genoma-evolution 1.0.0

package/.claude/worktrees/phase-2-mcp/backend/eval/engine.py

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+"""Evaluation engine orchestrating multiple scorers."""
+
+from typing import Optional
+
+from backend.eval.scorers import (
+    EvalScore,
+    OutcomeScorer,
+    ToolEfficiencyScorer,
+    TokenCostScorer,
+    ErrorRecoveryScorer,
+    DeltaScorer,
+)
+from backend.promethean.models import CanonicalRun
+from backend.storage import RunStore
+
+
+class EvaluationEngine:
+    """Evaluate canonical runs using composable scorers."""
+
+    DEFAULT_SCORERS = [
+        OutcomeScorer(),
+        ToolEfficiencyScorer(),
+        TokenCostScorer(),
+        ErrorRecoveryScorer(),
+        DeltaScorer(),
+    ]
+
+    def __init__(self, store: Optional[RunStore] = None, scorers: Optional[list] = None):
+        self.store = store or RunStore()
+        self.scorers = scorers if scorers is not None else self.DEFAULT_SCORERS
+
+    def evaluate(self, run: CanonicalRun) -> list[EvalScore]:
+        """Run applicable scorers on a run. Return list of scores."""
+        scores = []
+        for scorer in self.scorers:
+            if scorer.applies_to(run):
+                score = scorer.score(run)
+                if score:  # DeltaScorer may return None
+                    scores.append(score)
+                    # Optionally save to storage
+                    if self.store and hasattr(run, "run_id"):
+                        try:
+                            self._save_score(run.run_id, score)
+                        except Exception:
+                            pass
+        return scores
+
+    def evaluate_batch(self, runs: list[CanonicalRun]) -> dict:
+        """Evaluate batch of runs. Return {total, evaluated, errors}."""
+        result = {"total": len(runs), "evaluated": 0, "errors": 0}
+        for run in runs:
+            try:
+                self.evaluate(run)
+                result["evaluated"] += 1
+            except Exception:
+                result["errors"] += 1
+        return result
+
+    def get_aggregate_score(self, run: CanonicalRun) -> float:
+        """Weighted average of all applicable scores."""
+        scores = self.evaluate(run)
+        if not scores:
+            return 0.5  # Default if no scorers apply
+
+        # Equal weighting for now; can be customized per scorer
+        total = sum(s.score for s in scores)
+        return total / len(scores)
+
+    def detect_regression(
+        self, baseline_run_id: str, evolved_run_id: str, threshold: float = 0.05
+    ) -> dict:
+        """Compare baseline and evolved runs. Return {delta, regression, improvement, neutral}."""
+        baseline = self.store.get_run(baseline_run_id)
+        evolved = self.store.get_run(evolved_run_id)
+
+        if not baseline or not evolved:
+            return {
+                "error": "One or both runs not found",
+                "baseline_found": baseline is not None,
+                "evolved_found": evolved is not None,
+            }
+
+        baseline_score = self.get_aggregate_score(baseline)
+        evolved_score = self.get_aggregate_score(evolved)
+        delta = evolved_score - baseline_score
+
+        return {
+            "baseline_run_id": baseline_run_id,
+            "evolved_run_id": evolved_run_id,
+            "baseline_score": round(baseline_score, 3),
+            "evolved_score": round(evolved_score, 3),
+            "delta": round(delta, 3),
+            "threshold": threshold,
+            "regression": delta < -threshold,
+            "improvement": delta > threshold,
+            "neutral": abs(delta) <= threshold,
+        }
+
+    def _save_score(self, run_id: str, score: EvalScore):
+        """Save evaluation score to storage (optional)."""
+        conn = self.store.connect()
+        try:
+            conn.execute(
+                """INSERT INTO eval_scores (run_id, scorer, score, passed, details)
+                   VALUES (?, ?, ?, ?, ?)""",
+                (
+                    run_id,
+                    score.scorer,
+                    score.score,
+                    1 if score.passed else 0,
+                    str(score.details),
+                ),
+            )
+            conn.commit()
+        finally:
+            self.store.close(conn)

package/.claude/worktrees/phase-2-mcp/backend/eval/scorers.py

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+"""Evaluation scorers for CanonicalRun instances."""
+
+from dataclasses import dataclass, field
+from typing import Optional
+
+from backend.promethean.models import CanonicalRun
+
+
+@dataclass
+class EvalScore:
+    """Result of applying a scorer to a run."""
