feat: add codebase genome diff script for structural change detection

Introduces genome_diff.py — a tool for detecting structural changes between
two git refs: file-level changes, function/class signature modifications,
and dependency import changes.

Addresses #132.

docs/swarm-memory-design.md

@@ -1,207 +0,0 @@
-# Swarm Memory Architecture — Design Note
-
-**Issue:** #232 — [ATLAS][Research] Solve the swarm-memory gap for concurrent subagents  
-**Repo:** Timmy_Foundation/compounding-intelligence  
-**Status:** Research — Design Draft  
-**Author:** step35 (burn)  
-**Date:** 2026-04-26
-
----
-
-## 1. Problem Statement
-
-The compounding-intelligence pipelines assume a **session-bounded** memory model: each agent session starts with injected bootstrap context, runs, produces a transcript, then ends. Knowledge is harvested *after* the session and injected *before* the next.
-
-But **concurrent subagents** (multiple simultaneous agents working parallel tasks) break this model:
-
-- **No shared scratch space:** Each subagent operates in isolation; discoveries in sibling sessions aren't visible until the next harvest cycle.
-- **Race conditions on promotion:** Two subagents may discover the same fact; both write it, causing duplication or conflicts.
-- **Lost correlation:** Without a shared event log, you cannot reconstruct what happened across the swarm.
-- **Stale shared state:** If a fact is promoted to global memory while subagents are still running, they may act on outdated assumptions.
-
-**Core question:** What memory semantics should exist across concurrent subagents so they can cooperate without corrupting each other or losing important results?
-
----
-
-## 2. Session Memory vs Swarm Memory
-
-### Session Memory (Current)
-
-| Property | Description |
-|---|---|
-| **Scope** | Single agent process lifetime |
-| **Storage** | In-memory context window + transient tool state |
-| **Visibility** | Private to that session |
-| **Lifetime** | Ephemeral — disappears on exit |
-| **Promotion** | Post-session harvester extracts durable facts |
-| **Example** | "I read the config file and saw port 8080" |
-
-### Swarm Memory (What's Missing)
-
-| Property | Desired |
-|---|---|
-| **Scope** | All concurrent subagents in a task group |
-| **Storage** | Shared, durable, versioned |
-| **Visibility** | Readable by all siblings; write semantics TBD |
-| **Lifetime** | Persists for duration of the coordinated task |
-| **Promotion** | Real-time or near-real-time synchronization |
-| **Example** | "Agent A found that the API returns 405 on main; all agents should know this now" |
-
-**Key insight:** Session memory is **private and accumulated**; swarm memory is **shared and coordinated**. The harvester/bootstrapper loop is too slow for real-time coordination.
-
----
-
-## 3. Candidate Designs
-
-### Design A — Append-Only Event Log + Synthesis
-
-**Overview:** All subagents write to a shared, append-only event log. A background synthesis process reads the log and extracts high-level facts into the knowledge store. Subagents also read the log to stay current.
-
-**Data model:**
-```
-swarm-memory/
-  event-log.jsonl           # Immutable, ordered, concurrent-safe append
-  event-index/              # By agent, by type, by timestamp
-  synthesized-facts/        # Periodic distillation into durable facts
-  checkpoints/              # Snapshot every N events for fast replay
-```
-
-**Write path:**
-1. Subagent observes something → `event_log.append({agent, type, content, timestamp, session_id})`
-2. Other subagents can tail the log (like a changelog)
-
-**Read path:**
-1. Before each action, subagent queries recent events (last N minutes or last M entries)
-2. Background job periodically runs synthesis LLM to convert raw events → distilled facts
-
-**Pros:**
-- **Lossless:** Nothing is ever overwritten; full audit trail
-- **Concurrent-safe:** Append-only, no locking
-- **Causality preserved:** Order of discoveries is visible
-- **Replayable:** Any subagent can reconstruct state from checkpoint + tail
-
-**Cons:**
-- **Signal/noise:** Raw events are noisy; synthesis latency means swarm facts lag
-- **Storage growth:** Event log grows unbounded without pruning policy
-- **Query performance:** Finding "all facts about X" requires synthesis or full scan
-- **Coordination latency:** Subagents only learn of discoveries after they're written and tailed
-
-**Failure modes:**
-- **Duplication:** Multiple agents write the same observation → synthesis dedups
-- **Contradiction:** Two agents report conflicting facts → synthesis must reconcile
-- **Stale state:** Agent reads log at T0, then new events arrive before it acts
-
----
-
-### Design B — Shared Board + Evidence Links
-
-**Overview:** A shared, mutable board stores distilled facts. Each fact includes provenance links to the agent sessions that discovered it. Agents read-before-write and update via compare-and-swap.
