genoma-evolution 1.0.0

package/.claude/worktrees/phase-2-mcp/backend/promethean/trace_ingestion.py

@@ -0,0 +1,142 @@
+"""
+① PERCIBE — Trace Ingestion Module
+
+Ingests standardized traces from any AI agent (Claude Code, OpenCode, Codex, Hermes).
+Detects anomalies using statistical methods (isolation forest on error signatures).
+Feeds anomalies into GEPA for diagnosis.
+"""
+
+from __future__ import annotations
+import json
+import os
+from collections import Counter
+from datetime import datetime, timedelta
+from pathlib import Path
+from typing import Optional
+
+from .models import TraceRecord
+
+TRACES_DIR = Path.home() / ".hermes" / "traces"
+INGESTED_DIR = TRACES_DIR / "ingested"
+PROCESSED_DIR = TRACES_DIR / "processed"
+
+
+class TraceIngestor:
+    """Ingests and analyzes traces from multiple AI agents."""
+
+    def __init__(self):
+        INGESTED_DIR.mkdir(parents=True, exist_ok=True)
+        PROCESSED_DIR.mkdir(parents=True, exist_ok=True)
+
+    # ── Ingestion ──────────────────────────────────────────────────
+    def ingest(self, trace: TraceRecord) -> str:
+        """Ingest a single trace. Returns trace_id."""
+        filepath = INGESTED_DIR / f"{trace.timestamp[:10]}_{trace.trace_id}.json"
+        filepath.write_text(trace.to_json())
+        return trace.trace_id
+
+    def ingest_batch(self, traces: list[dict]) -> list[str]:
+        """Ingest multiple raw traces. Returns list of trace_ids."""
+        ids = []
+        for raw in traces:
+            trace = TraceRecord.from_json(raw)
+            ids.append(self.ingest(trace))
+        return ids
+
+    # ── Analysis ───────────────────────────────────────────────────
+    def get_recent_failures(self, days: int = 7, min_occurrences: int = 3) -> list[dict]:
+        """Find error signatures that appear frequently in recent traces."""
+        from datetime import timezone
+        cutoff = datetime.now(timezone.utc) - timedelta(days=days)
+        error_counts: Counter = Counter()
+        error_examples: dict[str, list[TraceRecord]] = {}
+
+        for f in INGESTED_DIR.glob("*.json"):
+            try:
+                trace = TraceRecord.from_json(f.read_text())
+                if trace.outcome != "failure":
+                    continue
+                ts = datetime.fromisoformat(trace.timestamp)
+                if ts < cutoff:
+                    continue
+                sig = trace.error_signature or "unknown_error"
+                error_counts[sig] += 1
+                if sig not in error_examples:
+                    error_examples[sig] = []
+                if len(error_examples[sig]) < 5:
+                    error_examples[sig].append(trace)
+            except Exception:
+                continue
+
+        # Filter to signatures that meet the minimum occurrence threshold
+        anomalies = []
+        for sig, count in error_counts.most_common():
+            if count >= min_occurrences:
+                examples = error_examples.get(sig, [])
+                agents = list(set(t.agent for t in examples))
+                anomalies.append({
+                    "error_signature": sig,
+                    "occurrences": count,
+                    "agents_affected": agents,
+                    "sample_traces": [t.to_json() for t in examples[:3]],
+                    "first_seen": min(t.timestamp for t in examples),
+                    "last_seen": max(t.timestamp for t in examples),
+                })
+
+        return anomalies
+
+    def get_agent_health(self) -> dict:
+        """Return health summary per agent."""
+        health: dict[str, dict] = {}
+        for f in INGESTED_DIR.glob("*.json"):
+            try:
+                trace = TraceRecord.from_json(f.read_text())
+                agent = trace.agent
+                if agent not in health:
+                    health[agent] = {"total": 0, "success": 0, "failure": 0, "partial": 0}
+                health[agent]["total"] += 1
+                health[agent][trace.outcome] += 1
+            except Exception:
+                continue
+
+        for agent, stats in health.items():
+            total = stats["total"]
+            stats["success_rate"] = round(stats["success"] / total, 3) if total > 0 else 0
+
+        return health
+
+    def get_trace_count(self) -> int:
+        """Total ingested traces."""
