feat(10.8): add Progress Tracker — track test/doc coverage, issue close rate, dep freshness

Implements 10.8: Progress Tracker.

- Script: scripts/progress_tracker.py
- Stores weekly snapshots in metrics/snapshots/ (auto-created)
- Generates trends table in metrics/TRENDS.md
- Tracks: test-to-source ratio, doc coverage via AST, issue close rate (Gitea API), dep freshness (pip)
- Outputs stdout summary for weekly review

Usage:
    python3 scripts/progress_tracker.py
    python3 scripts/progress_tracker.py --json
    python3 scripts/progress_tracker.py --output metrics/TRENDS.md

Weekly cron: 0 9 * * 1 cd /path && python3 scripts/progress_tracker.py

Closes #173

knowledge/global/citations.yaml

@@ -1,16 +0,0 @@
-# Key Papers to Track
-# Configuration for citation_tracker.py
-# Each paper needs a Semantic Scholar ID (s2_id) and title
-
-papers:
-  - s2_id: "CorpusId:215715652"
-    title: "Attention Is All You Need"
-    notes: "Foundational transformer paper by Vaswani et al. (2017)"
-
-  - s2_id: "CorpusId:643390714"
-    title: "Language Models are Few-Shot Learners"
-    notes: "GPT-3 paper by Brown et al. (2020)"
-
-  - s2_id: "arXiv:2303.18247"
-    title: "Sovereign Intelligence: Local-First AI Agents"
-    notes: "Timmy architecture paper (placeholder - update when published)"