-
-**Data model:**
-```
-swarm-memory/
-  board.yaml                # Current set of facts with version stamps
-  evidence-links/           # Mapping: fact_id → [session_id, turn_range]
-  fact-history/             # append-only log of fact revisions (for audit)
-```
-
-**Write path (compare-and-swap):**
-1. Agent reads current fact version
-2. Agent proposes update with new evidence
-3. System accepts if version unchanged since read; rejects with retry if conflict
-4. On accept → append to fact-history, increment board version
-
-**Read path:**
-1. Agent reads board.yaml (small, distilled)
-2. If deeper verification needed, follow evidence-links to source sessions
-
-**Pros:**
-- **Low-latency reads:** Board is small and current
-- **Explicit provenance:** Every fact knows which sessions contributed
-- **Conflict detection:** CAS catches concurrent updates
-- **Intentional updates:** Agents must justify changes with evidence
-
-**Cons:**
-- **Write contention:** Multiple agents writing same fact cause retry storms
-- **Central point:** board.yaml is a single source of truth (but versioned)
-- **Merge complexity:** CAS retry logic must be retry-with-backoff; could stall
-- **Staleness window:** Between read and act, board may change
-
-**Failure modes:**
-- **Thundering herd:** Many agents CAS-fail on same hot fact → exponential backoff needed
-- **Missing promotions:** A fact discovered but never written because agent crashed pre-write
-- **Board corruption:** If CAS not atomic, two writes could interleave
-- **Evidence loss:** If evidence-links point to deleted session transcripts, verification fails
-
----
-
-## 4. Trade-off Matrix
-
-| Dimension | Event Log | Shared Board |
-|---|---|---|
-| **Write concurrency** | Unbounded (append-only) | Contention on hot keys |
-| **Read latency** | Must scan/synthesize | Direct read (constant-time) |
-| **Storage efficiency** | Redundant raw events | Condensed facts |
-| **Auditability** | Full reconstruction | Requires fact-history |
-| **Coordination speed** | Lag between event → synthesis | Near-real-time (CAS cycle) |
-| **Complexity** | Log management + synthesis worker | CAS protocol + retry logic |
-
-**Verdict:** Start with **Event Log** (simpler, safer, no coordination overhead), then layer Board as a *view* over synthesized facts if read latency becomes a bottleneck.
-
----
-
-## 5. Proposed Experimental Prototype
-
-**Scope:** Minimal viable swarm-memory path for a controlled parallel task.
-
-**Task:** Have 3 concurrent subagents process a set of GitHub issues. Each agent:
-1. Reads issue details
-2. Searches codebase for relevant files
-3. Drafts a fix
-4. **Writes discovery events to swarm event log**
-5. Reads peer discoveries before next step
-
-**Metrics to collect:**
-- Duplication rate: how many agents found the same root cause independently?
-- Correlation lift: did reading peer discoveries change agent behavior?
-- Latency: time from discovery to visibility across swarm
-- Synthesis quality: can an LLM summarize raw events into coherent fact?
-
-**Implementation plan:**
-1. `scripts/swarm_event_log.py` — thread-safe JSONL append + tail API
-2. `scripts/swarm_synthesizer.py` — periodic batch that consumes event log, emits distilled facts
-3. Patch `hermes-agent` burn worker to emit events at key milestones
-4. Simple dashboard: `metrics/swarm_memory_dashboard.md`
-
-**Success criteria:** Prototype runs end-to-end with 3 agents; event log captures discoveries; synthesizer produces at least one cross-agent insight.
-
----
-
-## 6. Failure Modes to Watch
-
-| Mode | Symptom | Mitigation |
-|---|---|---|
-| Duplication | Same fact appears from 3 agents | Synthesis dedup; evidence links count |
-| Contradiction | Agent A says "port 8080", Agent B says "port 3000" | Evidence-weighted majority; timestamp priority |
-| Stale shared state | Agent reads board, acts, board changed under it | Version vectors; read-modify-write CAS with retry |
-| Missing promotion | Discovery lost on agent crash | Event log is durable before action; recovery from last checkpoint |
-| Race on hot fact | Two agents try to write same fact simultaneously | CAS backoff; random jitter |
-| Log unbounded | Event log grows 10GB/day | Checkpoint + prune: keep summary + recent window |
-
----
-
-## 7. Next Steps (Out of Scope for This Note)
-
-- Build the event log implementation (Design A, phase 1)
-- Wire hermes-agent to emit events
-- Run the 3-agent parallel experiment
-- Measure and compare Board vs Log read patterns
-- Decide: ship to prod or iterate
-
----
-
-## 8. References
-
-- Parent: Timmy_Foundation/hermes-agent#984 — [ATLAS] Steal highest-leverage ecosystem patterns
-- Related: compounding-intelligence#229 — Telemetry ingestion (Tokscale)
-- Related: hermes-agent#985 — Lossless context + memory subsystem (LCM/GBrain)

scripts/genome_diff.py

@@ -0,0 +1,288 @@
+#!/usr/bin/env python3
+"""
+Codebase Genome Diff — Detect structural changes between two versions.