+
+    scorer: str
+    score: float  # 0.0 to 1.0
+    passed: bool
+    details: dict = field(default_factory=dict)
+
+
+class OutcomeScorer:
+    """Score based on run outcome."""
+
+    name = "outcome"
+
+    def score(self, run: CanonicalRun) -> EvalScore:
+        """Map outcome to score: success=1.0, partial=0.5, failure=0.0, unknown=0.3."""
+        outcome_map = {
+            "success": 1.0,
+            "partial": 0.5,
+            "failure": 0.0,
+            "unknown": 0.3,
+        }
+        score = outcome_map.get(run.outcome, 0.3)
+        return EvalScore(
+            scorer=self.name,
+            score=score,
+            passed=score > 0.5,
+            details={"outcome": run.outcome},
+        )
+
+    def applies_to(self, run: CanonicalRun) -> bool:
+        """Applies to all runs."""
+        return True
+
+
+class ToolEfficiencyScorer:
+    """Score based on tool call efficiency (unique_tools / total_calls)."""
+
+    name = "tool_efficiency"
+
+    def score(self, run: CanonicalRun) -> EvalScore:
+        """Calculate tool efficiency ratio. Pass if > 0.3."""
+        if not run.tool_calls:
+            return EvalScore(
+                scorer=self.name,
+                score=1.0,
+                passed=True,
+                details={"reason": "no_tools_used"},
+            )
+
+        total = len(run.tool_calls)
+        unique = len(set(tc.name for tc in run.tool_calls))
+        ratio = unique / total if total > 0 else 0.0
+
+        return EvalScore(
+            scorer=self.name,
+            score=ratio,
+            passed=ratio > 0.3,
+            details={
+                "unique_tools": unique,
+                "total_calls": total,
+                "efficiency_ratio": round(ratio, 2),
+            },
+        )
+
+    def applies_to(self, run: CanonicalRun) -> bool:
+        """Applies to runs with tool calls."""
+        return len(run.tool_calls) > 0
+
+
+class TokenCostScorer:
+    """Score based on token usage: lower is better (up to 50k tokens)."""
+
+    name = "token_cost"
+
+    def score(self, run: CanonicalRun) -> EvalScore:
+        """Score = max(0, 1 - tokens/50000). Pass if < 50k."""
+        if not run.metrics or not run.metrics.input_tokens:
+            return EvalScore(
+                scorer=self.name,
+                score=1.0,
+                passed=True,
+                details={"reason": "no_metrics"},
+            )
+
+        total_tokens = (run.metrics.input_tokens or 0) + (run.metrics.output_tokens or 0)
+        threshold = 50000
+        score = max(0.0, 1.0 - (total_tokens / threshold))
+
+        return EvalScore(
+            scorer=self.name,
+            score=score,
+            passed=total_tokens < threshold,
+            details={
+                "input_tokens": run.metrics.input_tokens,
+                "output_tokens": run.metrics.output_tokens,
+                "total_tokens": total_tokens,
+                "threshold": threshold,
+            },
+        )
+
+    def applies_to(self, run: CanonicalRun) -> bool:
+        """Applies to runs with metrics."""
+        return run.metrics is not None
+
+
+class ErrorRecoveryScorer:
+    """Score based on error handling: success with no errors = 1.0, success with errors = 0.8, failure = 0.0."""
+
+    name = "error_recovery"
+
+    def score(self, run: CanonicalRun) -> EvalScore:
+        """Score based on outcome and error presence."""
+        if run.outcome == "success":
+            if not run.errors:
+                score = 1.0
+            else:
+                score = 0.8
+            passed = True
+        elif run.outcome == "partial":
+            score = 0.5
+            passed = False
+        else:  # failure or unknown
+            score = 0.0
+            passed = False
+
+        return EvalScore(
+            scorer=self.name,
+            score=score,
+            passed=passed,
+            details={
+                "outcome": run.outcome,
+                "error_count": len(run.errors),
+                "has_errors": len(run.errors) > 0,
+            },
+        )
+
+    def applies_to(self, run: CanonicalRun) -> bool:
+        """Applies to all runs."""
+        return True
+
+
+class DeltaScorer:
+    """Score based on delta validation (Hermes-specific).
+
+    Only applies to Hermes runs with context.skill_name.
+    Integrates with existing DeltaValidator from promethean module.
+    """
+
+    name = "delta"
+
+    def score(self, run: CanonicalRun) -> Optional[EvalScore]:
+        """Run delta validation if applicable. Return None if not applicable."""