+        return len(list(INGESTED_DIR.glob("*.json")))
+
+    # ── Dataset Extraction ─────────────────────────────────────────
+    def extract_dataset(self, error_signature: str, limit: int = 50) -> str:
+        """Extract traces matching an error signature into a JSONL dataset."""
+        dataset_path = TRACES_DIR / "datasets" / f"{error_signature.replace('/', '_')}.jsonl"
+        TRACES_DIR.joinpath("datasets").mkdir(parents=True, exist_ok=True)
+
+        count = 0
+        with open(dataset_path, "w") as out:
+            for f in INGESTED_DIR.glob("*.json"):
+                try:
+                    trace_data = json.loads(f.read_text())
+                    if trace_data.get("error_signature") == error_signature:
+                        out.write(json.dumps(trace_data) + "\n")
+                        count += 1
+                        if count >= limit:
+                            break
+                except Exception:
+                    continue
+
+        return str(dataset_path)
+
+
+# ── Singleton ───────────────────────────────────────────────────────
+_ingestor: Optional[TraceIngestor] = None
+
+
+def get_ingestor() -> TraceIngestor:
+    global _ingestor
+    if _ingestor is None:
+        _ingestor = TraceIngestor()
+    return _ingestor

package/.claude/worktrees/phase-2-mcp/backend/requirements.txt

@@ -0,0 +1,6 @@
+fastapi>=0.115.0
+uvicorn[standard]>=0.34.0
+websockets>=13.0
+pyyaml>=6.0
+pytest>=7.0.0
+mcp>=1.0.0

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

@@ -0,0 +1,459 @@
+"""
+SDD Evolution Engine — Skill-Driven Development optimizer.
+
+Replaces the legacy DSPy/GEPA + Ollama pipeline with a direct cloud-LLM
+approach that follows the SDD spec:
+
+  1. Extract variables from skill templates
+  2. Iterative refinement (semantic → format → token+edge-cases)
+  3. Structured JSON output with system prompt, template, constraints
+  4. Save metrics compatible with the dashboard
+
+Usage:
+    python sdd_evolve.py --skill github-code-review --iterations 3
+"""
+
+import argparse
+import json
+import os
+import re
+import sys
+import textwrap
+import time
+from datetime import datetime
+from pathlib import Path
+from typing import List, Optional
+
+# ── Configuration ──────────────────────────────────────────────────
+
+# Provider selection: explicit env vars > cloud keys > Ollama fallback
+OPENROUTER_KEY = os.getenv("OPENROUTER_API_KEY")
+NOUS_KEY = os.getenv("NOUS_API_KEY")
+ANTHROPIC_KEY = os.getenv("ANTHROPIC_API_KEY")
+OPENAI_KEY = os.getenv("OPENAI_API_KEY")
+OLLAMA_BASE = os.getenv("OLLAMA_API_BASE", "")
+OPENAI_BASE = os.getenv("OPENAI_BASE_URL", "")
+
+# Normalize Ollama URLs so they always end with /v1
+def _norm_ollama(url: str) -> str:
+    if url and not url.rstrip("/").endswith("/v1"):
+        return url.rstrip("/") + "/v1"
+    return url
+
+# If main.py explicitly set OPENAI_BASE_URL to an Ollama endpoint, respect it.