+
+Compares two git refs (commits, branches, tags) and produces a human-readable
+report of structural changes:
+  • Added/removed/renamed files
+  • Changed functions/classes (signature modifications)
+  • New dependencies (imports, requirements, etc.)
+
+Usage:
+    python3 scripts/genome_diff.py --ref1 <commit1> --ref2 <commit2>
+    python3 scripts/genome_diff.py --ref1 main --ref2 feature-branch
+    python3 scripts/genome_diff.py --ref1 v1.0 --ref2 v2.0 --output report.txt
+"""
+
+import argparse
+import json
+import os
+import re
+import subprocess
+import sys
+from dataclasses import dataclass, field
+from typing import List, Dict, Any, Optional
+
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+sys.path.insert(0, SCRIPT_DIR)
+from diff_analyzer import DiffAnalyzer, ChangeCategory
+
+
+@dataclass
+class FunctionChange:
+    file: str
+    name: str
+    kind: str  # 'function' or 'class'
+    change_type: str  # 'added' or 'removed' (simplified)
+    old_line: Optional[int] = None
+    new_line: Optional[int] = None
+
+
+@dataclass
+class DependencyChange:
+    file: str
+    module: str
+    change_type: str  # 'added' or 'removed' or 'modified'
+    line: int = 0
+
+
+@dataclass
+class GenomeDiffReport:
+    ref1: str
+    ref2: str
+    file_changes: List[Dict[str, Any]] = field(default_factory=list)
+    function_changes: List[FunctionChange] = field(default_factory=list)
+    dependency_changes: List[DependencyChange] = field(default_factory=list)
+    total_files_changed: int = 0
+    total_functions_changed: int = 0
+    total_dependencies_changed: int = 0
+
+    def to_dict(self) -> Dict[str, Any]:
+        return {
+            "ref1": self.ref1,
+            "ref2": self.ref2,
+            "summary": {
+                "files": self.total_files_changed,
+                "functions": self.total_functions_changed,
+                "dependencies": self.total_dependencies_changed,
+            },
+            "file_changes": self.file_changes,
+            "function_changes": [fc.__dict__ for fc in self.function_changes],
+            "dependency_changes": [dc.__dict__ for dc in self.dependency_changes],
+        }
+
+    def human_report(self) -> str:
+        lines = []
+        lines.append(f"Codebase Genome Diff: {self.ref1} → {self.ref2}")
+        lines.append("=" * 60)
+        lines.append(f"  Files changed: {self.total_files_changed}")
+        lines.append(f"  Functions changed: {self.total_functions_changed}")
+        lines.append(f"  Dependencies changed: {self.total_dependencies_changed}")
+        lines.append("")
+
+        for fc in self.file_changes:
+            kind = []
+            if fc.get('is_new'):
+                kind.append("NEW")
+            if fc.get('is_deleted'):
+                kind.append("DELETED")
+            if fc.get('is_renamed'):
+                kind.append("RENAMED")
+            if fc.get('is_binary'):
+                kind.append("BINARY")
+            kind_str = f" [{', '.join(kind)}]" if kind else ""
+            lines.append(f"  {fc['path']}{kind_str}  (+{fc['added_lines']}/-{fc['deleted_lines']})")
+        lines.append("")
+
+        for fc in self.function_changes:
+            op = {'added': '+', 'removed': '-', 'modified': '~'}.get(fc.change_type, '?')