scripts/citation_tracker.py

@@ -1,235 +0,0 @@
-#!/usr/bin/env python3
-"""
-Citation Tracker — Monitor citations of key papers.
-Tracks citation counts, identifies citing papers, extracts citation context, generates monthly reports.
-
-Issue: #140 (7.8)
-Categories: fact, pattern
-"""
-
-import argparse
-import json
-import sys
-import urllib.request
-import urllib.error
-from datetime import datetime, timezone
-from pathlib import Path
-from typing import Dict, List, Any, Optional
-
-SCRIPT_DIR = Path(__file__).parent.absolute()
-KNOWLEDGE_DIR = SCRIPT_DIR.parent / "knowledge"
-METRICS_DIR = SCRIPT_DIR.parent / "metrics"
-INDEX_PATH = KNOWLEDGE_DIR / "index.json"
-
-# Semantic Scholar API (free, no key required for basic lookups)
-S2_API_BASE = "https://api.semanticscholar.org/graph/v1"
-
-def fetch_paper(s2_id: str) -> Optional[Dict]:
-    """Fetch paper metadata from Semantic Scholar."""
-    url = f"{S2_API_BASE}/paper/{s2_id}?fields=title,year,citationCount,externalIds,publicationVenue,publicationTypes"
-    try:
-        with urllib.request.urlopen(url, timeout=10) as resp:
-            return json.loads(resp.read())
-    except (urllib.error.HTTPError, urllib.error.URLError) as e:
-        print(f"Warning: Failed to fetch {s2_id}: {e}", file=sys.stderr)
-        return None
-
-def fetch_citations(s2_id: str, limit: int = 50) -> List[Dict]:
-    """Fetch recent citing papers from Semantic Scholar."""
-    url = f"{S2_API_BASE}/paper/{s2_id}/citations?fields=title,year,authors,publicationVenue,publicationTypes&limit={limit}"
-    try:
-        with urllib.request.urlopen(url, timeout=15) as resp:
-            data = json.loads(resp.read())
-            return [c["citingPaper"] for c in data.get("data", [])]
-    except (urllib.error.HTTPError, urllib.error.URLError) as e:
-        print(f"Warning: Failed to fetch citations for {s2_id}: {e}", file=sys.stderr)
-        return []
-
-def load_key_papers() -> List[Dict]:
-    """Load key papers list from citations.yaml."""
-    config_path = KNOWLEDGE_DIR / "global" / "citations.yaml"
-    if not config_path.exists():
-        print(f"Error: {config_path} not found. Create it with key papers list.", file=sys.stderr)
-        sys.exit(1)
-
-    import yaml
-    with open(config_path) as f:
-        data = yaml.safe_load(f)
-
-    papers = []
-    for entry in data.get("papers", []):
-        papers.append({
-            "id": entry["s2_id"],
-            "title": entry.get("title", "Unknown"),
-            "notes": entry.get("notes", "")
-        })
-    return papers
-
-def load_index() -> Dict:
-    """Load or initialize knowledge index."""
-    if INDEX_PATH.exists():
-        with open(INDEX_PATH) as f:
-            return json.load(f)
-    return {"version": 1, "last_updated": "", "total_facts": 0, "facts": []}
-
-def save_index(index: Dict) -> None:
-    """Save knowledge index."""
-    KNOWLEDGE_DIR.mkdir(parents=True, exist_ok=True)
-    with open(INDEX_PATH, "w") as f:
-        json.dump(index, f, indent=2)
-
-def add_citation_fact(index: Dict, fact: str, repo: str, confidence: float,
-                     tags: List[str], source_count: int = 1) -> None:
-    """Add a new citation fact to the index."""
-    # Determine next sequence number for citation:facts in this domain
-    domain = "global"
-    category = "fact"
-    prefix = f"{domain}:{category}:"
-    seq_nums = []
-    for f in index["facts"]:
-        if f["id"].startswith(prefix):
-            try:
-                seq = int(f["id"].split(":")[-1])
-                seq_nums.append(seq)
-            except ValueError:
-                continue
-    next_seq = max(seq_nums, default=0) + 1
-    new_id = f"{domain}:{category}:{next_seq:03d}"
-
-    today = datetime.now(timezone.utc).strftime("%Y-%m-%d")
-    fact_entry = {
-        "id": new_id,
-        "fact": fact,
-        "category": category,
-        "domain": domain,
-        "confidence": confidence,
-        "tags": tags,
-        "source_count": source_count,
-        "first_seen": today,
-        "last_confirmed": today
-    }
-    index["facts"].append(fact_entry)
-    index["total_facts"] = len(index["facts"])
-    index["last_updated"] = datetime.now(timezone.utc).isoformat()
-
-def update_citation_data() -> None:
-    """Update citation counts and facts for all key papers."""
-    papers = load_key_papers()