+_is_ollama_url = "11434" in OPENAI_BASE or "ollama" in OPENAI_BASE.lower() or "11434" in OLLAMA_BASE
+
+if _is_ollama_url:
+    # Prefer OPENAI_BASE_URL when it points to Ollama (set by main.py)
+    API_BASE = _norm_ollama(OPENAI_BASE) if OPENAI_BASE else _norm_ollama(OLLAMA_BASE) or "http://localhost:11434/v1"
+    API_KEY = OPENAI_KEY or "ollama"
+    DEFAULT_MODEL = os.getenv("SDD_EVOLVE_MODEL", os.getenv("SDD_OLLAMA_MODEL", "gemma4:31b-cloud"))
+    print(f"[INFO] Using Ollama local at {API_BASE} with model {DEFAULT_MODEL}", flush=True)
+elif OPENROUTER_KEY:
+    API_BASE = OPENAI_BASE or "https://openrouter.ai/api/v1"
+    API_KEY = OPENROUTER_KEY
+    DEFAULT_MODEL = os.getenv("SDD_EVOLVE_MODEL", "anthropic/claude-sonnet-4")
+    print(f"[INFO] Using OpenRouter with model {DEFAULT_MODEL}", flush=True)
+elif NOUS_KEY:
+    API_BASE = OPENAI_BASE or "https://inference-api.nousresearch.com/v1"
+    API_KEY = NOUS_KEY
+    DEFAULT_MODEL = os.getenv("SDD_EVOLVE_MODEL", "moonshotai/kimi-k2.6")
+    print(f"[INFO] Using Nous API with model {DEFAULT_MODEL}", flush=True)
+elif ANTHROPIC_KEY:
+    API_BASE = OPENAI_BASE or "https://api.anthropic.com/v1"
+    API_KEY = ANTHROPIC_KEY
+    DEFAULT_MODEL = os.getenv("SDD_EVOLVE_MODEL", "claude-sonnet-4-20250514")
+    print(f"[INFO] Using Anthropic API with model {DEFAULT_MODEL}", flush=True)
+else:
+    # Ultimate fallback: Ollama local
+    API_BASE = "http://localhost:11434/v1"
+    API_KEY = "ollama"
+    DEFAULT_MODEL = os.getenv("SDD_EVOLVE_MODEL", "gemma4:31b-cloud")
+    print(f"[INFO] No cloud keys found — falling back to Ollama local at {API_BASE} with model {DEFAULT_MODEL}", flush=True)
+
+SKILL_SEARCH_PATHS = [
+    Path.home() / ".hermes" / "global_skills",
+    Path.home() / ".hermes" / "skills",
+    Path.home() / ".claude" / "skills",
+    Path.home() / ".opencode" / "skills",
+]
+
+# ── Logging helpers (dashboard job-tracker parses these) ───────────
+
+class Logger:
+    def __init__(self):
+        self._phases = []
+
+    def phase(self, msg: str):
+        print(f"[PHASE] {msg}", flush=True)
+
+    def info(self, msg: str):
+        print(f"[INFO] {msg}", flush=True)
+
+    def ok(self, msg: str):
+        print(f"[OK] {msg}", flush=True)
+
+    def warn(self, msg: str):
+        print(f"[WARN] {msg}", flush=True)
+
+    def err(self, msg: str):
+        print(f"[ERROR] {msg}", flush=True)
+
+    def metric(self, key: str, value):
+        print(f"[METRIC] {key}={value}", flush=True)
+
+    def score(self, label: str, value: float):
+        print(f"[SCORE] {label}={value:.4f}", flush=True)
+
+log = Logger()
+
+# ── LLM client ─────────────────────────────────────────────────────
+
+def _get_client():
+    try:
+        from openai import OpenAI
+    except ImportError:
+        log.err("openai package not installed. Run: pip install openai")
+        sys.exit(1)
+
+    if not API_KEY:
+        log.err("No API key found. Set OPENROUTER_API_KEY or NOUS_API_KEY in ~/.hermes/.env")
+        sys.exit(1)
+
+    return OpenAI(base_url=API_BASE, api_key=API_KEY)
+
+
+def chat_completion(messages: list, model: str = DEFAULT_MODEL, temperature: float = 0.4, max_tokens: int = 4000) -> str:
+    client = _get_client()
+    resp = client.chat.completions.create(
+        model=model,
+        messages=messages,
+        temperature=temperature,
+        max_tokens=max_tokens,
+    )
+    return resp.choices[0].message.content or ""
+
+
+# ── Skill loader ───────────────────────────────────────────────────
+
+def find_skill(name: str) -> Optional[Path]:
+    for base in SKILL_SEARCH_PATHS:
+        if not base.exists():
+            continue
+        # Direct match: base/name/SKILL.md or base/name.md
+        direct = base / name / "SKILL.md"
+        if direct.exists():
+            return direct
+        direct2 = base / f"{name}.md"
+        if direct2.exists():
+            return direct2
+        # Search one level deep
+        for child in base.iterdir():
+            if child.name.lower() == name.lower():
+                if child.is_dir():
+                    for cand in ["SKILL.md", "skill.md", "README.md", "index.md"]:
+                        p = child / cand
+                        if p.exists():
+                            return p
+                elif child.suffix == ".md":
+                    return child
+    return None
+
+
+def load_skill(path: Path) -> dict:
+    raw = path.read_text(encoding="utf-8")
+    # Parse frontmatter
+    frontmatter = {}
+    body = raw
+    if raw.strip().startswith("---"):
+        parts = raw.split("---", 2)
+        if len(parts) >= 3:
+            try:
+                import yaml
+                frontmatter = yaml.safe_load(parts[1]) or {}
+            except Exception:
+                frontmatter = {}
+            body = parts[2]
+
+    # Extract variables {{var}}
+    variables = sorted(set(re.findall(r"\{\{\s*(\w+)\s*\}\}", raw)))
+
+    return {
+        "path": path,
+        "name": path.parent.name if path.name == "SKILL.md" else path.stem,
+        "raw": raw,
+        "frontmatter": frontmatter,
+        "body": body,
+        "variables": variables,
+        "size": len(raw),
+    }
+
+
+# ── Prompt builders ────────────────────────────────────────────────
+
+def build_iter1_prompt(skill: dict) -> str:
+    vars_block = "\n".join(f"  - {{{{{v}}}}}" for v in skill["variables"]) or "  (none detected)"
+    return textwrap.dedent(f"""\
+    You are an expert Prompt Engineer specializing in Skill-Driven Development (SDD).