+            lines.append(f"  [{op}] {fc.file}: {fc.kind} '{fc.name}'")
+        lines.append("")
+
+        for dc in self.dependency_changes:
+            op = '+' if dc.change_type == 'added' else '-'
+            lines.append(f"  [{op}] {dc.file}: {dc.module}")
+        lines.append("")
+
+        return "\n".join(lines)
+
+
+def run_git_diff(ref1: str, ref2: str) -> str:
+    result = subprocess.run(
+        ['git', 'diff', '--unified=0', f'{ref1}...{ref2}'],
+        capture_output=True, text=True, cwd=SCRIPT_DIR
+    )
+    if result.returncode not in (0, 1):
+        print(f"git diff failed: {result.stderr}", file=sys.stderr)
+        sys.exit(1)
+    return result.stdout
+
+
+def extract_function_changes(diff_text: str) -> List[FunctionChange]:
+    changes: List[FunctionChange] = []
+    pattern = re.compile(r'^([+\-])\s*(def|class)\s+(\w+)', re.MULTILINE)
+    hunk_header_re = re.compile(r'^@@\s+-(\d+)(?:,(\d+))?\s+\+(\d+)(?:,(\d+))?\s+@@')
+    current_old_line: Optional[int] = None
+    current_new_line: Optional[int] = None
+
+    for line in diff_text.split('\n'):
+        hdr = hunk_header_re.match(line)
+        if hdr:
+            current_old_line = int(hdr.group(1))
+            current_new_line = int(hdr.group(3))
+            continue
+        m = pattern.match(line)
+        if m:
+            op = m.group(1)
+            kind = m.group(2)
+            name = m.group(3)
+            change_type = "added" if op == '+' else "removed"
+            line_num = current_new_line if change_type == "added" else current_old_line
+            changes.append(FunctionChange(
+                file="<unknown>",
+                name=name,
+                kind=kind,
+                change_type=change_type,
+                new_line=line_num if change_type == "added" else None,
+                old_line=line_num if change_type == "removed" else None,
+            ))
+            # Advance line counters heuristically
+            if op == '-':
+                if current_old_line is not None:
+                    current_old_line += 1
+            elif op == '+':
+                if current_new_line is not None:
+                    current_new_line += 1
+        elif line.startswith(' '):
+            if current_old_line is not None:
+                current_old_line += 1
+            if current_new_line is not None:
+                current_new_line += 1
+        # lines starting with other prefixes (like \\ No newline) ignored
+    return changes
+
+
+def extract_dependency_changes(diff_text: str, analyzer: DiffAnalyzer) -> List[DependencyChange]:
+    changes: List[DependencyChange] = []
+    import_pattern = re.compile(
+        r'^([+\-])\s*(?:import\s+([\w\.]+)|from\s+([\w\.]+)\s+import)',
+        re.MULTILINE
+    )
+    file_diffs = analyzer._split_files(diff_text)
+    for file_diff in file_diffs:
+        file_match = re.search(r'^diff --git a/.*? b/(.*?)$', file_diff, re.MULTILINE)
+        if not file_match:
+            continue
+        filepath = file_match.group(1)
+
+        # Scan each line for import changes
+        for line in file_diff.split('\n'):
+            m = import_pattern.match(line)
+            if m:
+                change_type = "added" if m.group(1) == '+' else "removed"
+                module = m.group(2) or m.group(3)
+                changes.append(DependencyChange(
+                    file=filepath,
+                    module=module,
+                    change_type=change_type,
+                    line=0
+                ))
+
+        # Detect if this file is a dependency manifest
+        req_file_pattern = re.compile(
+            r'^[\+\-].*?(requirements(.*?)\.txt|pyproject\.toml|setup\.py|Pipfile)'
+        )
+        if any(req_file_pattern.match(line) for line in file_diff.split('\n')):
+            if not any(c.file == filepath and c.module == "<file>" for c in changes):
+                changes.append(DependencyChange(
+                    file=filepath,
+                    module="<file>",
+                    change_type="modified",
+                    line=0
+                ))
+    return changes
+
+
+def correlate_function_changes_with_files(diff_text: str, functions: List[FunctionChange]) -> List[FunctionChange]:
+    result: List[FunctionChange] = []
+    # Split diff into per-file sections
+    file_sections: List[tuple[str, str]] = []
+    current_file: Optional[str] = None
+    current_lines: List[str] = []
+    for line in diff_text.split('\n'):
+        if line.startswith('diff --git'):
+            if current_file is not None:
+                file_sections.append((current_file, '\n'.join(current_lines)))
+            m = re.match(r'^diff --git a/.*? b/(.*?)$', line)
+            current_file = m.group(1) if m else "unknown"
+            current_lines = [line]
+        else:
+            current_lines.append(line)
+    if current_file is not None:
+        file_sections.append((current_file, '\n'.join(current_lines)))
+
+    pattern = re.compile(r'^([+\-])\s*(def|class)\s+(\w+)', re.MULTILINE)
+    for filepath, section in file_sections:
+        for m in pattern.finditer(section):
+            op = m.group(1)
+            kind = m.group(2)
+            name = m.group(3)
+            change_type = "added" if op == '+' else "removed"
+            result.append(FunctionChange(
+                file=filepath,
+                name=name,
+                kind=kind,
+                change_type=change_type
+            ))
+    return result
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Codebase Genome Diff — structural changes between versions")
+    parser.add_argument("--ref1", required=True, help="First git ref (commit, branch, tag)")
+    parser.add_argument("--ref2", required=True, help="Second git ref")
+    parser.add_argument("--output", help="Write report to file")
+    parser.add_argument("--json", action="store_true", help="Output JSON instead of human report")
+    args = parser.parse_args()
+
+    try:
+        diff_text = run_git_diff(args.ref1, args.ref2)
+    except Exception as e:
+        print(f"Error: {e}", file=sys.stderr)
+        sys.exit(1)
+
+    if not diff_text.strip():
+        print(f"No differences between {args.ref1} and {args.ref2}.")