+        if not self.applies_to(run):
+            return None
+
+        # Try to import DeltaValidator
+        try:
+            from backend.promethean.delta_validator import get_validator
+
+            validator = get_validator()
+            skill_name = run.context.get("skill_name")
+
+            # Get baseline from context or infer
+            baseline = run.context.get("baseline_version")
+            if not baseline:
+                baseline = "unknown"
+
+            # Run validation
+            result = validator.validate(skill_name, baseline=baseline)
+
+            # Map validation result to score
+            passed = result.get("passed", False)
+            score = 1.0 if passed else 0.0
+
+            return EvalScore(
+                scorer=self.name,
+                score=score,
+                passed=passed,
+                details=result,
+            )
+        except Exception:
+            # DeltaValidator not available or error occurred
+            return None
+
+    def applies_to(self, run: CanonicalRun) -> bool:
+        """Applies to Hermes runs with skill_name in context."""
+        return (
+            run.agent_name == "hermes"
+            and run.context
+            and "skill_name" in run.context
+        )

package/.claude/worktrees/phase-2-mcp/backend/generate_dataset.py

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+"""
+Dataset Generator — Genera ejemplos de validación sintéticos para skills.
+
+Usage:
+    python generate_dataset.py --skill code-review --count 10 --output ~/.hermes/datasets/code-review/train.jsonl
+"""
+import argparse
+import json
+import sys
+from pathlib import Path
+from openai import OpenAI
+
+OLLAMA_BASE = "http://localhost:11434/v1"
+OLLAMA_MODEL = "gemma4:31b-cloud"
+
+client = OpenAI(base_url=OLLAMA_BASE, api_key="ollama")
+
+SKILL_PROMPTS = {
+    "code-review": """Para la skill 'code-review', generá exactamente {count} ejemplos de revisión de código.
+Cada ejemplo debe ser un objeto JSON con:
+- "input": código con bugs/problemas (Python, TypeScript, o Go)
+- "expected": la revisión esperada (bugs específicos que deberían detectarse)
+
+Cubrí estos casos:
+1. Python: SQL injection, type hints faltantes, async mal usado, raw dicts en vez de Pydantic
+2. TypeScript/React: useEffect sin deps, componentes no memoizados, keys faltantes en maps
+3. Go: error handling ignorado, goroutines sin sync, nil pointer dereference
+4. General: dead code, secretos hardcodeados, logs con PII
+
+IMPORTANTE: El expected NO debe ser el código corregido, sino una LISTA de bugs que deben detectarse.
+
+OUTPUT: Array JSON de objetos {{"input": "...", "expected": "..."}}. Sin markdown fences.
+Generá EXACTAMENTE {count} ejemplos. Comenzá YA:""",
+}
+
+
+def generate_dataset(skill: str, count: int, output_path: str):
+    prompt = SKILL_PROMPTS.get(skill, SKILL_PROMPTS["code-review"]).format(count=count)
+    
+    print(f"🎯 Generating {count} examples for '{skill}'...", flush=True)
+    
+    resp = client.chat.completions.create(
+        model=OLLAMA_MODEL,
+        messages=[
+            {"role": "system", "content": "Sos un experto en code review. Generás datasets de validación en JSON. Output: solo JSON válido, sin explicaciones."},
+            {"role": "user", "content": prompt}
+        ],
+        temperature=0.7,
+        max_tokens=4000,
+    )
+    
+    raw = resp.choices[0].message.content or ""
+    raw = raw.strip()
+    if raw.startswith("```"):
+        raw = raw.split("```")[1]
+        if raw.startswith("json"):
+            raw = raw[4:]
+    raw = raw.strip()
+    
+    try:
+        examples = json.loads(raw)
+    except json.JSONDecodeError:
+        print(f"❌ Failed to parse JSON. Raw output:", file=sys.stderr)
+        print(raw[:500], file=sys.stderr)
+        sys.exit(1)
+    
+    if not isinstance(examples, list):
+        examples = [examples]
+    
+    # Write to file
+    out = Path(output_path)
+    out.parent.mkdir(parents=True, exist_ok=True)
+    with open(out, "w") as f:
+        for ex in examples:
+            f.write(json.dumps(ex, ensure_ascii=False) + "\n")
+    
+    print(f"✅ Saved {len(examples)} examples to {out}")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Generate synthetic validation dataset")
+    parser.add_argument("--skill", required=True, help="Skill name")
+    parser.add_argument("--count", type=int, default=10, help="Number of examples")
+    parser.add_argument("--output", required=True, help="Output .jsonl file")
+    args = parser.parse_args()
+    generate_dataset(args.skill, args.count, args.output)

package/.claude/worktrees/phase-2-mcp/backend/job_tracker.py

@@ -0,0 +1,232 @@
+"""Evolution job tracking — persistent state for active and completed jobs."""