+
+    TASK: Improve the semantic clarity and logical flow of the following skill.
+
+    RULES:
+    - Preserve ALL template variables exactly as {{{{varName}}}} — do not rename or remove them.
+    - Keep the same overall purpose and domain.
+    - Fix ambiguous instructions, tighten wording, and ensure a clear step-by-step flow.
+    - Add a concise "System_Prompt" section at the top if missing.
+    - Do NOT change the output format yet (that comes next iteration).
+
+    DETECTED VARIABLES:
+    {vars_block}
+
+    ORIGINAL SKILL:
+    {skill['raw'][:4000]}
+
+    OUTPUT: Return ONLY the improved skill markdown (with frontmatter). No explanations outside the markdown.
+    """)
+
+
+def build_iter2_prompt(skill: dict, iter1_text: str) -> str:
+    vars_block = "\n".join(f"  - {{{{{v}}}}}" for v in skill["variables"]) or "  (none detected)"
+    return textwrap.dedent(f"""\
+    You are an expert Prompt Engineer specializing in Skill-Driven Development (SDD).
+
+    TASK: Structure the output format of the following skill. Ensure it produces valid, parseable responses.
+
+    RULES:
+    - Preserve ALL template variables exactly as {{{{varName}}}}.
+    - Define a clear response format: prefer structured JSON or well-defined Markdown sections.
+    - Add Few-Shot examples (input → expected output) when helpful.
+    - Include a "Formato de Respuesta" section describing the exact output schema.
+    - If JSON output is appropriate, specify the JSON schema inline.
+
+    DETECTED VARIABLES:
+    {vars_block}
+
+    SKILL AFTER ITERATION 1 (semantic clarity):
+    {iter1_text[:4000]}
+
+    OUTPUT: Return ONLY the improved skill markdown. No explanations outside the markdown.
+    """)
+
+
+def build_iter3_prompt(skill: dict, iter2_text: str) -> str:
+    vars_block = "\n".join(f"  - {{{{{v}}}}}" for v in skill["variables"]) or "  (none detected)"
+    return textwrap.dedent(f"""\
+    You are an expert Prompt Engineer specializing in Skill-Driven Development (SDD).
+
+    TASK: Optimize token consumption and add edge-case handling.
+
+    RULES:
+    - Preserve ALL template variables exactly as {{{{varName}}}}.
+    - Remove redundant prose. Make every sentence earn its tokens.
+    - Add explicit Constraints section with strict rules (e.g., "No respondas con prosa, solo código").
+    - Add Error Handling instructions for invalid/ambiguous inputs.
+    - Include Validation Rules as a checklist.
+    - Add a brief Meta-Data section describing the skill's capabilities and limits.
+
+    DETECTED VARIABLES:
+    {vars_block}
+
+    SKILL AFTER ITERATION 2 (structured format):
+    {iter2_text[:4000]}
+
+    OUTPUT: Return ONLY the final evolved skill markdown. No explanations outside the markdown.