+        sys.exit(0)
+
+    analyzer = DiffAnalyzer()
+    summary = analyzer.analyze(diff_text)
+
+    file_changes = [fc.to_dict() for fc in summary.files]
+    func_changes = extract_function_changes(diff_text)
+    func_changes = correlate_function_changes_with_files(diff_text, func_changes)
+    dep_changes = extract_dependency_changes(diff_text, analyzer)
+
+    report = GenomeDiffReport(
+        ref1=args.ref1,
+        ref2=args.ref2,
+        file_changes=file_changes,
+        function_changes=func_changes,
+        dependency_changes=dep_changes,
+        total_files_changed=len(file_changes),
+        total_functions_changed=len(func_changes),
+        total_dependencies_changed=len(dep_changes),
+    )
+
+    output = json.dumps(report.to_dict(), indent=2) if args.json else report.human_report()
+
+    if args.output:
+        with open(args.output, 'w') as f:
+            f.write(output + '\n')
+        print(f"Report written to {args.output}")
+    else:
+        print(output)
+
+
+if __name__ == '__main__':
+    main()

scripts/pr_complexity_scorer.py

@@ -1,351 +0,0 @@
-#!/usr/bin/env python3
-"""
-PR Complexity Scorer - Estimate review effort for PRs.
-"""
-
-import argparse
-import json
-import os
-import re
-import sys
-from dataclasses import dataclass, asdict
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Any, Dict, List, Optional
-import urllib.request
-import urllib.error
-
-GITEA_BASE = "https://forge.alexanderwhitestone.com/api/v1"
-
-DEPENDENCY_FILES = {
-    "requirements.txt", "pyproject.toml", "setup.py", "setup.cfg",
-    "Pipfile", "poetry.lock", "package.json", "yarn.lock", "Gemfile",
-    "go.mod", "Cargo.toml", "pom.xml", "build.gradle"
-}
-
-TEST_PATTERNS = [
-    r"tests?/.*\.py$", r".*_test\.py$", r"test_.*\.py$",
-    r"spec/.*\.rb$", r".*_spec\.rb$",
-    r"__tests__/", r".*\.test\.(js|ts|jsx|tsx)$"
-]
-
-WEIGHT_FILES = 0.25
-WEIGHT_LINES = 0.25
-WEIGHT_DEPS = 0.30
-WEIGHT_TEST_COV = 0.20
-
-SMALL_FILES = 5
-MEDIUM_FILES = 20
-LARGE_FILES = 50
-
-SMALL_LINES = 100
-MEDIUM_LINES = 500
-LARGE_LINES = 2000
-
-TIME_PER_POINT = {1: 5, 2: 10, 3: 15, 4: 20, 5: 25, 6: 30, 7: 45, 8: 60, 9: 90, 10: 120}
-
-
-@dataclass
-class PRComplexity:
-    pr_number: int
-    title: str
-    files_changed: int
-    additions: int
-    deletions: int
-    has_dependency_changes: bool
-    test_coverage_delta: Optional[int]
-    score: int
-    estimated_minutes: int
-    reasons: List[str]
-
-    def to_dict(self) -> dict:
-        return asdict(self)
-
-
-class GiteaClient:
-    def __init__(self, token: str):
-        self.token = token
-        self.base_url = GITEA_BASE.rstrip("/")
-
-    def _request(self, path: str, params: Dict = None) -> Any:
-        url = f"{self.base_url}{path}"
-        if params:
-            qs = "&".join(f"{k}={v}" for k, v in params.items() if v is not None)
-            url += f"?{qs}"
-
-        req = urllib.request.Request(url)
-        req.add_header("Authorization", f"token {self.token}")
-        req.add_header("Content-Type", "application/json")
-
-        try:
-            with urllib.request.urlopen(req, timeout=30) as resp:
-                return json.loads(resp.read().decode())
-        except urllib.error.HTTPError as e:
-            print(f"API error {e.code}: {e.read().decode()[:200]}", file=sys.stderr)
-            return None
-        except urllib.error.URLError as e:
-            print(f"Network error: {e}", file=sys.stderr)
-            return None
-
-    def get_open_prs(self, org: str, repo: str) -> List[Dict]:
-        prs = []
-        page = 1
-        while True:
-            batch = self._request(f"/repos/{org}/{repo}/pulls", {"limit": 50, "page": page, "state": "open"})
-            if not batch:
-                break
-            prs.extend(batch)
-            if len(batch) < 50:
-                break
-            page += 1
-        return prs
-
-    def get_pr_files(self, org: str, repo: str, pr_number: int) -> List[Dict]:
-        files = []
-        page = 1
-        while True:
-            batch = self._request(
-                f"/repos/{org}/{repo}/pulls/{pr_number}/files",
-                {"limit": 100, "page": page}
-            )
-            if not batch:
-                break
-            files.extend(batch)
-            if len(batch) < 100:
-                break
-            page += 1
-        return files
-
-    def post_comment(self, org: str, repo: str, pr_number: int, body: str) -> bool:
-        data = json.dumps({"body": body}).encode("utf-8")
-        req = urllib.request.Request(
-            f"{self.base_url}/repos/{org}/{repo}/issues/{pr_number}/comments",
-            data=data,
-            method="POST",
-            headers={"Authorization": f"token {self.token}", "Content-Type": "application/json"}
-        )
-        try:
-            with urllib.request.urlopen(req, timeout=30) as resp:
-                return resp.status in (200, 201)
-        except urllib.error.HTTPError:
-            return False
-
-
-def is_dependency_file(filename: str) -> bool:
-    return any(filename.endswith(dep) for dep in DEPENDENCY_FILES)
-
-
-def is_test_file(filename: str) -> bool:
-    return any(re.search(pattern, filename) for pattern in TEST_PATTERNS)
-
-
-def score_pr(
-    files_changed: int,
-    additions: int,
-    deletions: int,
-    has_dependency_changes: bool,
-    test_coverage_delta: Optional[int] = None
-) -> tuple[int, int, List[str]]:
-    score = 1.0
-    reasons = []
-
-    # Files changed
-    if files_changed <= SMALL_FILES:
-        fscore = 1.0
-        reasons.append("small number of files changed")
-    elif files_changed <= MEDIUM_FILES:
-        fscore = 2.0
-        reasons.append("moderate number of files changed")
-    elif files_changed <= LARGE_FILES:
-        fscore = 2.5
-        reasons.append("large number of files changed")
-    else:
-        fscore = 3.0
-        reasons.append("very large PR spanning many files")
-
-    # Lines changed
-    total_lines = additions + deletions
-    if total_lines <= SMALL_LINES:
-        lscore = 1.0
-        reasons.append("small change size")
-    elif total_lines <= MEDIUM_LINES:
-        lscore = 2.0
-        reasons.append("moderate change size")
-    elif total_lines <= LARGE_LINES:
-        lscore = 3.0
-        reasons.append("large change size")
-    else:
-        lscore = 4.0
-        reasons.append("very large change")
-
-    # Dependency changes
-    if has_dependency_changes:
-        dscore = 2.5
-        reasons.append("dependency changes (architectural impact)")
-    else:
-        dscore = 0.0
-
-    # Test coverage delta
-    tscore = 0.0
-    if test_coverage_delta is not None:
-        if test_coverage_delta > 0:
-            reasons.append(f"test additions (+{test_coverage_delta} test files)")
-            tscore = -min(2.0, test_coverage_delta / 2.0)
-        elif test_coverage_delta < 0:
-            reasons.append(f"test removals ({abs(test_coverage_delta)} test files)")
-            tscore = min(2.0, abs(test_coverage_delta) * 0.5)
-    else:
-        reasons.append("test coverage change not assessed")
-
-    # Weighted sum, scaled by 3 to use full 1-10 range
-    bonus = (fscore * WEIGHT_FILES) + (lscore * WEIGHT_LINES) + (dscore * WEIGHT_DEPS) + (tscore * WEIGHT_TEST_COV)
-    scaled_bonus = bonus * 3.0
-    score = 1.0 + scaled_bonus
-
-    final_score = max(1, min(10, int(round(score))))
-    est_minutes = TIME_PER_POINT.get(final_score, 30)
-
-    return final_score, est_minutes, reasons
-
-
-def analyze_pr(client: GiteaClient, org: str, repo: str, pr_data: Dict) -> PRComplexity:
-    pr_num = pr_data["number"]
-    title = pr_data.get("title", "")
-    files = client.get_pr_files(org, repo, pr_num)
-
-    additions = sum(f.get("additions", 0) for f in files)
-    deletions = sum(f.get("deletions", 0) for f in files)
-    filenames = [f.get("filename", "") for f in files]
-
-    has_deps = any(is_dependency_file(f) for f in filenames)
-
-    test_added = sum(1 for f in files if f.get("status") == "added" and is_test_file(f.get("filename", "")))
-    test_removed = sum(1 for f in files if f.get("status") == "removed" and is_test_file(f.get("filename", "")))
-    test_delta = test_added - test_removed if (test_added or test_removed) else None
-
-    score, est_min, reasons = score_pr(
-        files_changed=len(files),
-        additions=additions,
-        deletions=deletions,
-        has_dependency_changes=has_deps,
-        test_coverage_delta=test_delta
-    )
-
-    return PRComplexity(
-        pr_number=pr_num,
-        title=title,
-        files_changed=len(files),
-        additions=additions,
-        deletions=deletions,
-        has_dependency_changes=has_deps,
-        test_coverage_delta=test_delta,
-        score=score,
-        estimated_minutes=est_min,
-        reasons=reasons
-    )
-
-
