self.assertNotEqual(result.confidence, 0.95)
 
     def test_fact_signed_by_pinned_trusted_key_verifies(self):
+        """A THIRD assertion whose meaning changed in slice C — re-derived, not nudged.
+
+        The architecture named two such assertions (`test_evidence_provenance.py:97`
+        and `:123`). This is a third, found only by RUNNING this file — which is
+        exactly AM-14's point, since before slice C no run command named it.
+
+        What changed: `create_issuer_signed_fact` used to mint a **v1** fact, and v1 is
+        exempt from the source-tier ceiling (D-20's lower edge). It now mints **v3**,
+        so the third ceiling applies and the documented chain
+        `min(trust, evidence, tier)` is finally computed in full for this factory.
+        `nature.com` is tier B (0.80), so 0.80 — not 0.95 — is the formula being
+        HONOURED, not a downgrade bug. The assertion is written against
+        `source_tier_ceiling(fact)` so it states the reason, not just the number.
+        """
         signer, verifier = self.make_pinned_pair()
 
         fact = signer.create_issuer_signed_fact(
@@ -46,13 +95,17 @@ class Ed25519VerifierSecurityTests(unittest.TestCase):
             source_url="https://nature.com/articles/example",
             source_content="source content",
             issuer="nature.com",
+            study_population=_pop(),
         )
 
         result = verifier.verify_fact(fact)
 
         self.assertTrue(result.verified)
         self.assertEqual(result.trust_class, ev.TRUST_CLASS_ISSUER_SIGNED)
-        self.assertEqual(result.confidence, 0.95)
+        self.assertEqual(ev.fact_schema_version(fact), 3, "every newly created fact is v3")
+        self.assertEqual(ev.source_tier_ceiling(fact), 0.80, "nature.com is a tier-B source")
+        self.assertEqual(result.confidence, 0.80,
+                         "min(trust 0.95, evidence 1.0, tier 0.80) — the tier term is the binding one")
 
     def test_relabelled_or_moved_fact_fails(self):
         signer, verifier = self.make_pinned_pair()
@@ -61,6 +114,7 @@ class Ed25519VerifierSecurityTests(unittest.TestCase):
             source_url="https://nature.com/articles/example",
             source_content="source content",
             issuer="nature.com",
+            study_population=_pop(),
         )
 
         relabelled = copy.deepcopy(fact)
@@ -87,6 +141,7 @@ class Ed25519VerifierSecurityTests(unittest.TestCase):
                     source_url=f"https://nature.com/articles/{index}",
                     source_content=f"source content {index}",
                     issuer="nature.com",
+                    study_population=_pop(),
                 )
             )