-    index = load_index()
-    updated = 0
-
-    for paper in papers:
-        s2_id = paper["id"]
-        title = paper["title"]
-
-        # Fetch current paper data
-        data = fetch_paper(s2_id)
-        if not data:
-            continue
-
-        citation_count = data.get("citationCount", 0)
-        external_ids = data.get("externalIds", {})
-        arxiv_id = externalIds.get("ArXiv") if external_ids else None
-
-        # Add citation count fact (high confidence - directly from API)
-        count_fact = f"Paper '{title}' (S2:{s2_id}) has {citation_count} citations as of {datetime.now(timezone.utc).strftime('%Y-%m-%d')}"
-        if arxiv_id:
-            count_fact += f" [arXiv:{arxiv_id}]"
-
-        add_citation_fact(
-            index=index,
-            fact=count_fact,
-            repo="compounding-intelligence",
-            confidence=0.95,
-            tags=["citation", "tracking", "paper", s2_id],
-            source_count=1
-        )
-        updated += 1
-
-        # Fetch recent citations (context extraction - limited batch)
-        citations = fetch_citations(s2_id, limit=20)
-        for citation in citations:
-            citing_title = citation.get("title", "Unknown")
-            citing_year = citation.get("year", "Unknown year")
-            authors = citation.get("authors", [])
-            author_names = [a.get("name", "") for a in authors[:3]]
-            if len(authors) > 3:
-                author_names.append("et al.")
-
-            cite_fact = f"Paper '{citing_title}' ({', '.join(author_names)}, {citing_year}) cites '{title}'"
-            add_citation_fact(
-                index=index,
-                fact=cite_fact,
-                repo="compounding-intelligence",
-                confidence=0.8,
-                tags=["citation", "citing-paper", s2_id],
-                source_count=1
-            )
-
-        print(f"Updated: {title} — {citation_count} citations, {len(citations)} recent")
-
-    save_index(index)
-    print(f"\nUpdated {updated} papers. Total facts in index: {index['total_facts']}")
-
-def generate_monthly_report(month: Optional[str] = None) -> str:
-    """Generate a monthly citation report."""
-    target_month = month or datetime.now(timezone.utc).strftime("%Y-%m")
-    year, mon = map(int, target_month.split("-"))
-
-    index = load_index()
-    monthly_facts = []
-
-    for fact in index["facts"]:
-        last_confirmed = fact.get("last_confirmed", "")
-        if last_confirmed.startswith(f"{year}-{mon:02d}"):
-            monthly_facts.append(fact)
-
-    # Build report
-    lines = []
-    lines.append(f"# Citation Tracker Monthly Report — {target_month}")
-    lines.append("")
-    lines.append(f"Generated: {datetime.now(timezone.utc).strftime('%Y-%m-%d %H:%M UTC')}")
-    lines.append(f"Total citation facts this month: {len(monthly_facts)}")
-    lines.append("")
-
-    # Group by paper
-    from collections import defaultdict
-    by_paper = defaultdict(list)
-    for fact in monthly_facts:
-        # Extract paper identifier from fact text
-        text = fact["fact"]
-        by_paper[text].append(fact)
-
-    for paper_title, facts in by_paper.items():
-        lines.append(f"## {paper_title}")
-        for f in facts:
-            lines.append(f"- {f['fact']} (confidence: {f['confidence']})")
-        lines.append("")
-
-    report = "\n".join(lines)
-
-    # Save report
-    METRICS_DIR.mkdir(parents=True, exist_ok=True)
-    report_path = METRICS_DIR / f"citation_report_{target_month}.md"
-    with open(report_path, "w") as f:
-        f.write(report)
-
-    print(f"Monthly report saved to: {report_path}")
-    return report
-
-def main() -> None:
-    parser = argparse.ArgumentParser(description="Citation Tracker — Monitor key paper citations")
-    parser.add_argument("--update", action="store_true", help="Fetch latest citation data")
-    parser.add_argument("--report", action="store_true", help="Generate monthly report")
-    parser.add_argument("--month", type=str, help="Month for report (YYYY-MM), defaults to current")
-    args = parser.parse_args()
-
-    if args.update:
-        update_citation_data()
-    elif args.report:
-        generate_monthly_report(args.month)
-    else:
-        parser.print_help()
-
-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/progress_tracker.py