-def build_comment(complexity: PRComplexity) -> str:
-    change_desc = f"{complexity.files_changed} files, +{complexity.additions}/-{complexity.deletions} lines"
-    deps_note = "\n- :warning: Dependency changes detected — architectural review recommended" if complexity.has_dependency_changes else ""
-    test_note = ""
-    if complexity.test_coverage_delta is not None:
-        if complexity.test_coverage_delta > 0:
-            test_note = f"\n- :+1: {complexity.test_coverage_delta} test file(s) added"
-        elif complexity.test_coverage_delta < 0:
-            test_note = f"\n- :warning: {abs(complexity.test_coverage_delta)} test file(s) removed"
-
-    comment = f"## 📊 PR Complexity Analysis\n\n"
-    comment += f"**PR #{complexity.pr_number}: {complexity.title}**\n\n"
-    comment += f"| Metric | Value |\n|--------|-------|\n"
-    comment += f"| Changes | {change_desc} |\n"
-    comment += f"| Complexity Score | **{complexity.score}/10** |\n"
-    comment += f"| Estimated Review Time | ~{complexity.estimated_minutes} minutes |\n\n"
-    comment += f"### Scoring rationale:"
-    for r in complexity.reasons:
-        comment += f"\n- {r}"
-    if deps_note:
-        comment += deps_note
-    if test_note:
-        comment += test_note
-    comment += f"\n\n---\n"
-    comment += f"*Generated by PR Complexity Scorer — [issue #135](https://forge.alexanderwhitestone.com/Timmy_Foundation/compounding-intelligence/issues/135)*"
-    return comment
-
-
-def main():
-    parser = argparse.ArgumentParser(description="PR Complexity Scorer")
-    parser.add_argument("--org", default="Timmy_Foundation")
-    parser.add_argument("--repo", default="compounding-intelligence")
-    parser.add_argument("--token", default=os.environ.get("GITEA_TOKEN") or os.path.expanduser("~/.config/gitea/token"))
-    parser.add_argument("--dry-run", action="store_true")
-    parser.add_argument("--apply", action="store_true")
-    parser.add_argument("--output", default="metrics/pr_complexity.json")
-    args = parser.parse_args()
-
-    token_path = args.token
-    if os.path.exists(token_path):
-        with open(token_path) as f:
-            token = f.read().strip()
-    else:
-        token = args.token
-
-    if not token:
-        print("ERROR: No Gitea token provided", file=sys.stderr)
-        sys.exit(1)
-
-    client = GiteaClient(token)
-
-    print(f"Fetching open PRs for {args.org}/{args.repo}...")
-    prs = client.get_open_prs(args.org, args.repo)
-    if not prs:
-        print("No open PRs found.")
-        sys.exit(0)
-
-    print(f"Found {len(prs)} open PR(s). Analyzing...")
-
-    results = []
-    Path(args.output).parent.mkdir(parents=True, exist_ok=True)
-
-    for pr in prs:
-        pr_num = pr["number"]
-        title = pr.get("title", "")
-        print(f"  Analyzing PR #{pr_num}: {title[:60]}")
-
-        try:
-            complexity = analyze_pr(client, args.org, args.repo, pr)
-            results.append(complexity.to_dict())
-
-            comment = build_comment(complexity)
-
-            if args.dry_run:
-                print(f"    → Score: {complexity.score}/10, Est: {complexity.estimated_minutes}min [DRY-RUN]")
-            elif args.apply:
-                success = client.post_comment(args.org, args.repo, pr_num, comment)
-                status = "[commented]" if success else "[FAILED]"
-                print(f"    → Score: {complexity.score}/10, Est: {complexity.estimated_minutes}min {status}")
-            else:
-                print(f"    → Score: {complexity.score}/10, Est: {complexity.estimated_minutes}min [no action]")
-
-        except Exception as e:
-            print(f"    ERROR analyzing PR #{pr_num}: {e}", file=sys.stderr)
-
-    with open(args.output, "w") as f:
-        json.dump({
-            "org": args.org,
-            "repo": args.repo,
-            "timestamp": datetime.now(timezone.utc).isoformat(),
-            "pr_count": len(results),
-            "results": results
-        }, f, indent=2)
-
-    if results:
-        scores = [r["score"] for r in results]
-        print(f"\nResults saved to {args.output}")
-        print(f"Summary: {len(results)} PRs, scores range {min(scores):.0f}-{max(scores):.0f}")
-    else:
-        print("\nNo results to save.")
-
-
-if __name__ == "__main__":
-    main()

scripts/test_pr_complexity_scorer.py

@@ -1,170 +0,0 @@
-#!/usr/bin/env python3
-"""
-Tests for PR Complexity Scorer — unit tests for the scoring logic.