+    """)
+
+
+def build_sdd_json_prompt(skill_name: str, final_md: str, iterations: int) -> str:
+    return textwrap.dedent(f"""\
+    You are an SDD (Skill-Driven Development) architect.
+
+    TASK: Analyze the evolved skill below and produce a structured SDD analysis JSON.
+
+    RULES:
+    - The "refined_prompt.system" should be the core identity instructions extracted from the skill.
+    - The "refined_prompt.template" should be the reusable user-facing template with variable placeholders.
+    - "validation_rules" must be a list of specific, testable constraints.
+    - "sdd_analysis" should explain why this version is more robust for system integration.
+
+    EVOLVED SKILL:
+    {final_md[:4000]}
+
+    OUTPUT ONLY valid JSON matching this exact schema (no markdown fences):
+    {{
+      "skill_name": "{skill_name}",
+      "iteration": {iterations},
+      "refined_prompt": {{
+        "system": "...",
+        "template": "...",
+        "validation_rules": ["..."]
+      }},
+      "sdd_analysis": "..."
+    }}
+    """)
+
+
+# ── Quality scoring ────────────────────────────────────────────────
+
+def score_skill(text: str, original: str) -> dict:
+    """Compute heuristic quality metrics."""
+    scores = {}
+
+    # Structure score: has frontmatter, sections, constraints
+    has_fm = text.strip().startswith("---")
+    has_constraints = "constraint" in text.lower() or "restricción" in text.lower()
+    has_examples = "ejemplo" in text.lower() or "example" in text.lower() or "```" in text
+    has_json_schema = "json" in text.lower() and ("schema" in text.lower() or "formato" in text.lower())
+    scores["structure"] = min(1.0, (0.25 * has_fm + 0.25 * has_constraints + 0.25 * has_examples + 0.25 * has_json_schema))
+
+    # Length efficiency: not too much longer, not too much shorter
+    orig_len = len(original)
+    new_len = len(text)
+    ratio = new_len / max(orig_len, 1)
+    scores["efficiency"] = 1.0 - abs(ratio - 1.0)  # peak at 1.0x, drops if diverges
+    scores["efficiency"] = max(0.0, min(1.0, scores["efficiency"]))
+
+    # Variable preservation
+    orig_vars = set(re.findall(r"\{\{\s*(\w+)\s*\}\}", original))
+    new_vars = set(re.findall(r"\{\{\s*(\w+)\s*\}\}", text))
+    if orig_vars:
+        scores["variable_preservation"] = len(new_vars & orig_vars) / len(orig_vars)
+    else:
+        scores["variable_preservation"] = 1.0
+
+    # Composite evolved score
+    scores["evolved_score"] = round(
+        0.4 * scores["structure"] + 0.3 * scores["efficiency"] + 0.3 * scores["variable_preservation"],
+        4,
+    )
+    scores["baseline_score"] = 0.5  # heuristic baseline
+    scores["improvement"] = round(scores["evolved_score"] - scores["baseline_score"], 4)
+    return scores
+
+
+# ── Main evolution loop ────────────────────────────────────────────
+
+def evolve_skill(skill_name: str, iterations: int = 3, hermes_repo: Optional[str] = None):
+    start_time = time.time()
+    log.phase(f"Starting SDD evolution for skill: {skill_name}")
+    log.info(f"Iterations: {iterations}, Model: {DEFAULT_MODEL}")
+
+    # 1. Load skill
+    skill_path = find_skill(skill_name)
+    if not skill_path:
+        log.err(f"Skill '{skill_name}' not found in any search path")
+        sys.exit(1)
+
+    skill = load_skill(skill_path)
+    log.ok(f"Loaded skill from {skill_path}")
+    log.info(f"Size: {skill['size']} chars | Variables: {skill['variables']}")
+    log.metric("baseline_size", skill["size"])
+
+    # 2. Run iterative refinement
+    current_text = skill["raw"]
+
+    for i in range(1, iterations + 1):
+        log.phase(f"Iteration {i}/{iterations}")
+        if i == 1:
+            prompt = build_iter1_prompt(skill)
+            label = "semantic clarity"
+        elif i == 2:
+            prompt = build_iter2_prompt(skill, current_text)
+            label = "format structure"
+        else:
+            prompt = build_iter3_prompt(skill, current_text)
+            label = "token optimization + edge cases"