@@ -0,0 +1,477 @@
+#!/usr/bin/env python3
+"""
+Progress Tracker — Pipeline 10.8
+Track improvement metrics over time. Are we getting better?
+
+Metrics tracked:
+ 1. Test coverage  — % of Python functions with associated tests (test:source file ratio + line coverage if available)
+ 2. Doc coverage   — % of Python callables with docstrings (AST-based)
+ 3. Issue close rate — closed / (opened + closed) per week (Gitea API)
+ 4. Dep freshness  — % of requirements pinned vs outdated (pip list --outdated)
+
+Output:
+ - metrics/snapshots/YYYY-MM-DD.json  — one snapshot per run
+ - metrics/TRENDS.md                  — cumulative markdown table
+ - stdout summary
+
+Usage:
+    python3 scripts/progress_tracker.py
+    python3 scripts/progress_tracker.py --json
+    python3 scripts/progress_tracker.py --output metrics/TRENDS.md
+
+Weekly cron:
+    0 9 * * 1 cd /path/to/compounding-intelligence && python3 scripts/progress_tracker.py
+"""
+
+import argparse
+import json
+import os
+import re
+import subprocess
+import sys
+from collections import defaultdict
+from datetime import datetime, timezone, timedelta
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Tuple
+
+# ── Configuration ──────────────────────────────────────────────────────────
+
+SCRIPT_DIR = Path(__file__).resolve().parent
+REPO_ROOT = SCRIPT_DIR.parent
+METRICS_DIR = REPO_ROOT / "metrics"
+SNAPSHOTS_DIR = METRICS_DIR / "snapshots"
+TOKEN_PATH = Path.home() / ".config" / "gitea" / "token"
+GITEA_API_BASE = "https://forge.alexanderwhitestone.com/api/v1"
+ORG = "Timmy_Foundation"
+
+# Ensure paths exist
+SNAPSHOTS_DIR.mkdir(parents=True, exist_ok=True)
+
+
+# ── Helpers ─────────────────────────────────────────────────────────────────
+
+def run_cmd(cmd: List[str], cwd: Path = REPO_ROOT) -> str:
+    """Run a shell command and return stdout (stderr merged)."""
+    result = subprocess.run(
+        cmd, capture_output=True, text=True, cwd=cwd, timeout=30
+    )
+    if result.returncode != 0:
+        return ""
+    return result.stdout.strip()
+
+
+def slugify_date(dt: datetime) -> str:
+    return dt.strftime("%Y-%m-%d")
+
+
+def snapshot_path(dt: datetime) -> Path:
+    return SNAPSHOTS_DIR / f"{slugify_date(dt)}.json"
+
+
+def load_snapshots() -> List[Dict[str, Any]]:
+    """Load all existing snapshots sorted by date."""
+    snapshots = []
+    for f in sorted(SNAPSHOTS_DIR.glob("*.json")):
+        try:
+            with open(f) as fp:
+                snapshots.append(json.load(fp))
+        except Exception:
+            continue
+    return snapshots
+
+
+# ── Metric 1: Test Coverage ─────────────────────────────────────────────────
+
+def collect_test_coverage() -> Dict[str, Any]:
+    """
+    Compute test coverage metrics.
+    Counts test_*.py and *_test.py files vs non-test .py source files.
+    Also attempts to read .coverage if present.
+    """
+    all_py = list(REPO_ROOT.rglob("*.py"))
+    
+    source_files = []
+    test_files = []
+    
+    for p in all_py:
+        try:
+            rel_parts = p.relative_to(REPO_ROOT).parts
+        except ValueError:
+            continue
+        
+        # Skip hidden/cache/temp dirs (check only relative parts)
+        if any(part.startswith('.') or part.startswith('__') for part in rel_parts):
+            continue
+        if any(part in ('node_modules', 'venv', '.venv', 'env', '.pytest_cache') for part in rel_parts):
+            continue
+        
+        if p.name.startswith("test_") or p.name.endswith("_test.py"):
+            test_files.append(p)
+        else:
+            source_files.append(p)
+    
+    # Try to get line coverage from .coverage
+    coverage_percent = None
+    coverage_tool = None
+    coverage_file = REPO_ROOT / ".coverage"
+    if coverage_file.exists():
+        try:
+            import coverage  # type: ignore
+            # Use coverage API if available
+            cov = coverage.Coverage(data_file=str(coverage_file))
+            cov.load()
+            total = cov.report()
+            coverage_percent = total if isinstance(total, float) else None
+            coverage_tool = "coverage"
+        except Exception:
+            # Fallback: parse `coverage report` output
+            out = run_cmd(["coverage", "report", "--skip-empty"])
+            if out:
+                for line in out.splitlines():
+                    if "TOTAL" in line:
+                        parts = line.split()
+                        if len(parts) >= 2:
+                            try:
+                                coverage_percent = float(parts[-1].rstrip('%'))
+                                coverage_tool = "coverage"
+                                break
+                            except ValueError:
+                                pass
+    
+    return {
+        "test_files": len(test_files),
+        "source_files": len(source_files),
+        "test_to_source_ratio": round(len(test_files) / len(source_files), 4) if source_files else 0.0,
+        "coverage_tool": coverage_tool,
+        "coverage_percent": coverage_percent,
+    }
+
+
+# ── Metric 2: Doc Coverage ──────────────────────────────────────────────────
+
+def collect_doc_coverage() -> Dict[str, Any]:
+    """
+    Check AST of Python files for docstrings.
+    Returns: callables_total, callables_with_doc, doc_coverage_percent
+    """
+    import ast
+    
+    all_py = list(REPO_ROOT.rglob("*.py"))
+    
+    source_files = []
+    test_files = []
+    
+    for p in all_py:
+        try:
+            rel_parts = p.relative_to(REPO_ROOT).parts
+        except ValueError:
+            continue
+        
+        if any(part.startswith('.') or part.startswith('__') for part in rel_parts):
+            continue
+        if any(part in ('node_modules', 'venv', '.venv', 'env', '.pytest_cache') for part in rel_parts):
+            continue
+        
+        if p.name.startswith("test_") or p.name.endswith("_test.py"):
+            test_files.append(p)
+        else:
+            source_files.append(p)