-"""
-
-import sys
-from pathlib import Path
-
-sys.path.insert(0, str(Path(__file__).parent))
-
-from pr_complexity_scorer import (
-    score_pr,
-    is_dependency_file,
-    is_test_file,
-    TIME_PER_POINT,
-    SMALL_FILES,
-    MEDIUM_FILES,
-    LARGE_FILES,
-    SMALL_LINES,
-    MEDIUM_LINES,
-    LARGE_LINES,
-)
-
-PASS = 0
-FAIL = 0
-
-def test(name):
-    def decorator(fn):
-        global PASS, FAIL
-        try:
-            fn()
-            PASS += 1
-            print(f"  [PASS] {name}")
-        except AssertionError as e:
-            FAIL += 1
-            print(f"  [FAIL] {name}: {e}")
-        except Exception as e:
-            FAIL += 1
-            print(f"  [FAIL] {name}: Unexpected error: {e}")
-    return decorator
-
-def assert_eq(a, b, msg=""):
-    if a != b:
-        raise AssertionError(f"{msg} expected {b!r}, got {a!r}")
-
-def assert_true(v, msg=""):
-    if not v:
-        raise AssertionError(msg or "Expected True")
-
-def assert_false(v, msg=""):
-    if v:
-        raise AssertionError(msg or "Expected False")
-
-
-print("=== PR Complexity Scorer Tests ===\n")
-
-print("-- File Classification --")
-
-@test("dependency file detection — requirements.txt")
-def _():
-    assert_true(is_dependency_file("requirements.txt"))
-    assert_true(is_dependency_file("src/requirements.txt"))
-    assert_false(is_dependency_file("requirements_test.txt"))
-
-@test("dependency file detection — pyproject.toml")
-def _():
-    assert_true(is_dependency_file("pyproject.toml"))
-    assert_false(is_dependency_file("myproject.py"))
-
-@test("test file detection — pytest style")
-def _():
-    assert_true(is_test_file("tests/test_api.py"))
-    assert_true(is_test_file("test_module.py"))
-    assert_true(is_test_file("src/module_test.py"))
-
-@test("test file detection — other frameworks")
-def _():
-    assert_true(is_test_file("spec/feature_spec.rb"))
-    assert_true(is_test_file("__tests__/component.test.js"))
-    assert_false(is_test_file("testfixtures/helper.py"))
-
-
-print("\n-- Scoring Logic --")
-
-@test("small PR gets low score (1-3)")
-def _():
-    score, minutes, _ = score_pr(
-        files_changed=3,
-        additions=50,
-        deletions=10,
-        has_dependency_changes=False,
-        test_coverage_delta=None
-    )
-    assert_true(1 <= score <= 3, f"Score should be low, got {score}")
-    assert_true(minutes < 20)
-
-@test("medium PR gets medium score (4-6)")
-def _():
-    score, minutes, _ = score_pr(
-        files_changed=15,
-        additions=400,
-        deletions=100,
-        has_dependency_changes=False,
-        test_coverage_delta=None
-    )
-    assert_true(4 <= score <= 6, f"Score should be medium, got {score}")
-    assert_true(20 <= minutes <= 45)
-
-@test("large PR gets high score (7-9)")
-def _():
-    score, minutes, _ = score_pr(
-        files_changed=60,
-        additions=3000,
-        deletions=1500,
-        has_dependency_changes=True,
-        test_coverage_delta=None
-    )
-    assert_true(7 <= score <= 9, f"Score should be high, got {score}")
-    assert_true(minutes >= 45)
-
-@test("dependency changes boost score")
-def _():
-    base_score, _, _ = score_pr(
-        files_changed=10, additions=200, deletions=50,
-        has_dependency_changes=False, test_coverage_delta=None
-    )
-    dep_score, _, _ = score_pr(
-        files_changed=10, additions=200, deletions=50,
-        has_dependency_changes=True, test_coverage_delta=None
-    )
-    assert_true(dep_score > base_score, f"Deps: {base_score} -> {dep_score}")
-
-@test("adding tests lowers complexity")
-def _():
-    base_score, _, _ = score_pr(
-        files_changed=8, additions=150, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=None
-    )
-    better_score, _, _ = score_pr(
-        files_changed=8, additions=180, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=3
-    )
-    assert_true(better_score < base_score, f"Tests: {base_score} -> {better_score}")
-
-@test("removing tests increases complexity")
-def _():
-    base_score, _, _ = score_pr(
-        files_changed=8, additions=150, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=None
-    )
-    worse_score, _, _ = score_pr(
-        files_changed=8, additions=150, deletions=20,
-        has_dependency_changes=False, test_coverage_delta=-2
-    )
-    assert_true(worse_score > base_score, f"Remove tests: {base_score} -> {worse_score}")
-
-@test("score bounded 1-10")
-def _():
-    for files, adds, dels in [(1, 10, 5), (100, 10000, 5000)]:
-        score, _, _ = score_pr(files, adds, dels, False, None)
-        assert_true(1 <= score <= 10, f"Score {score} out of range")
-
-@test("estimated minutes exist for all scores")
-def _():
-    for s in range(1, 11):
-        assert_true(s in TIME_PER_POINT, f"Missing time for score {s}")
-
-
-print(f"\n=== Results: {PASS} passed, {FAIL} failed ===")
-sys.exit(0 if FAIL == 0 else 1)