+
+import json
+import re
+import uuid
+import asyncio
+from datetime import datetime
+from enum import Enum
+from pathlib import Path
+from dataclasses import dataclass, field, asdict
+from typing import Optional
+
+LOG_DIR = Path.home() / ".hermes" / "evolution-logs"
+
+
+class JobStatus(str, Enum):
+    QUEUED = "queued"
+    LOADING_SKILL = "loading_skill"
+    BUILDING_DATASET = "building_dataset"
+    VALIDATING = "validating"
+    CONFIGURING = "configuring"
+    OPTIMIZING = "optimizing"
+    EVALUATING = "evaluating"
+    SAVING = "saving"
+    COMPLETED = "completed"
+    FAILED = "failed"
+
+
+# Phases in order (for progress calculation)
+PHASE_ORDER = [
+    JobStatus.LOADING_SKILL,
+    JobStatus.BUILDING_DATASET,
+    JobStatus.VALIDATING,
+    JobStatus.CONFIGURING,
+    JobStatus.OPTIMIZING,
+    JobStatus.EVALUATING,
+    JobStatus.SAVING,
+]
+
+
+@dataclass
+class EvolutionJob:
+    id: str
+    skill_name: str
+    status: JobStatus = JobStatus.QUEUED
+    iterations: int = 3
+    current_iteration: int = 0
+    pid: Optional[int] = None
+    started_at: str = ""
+    completed_at: str = ""
+    baseline_score: Optional[float] = None
+    current_best_score: Optional[float] = None
+    evolved_score: Optional[float] = None
+    improvement: Optional[float] = None
+    error: str = ""
+    logs: list[str] = field(default_factory=list)
+
+    def to_dict(self) -> dict:
+        d = asdict(self)
+        d["status"] = self.status.value
+        return d
+
+    @property
+    def progress(self) -> float:
+        """0.0 to 1.0 progress estimate."""
+        if self.status == JobStatus.COMPLETED:
+            return 1.0
+        if self.status == JobStatus.FAILED:
+            return 0.0
+        if self.status == JobStatus.QUEUED:
+            return 0.0
+
+        # Phase-based progress
+        phase_idx = 0
+        try:
+            phase_idx = PHASE_ORDER.index(self.status)
+        except ValueError:
+            pass
+
+        phase_weight = 1.0 / len(PHASE_ORDER)
+
+        # Within OPTIMIZING phase, use iteration progress
+        if self.status == JobStatus.OPTIMIZING and self.iterations > 0:
+            iter_progress = self.current_iteration / self.iterations
+            base = phase_idx * phase_weight
+            return base + (iter_progress * phase_weight)
+
+        return phase_idx * phase_weight
+
+    def add_log(self, message: str):
+        timestamp = datetime.now().isoformat()[:19]
+        self.logs.append(f"[{timestamp}] {message}")
+        # Keep last 500 lines
+        if len(self.logs) > 500:
+            self.logs = self.logs[-500:]
+
+    def save_log(self):
+        LOG_DIR.mkdir(parents=True, exist_ok=True)
+        log_file = LOG_DIR / f"{self.id}.json"
+        log_file.write_text(json.dumps(self.to_dict(), indent=2))
+
+
+class JobTracker:
+    def __init__(self):
+        self._jobs: dict[str, EvolutionJob] = {}
+        self._processes: dict[str, asyncio.subprocess.Process] = {}
+        LOG_DIR.mkdir(parents=True, exist_ok=True)
+
+    def create_job(self, skill_name: str, iterations: int) -> EvolutionJob:
+        job_id = f"{skill_name}_{datetime.now().strftime('%Y%m%d_%H%M%S')}_{uuid.uuid4().hex[:6]}"
+        job = EvolutionJob(
+            id=job_id,
+            skill_name=skill_name,
+            iterations=iterations,
+            started_at=datetime.now().isoformat(),
+        )
+        self._jobs[job_id] = job
+        return job
+
+    def get_job(self, job_id: str) -> Optional[EvolutionJob]:
+        return self._jobs.get(job_id)
+
+    def get_active_jobs(self) -> list[EvolutionJob]:
+        return [
+            j for j in self._jobs.values()
+            if j.status not in (JobStatus.COMPLETED, JobStatus.FAILED)
+        ]
+
+    def get_all_jobs(self, limit: int = 50) -> list[EvolutionJob]:
+        sorted_jobs = sorted(
+            self._jobs.values(),
+            key=lambda j: j.started_at,
+            reverse=True,
+        )
+        return sorted_jobs[:limit]
+