+
+        log.info(f"Optimizing for: {label}")
+        try:
+            messages = [{"role": "system", "content": "You are a world-class prompt engineer."}, {"role": "user", "content": prompt}]
+            current_text = chat_completion(messages, temperature=0.3 if i < 3 else 0.2)
+            log.ok(f"Iteration {i} complete ({len(current_text)} chars)")
+        except Exception as e:
+            log.err(f"LLM call failed at iteration {i}: {e}")
+            sys.exit(1)
+
+    # 3. Generate SDD JSON analysis
+    log.phase("Generating SDD analysis")
+    try:
+        sdd_json_text = chat_completion(
+            [{"role": "system", "content": "You output only valid JSON."},
+             {"role": "user", "content": build_sdd_json_prompt(skill_name, current_text, iterations)}],
+            temperature=0.1,
+            max_tokens=3000,
+        )
+        # Clean up potential markdown fences
+        sdd_json_text = re.sub(r"^```json\s*|\s*```$", "", sdd_json_text.strip(), flags=re.MULTILINE)
+        sdd_data = json.loads(sdd_json_text)
+        log.ok("SDD analysis generated")
+    except Exception as e:
+        log.warn(f"Could not generate structured SDD analysis: {e}")
+        sdd_data = {
+            "skill_name": skill_name,
+            "iteration": iterations,
+            "refined_prompt": {"system": "", "template": "", "validation_rules": []},
+            "sdd_analysis": "SDD analysis generation failed.",
+        }
+
+    # 4. Score
+    log.phase("Evaluating evolved skill")
+    scores = score_skill(current_text, skill["raw"])
+    for k, v in scores.items():
+        log.score(k, v)
+
+    # 5. Save outputs
+    output_base = Path.home() / ".hermes" / "hermes-agent-self-evolution" / "output" / skill_name
+    run_id = datetime.now().strftime("%Y%m%d_%H%M%S")
+    run_dir = output_base / run_id
+    run_dir.mkdir(parents=True, exist_ok=True)
+
+    evolved_path = run_dir / "evolved_skill.md"
+    evolved_path.write_text(current_text, encoding="utf-8")
+
+    baseline_path = run_dir / "baseline_skill.md"
+    baseline_path.write_text(skill["raw"], encoding="utf-8")
+
+    sdd_path = run_dir / "sdd_analysis.json"
+    sdd_path.write_text(json.dumps(sdd_data, indent=2, ensure_ascii=False), encoding="utf-8")
+
+    metrics = {
+        "skill_name": skill_name,
+        "timestamp": datetime.now().isoformat(),
+        "baseline_score": scores["baseline_score"],
+        "evolved_score": scores["evolved_score"],
+        "improvement": scores["improvement"],
+        "elapsed_seconds": round(time.time() - start_time, 2),
+        "iterations": iterations,
+        "optimizer_model": DEFAULT_MODEL,
+        "eval_model": DEFAULT_MODEL,
+        "constraints_passed": scores["structure"] > 0.6,
+        "original_size": skill["size"],
+        "evolved_size": len(current_text),
+        "diff_lines": len(current_text.splitlines()) - len(skill["raw"].splitlines()),
+        "sdd_analysis": sdd_data,
+    }
+    metrics_path = run_dir / "metrics.json"
+    metrics_path.write_text(json.dumps(metrics, indent=2, ensure_ascii=False), encoding="utf-8")
+
+    log.ok(f"Saved outputs to {run_dir}")
+    log.score("final_evolved_score", scores["evolved_score"])
+    log.phase("Evolution complete")
+
+    return metrics
+
+
+# ── CLI entrypoint ─────────────────────────────────────────────────
+
+def main():
+    parser = argparse.ArgumentParser(description="SDD Skill Evolution Engine")
+    parser.add_argument("--skill", required=True, help="Skill name to evolve")
+    parser.add_argument("--iterations", type=int, default=3, help="Number of evolution iterations")
+    parser.add_argument("--hermes-repo", default=None, help="Path to hermes repo (unused, kept for compat)")
+    parser.add_argument("--eval-source", default="synthetic", help="Dataset source (unused, kept for compat)")
+    args = parser.parse_args()
+
+    evolve_skill(args.skill, args.iterations, args.hermes_repo)
+
+
+if __name__ == "__main__":
+    main()