+    def set_process(self, job_id: str, process: asyncio.subprocess.Process):
+        self._processes[job_id] = process
+
+    def get_process(self, job_id: str) -> Optional[asyncio.subprocess.Process]:
+        return self._processes.get(job_id)
+
+    def cleanup_process(self, job_id: str):
+        self._processes.pop(job_id, None)
+
+    # ── Log parsing ─────────────────────────────────────────────────
+
+    # Patterns to detect phase changes from Rich output
+    PHASE_PATTERNS = [
+        (r"Loaded:.*\.md", JobStatus.LOADING_SKILL),
+        (r"Building evaluation dataset", JobStatus.BUILDING_DATASET),
+        (r"Generated.*synthetic examples", JobStatus.BUILDING_DATASET),
+        (r"Mined.*examples from session", JobStatus.BUILDING_DATASET),
+        (r"Loaded golden dataset", JobStatus.BUILDING_DATASET),
+        (r"Validating baseline constraints", JobStatus.VALIDATING),
+        (r"Configuring optimizer", JobStatus.CONFIGURING),
+        (r"Running GEPA optimization", JobStatus.OPTIMIZING),
+        (r"Running MIPROv2", JobStatus.OPTIMIZING),
+        (r"Optimization completed", JobStatus.OPTIMIZING),
+        (r"Validating evolved skill", JobStatus.EVALUATING),
+        (r"Evaluating on holdout", JobStatus.EVALUATING),
+        (r"Evolution Results", JobStatus.SAVING),
+        (r"Saved.*to output", JobStatus.SAVING),
+        (r"✓ Skill evolved", JobStatus.COMPLETED),
+    ]
+
+    # Pattern to extract scores
+    SCORE_PATTERN = re.compile(r"baseline[=_:\s]+(\d+\.?\d*)|evolved[=_:\s]+(\d+\.?\d*)|score[=_:\s]+(\d+\.?\d*)|improvement[=_:\s]+([+-]?\d+\.?\d*)", re.IGNORECASE)
+
+    # Pattern to extract iteration number
+    ITER_PATTERN = re.compile(r"iteration[=:\s]+(\d+)|eval[=:\s#]+(\d+)/(\d+)", re.IGNORECASE)
+
+    def parse_line(self, job: EvolutionJob, line: str):
+        """Parse a log line and update job state."""
+        # Strip ANSI codes
+        clean = re.sub(r"\x1b\[[0-9;]*m", "", line).strip()
+        if not clean:
+            return
+
+        job.add_log(clean)
+
+        # Check phase transitions
+        for pattern, phase in self.PHASE_PATTERNS:
+            if re.search(pattern, clean, re.IGNORECASE):
+                if phase != job.status:
+                    job.status = phase
+
+        # Check for optimization iteration progress
+        iter_match = self.ITER_PATTERN.search(clean)
+        if iter_match:
+            num = iter_match.group(1) or iter_match.group(2)
+            if num:
+                job.current_iteration = int(num)
+            total = iter_match.group(3)
+            if total:
+                job.iterations = int(total)
+
+        # Check for scores
+        score_match = self.SCORE_PATTERN.search(clean)
+        if score_match:
+            val = score_match.group(1) or score_match.group(2) or score_match.group(3) or score_match.group(4)
+            if val:
+                try:
+                    score = float(val)
+                    if "baseline" in clean.lower():
+                        job.baseline_score = score
+                    elif "evolved" in clean.lower() or "best" in clean.lower():
+                        job.current_best_score = score
+                    elif "improvement" in clean.lower():
+                        job.improvement = score
+                except ValueError:
+                    pass
+
+        # Check for completion
+        if "evolved_skill.md" in clean and "Saved" in clean:
+            job.status = JobStatus.COMPLETED
+            job.completed_at = datetime.now().isoformat()
+
+        # Check for failure
+        if "FAILED" in clean or "not found" in clean.lower():
+            if "✗" in clean or "Error" in clean or "error" in clean:
+                job.error = clean
+                job.status = JobStatus.FAILED
+                job.completed_at = datetime.now().isoformat()
+
+        # Persist periodically
+        if len(job.logs) % 10 == 0:
+            job.save_log()
+
+
+# Global tracker instance
+tracker = JobTracker()