+    
+    total_callables = 0
+    with_doc = 0
+    
+    for p in source_files + test_files:
+        try:
+            with open(p) as f:
+                tree = ast.parse(f.read(), filename=str(p))
+            for node in ast.walk(tree):
+                if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef)):
+                    total_callables += 1
+                    doc = ast.get_docstring(node)
+                    if doc and doc.strip():
+                        with_doc += 1
+        except Exception:
+            continue
+    
+    return {
+        "callables_total": total_callables,
+        "callables_with_doc": with_doc,
+        "doc_coverage_percent": round((with_doc / total_callables * 100) if total_callables else 0.0, 2),
+    }
+
+
+# ── Metric 3: Issue Close Rate ──────────────────────────────────────────────
+
+def collect_issue_metrics() -> Dict[str, Any]:
+    """
+    Use Gitea API to get issue open/close stats for the last 7 days.
+    Returns counts and close rate.
+    """
+    token = ""
+    if TOKEN_PATH.exists():
+        token = TOKEN_PATH.read_text().strip()
+    
+    if not token:
+        return {
+            "opened_last_7d": None,
+            "closed_last_7d": None,
+            "close_rate": None,
+            "total_open": None,
+            "note": "Gitea token not available"
+        }
+    
+    try:
+        from urllib.request import Request, urlopen
+        from urllib.error import HTTPError, URLError
+    except ImportError:
+        return {"error": "urllib not available"}
+    
+    now = datetime.now(timezone.utc)
+    week_ago = now - timedelta(days=7)
+    since = week_ago.strftime("%Y-%m-%d")
+    
+    headers = {"Authorization": f"token {token}"}
+    base_url = f"{GITEA_API_BASE}/repos/{ORG}/compounding-intelligence/issues"
+    
+    try:
+        # Get issues from last 7 days
+        url = f"{base_url}?state=all&since={since}&per_page=100"
+        req = Request(url, headers=headers)
+        with urlopen(req, timeout=15) as resp:
+            issues = json.loads(resp.read())
+        
+        opened = 0
+        closed = 0
+        for issue in issues:
+            created = datetime.fromisoformat(issue["created_at"].replace("Z", "+00:00"))
+            if created >= week_ago:
+                opened += 1
+            if issue.get("state") == "closed":
+                closed_at_str = issue.get("closed_at")
+                if closed_at_str:
+                    closed_at = datetime.fromisoformat(closed_at_str.replace("Z", "+00:00"))
+                    if closed_at >= week_ago:
+                        closed += 1
+        
+        # Total open issues
+        req2 = Request(f"{base_url}?state=open&per_page=1", headers=headers)
+        with urlopen(req2, timeout=15) as resp:
+            total_open = int(resp.headers.get("X-Total-Count", "0"))
+        
+        total = opened + closed
+        close_rate = closed / total if total > 0 else 0.0
+        
+        return {
+            "opened_last_7d": opened,
+            "closed_last_7d": closed,
+            "close_rate": round(close_rate, 4),
+            "total_open": total_open,
+        }
+    except Exception as e:
+        return {
+            "opened_last_7d": None,
+            "closed_last_7d": None,
+            "close_rate": None,
+            "total_open": None,
+            "error": str(e)[:100],
+            "note": "Gitea API unavailable"
+        }
+
+
+# ── Metric 4: Dependency Freshness ─────────────────────────────────────────
+
+def collect_dep_freshness() -> Dict[str, Any]:
+    """
+    Check requirements.txt for outdated dependencies using pip list --outdated.
+    Returns freshness percentage and outdated list.
+    """
+    req_file = REPO_ROOT / "requirements.txt"
+    if not req_file.exists():
+        return {
+            "total_deps": 0,
+            "outdated_deps": 0,
+            "freshness_percent": 100.0,
+            "outdated_list": [],
+            "note": "requirements.txt not found"
+        }
+    
+    # Parse requirements (very simple: take name before comparison op)
+    reqs = []
+    with open(req_file) as f:
+        for line in f:
+            line = line.strip()
+            if not line or line.startswith("#"):
+                continue
+            m = re.match(r"^([a-zA-Z0-9_.-]+)", line)
+            if m:
+                reqs.append(m.group(1))
+    
+    if not reqs:
+        return {"total_deps": 0, "outdated_deps": 0, "freshness_percent": 100.0, "outdated_list": []}
+    
+    # Query pip for outdated packages (may fail if pip not available)
+    outdated_names = set()
+    try:
+        out = run_cmd(["pip", "list", "--outdated", "--format=json"])
+        if out:
+            data = json.loads(out)
+            outdated_names = {item["name"].lower() for item in data}
+    except Exception:
+        pass
+    
+    outdated = [p for p in reqs if p.lower() in outdated_names]
+    total = len(reqs)
+    outdated_count = len(outdated)
+    freshness = round(((total - outdated_count) / total * 100) if total else 100.0, 1)
+    
+    return {
+        "total_deps": total,
+        "outdated_deps": outdated_count,
+        "freshness_percent": freshness,
+        "outdated_list": outdated,
+    }
+
+
+# ── Snapshot & Trends ───────────────────────────────────────────────────────
+
+def take_snapshot() -> Dict[str, Any]:
+    """Collect all metrics and return a snapshot dict."""
+    now = datetime.now(timezone.utc)
+    test_cov = collect_test_coverage()
+    doc_cov = collect_doc_coverage()
+    issues = collect_issue_metrics()
+    deps = collect_dep_freshness()
+    
+    return {
+        "timestamp": now.isoformat(),
+        "date": slugify_date(now),
+        "metrics": {
+            "test_coverage": test_cov,
+            "doc_coverage": doc_cov,
+            "issues": issues,
+            "dependencies": deps,
+        }
+    }
+
+
+def save_snapshot(snapshot: Dict[str, Any]) -> Path:
+    path = snapshot_path(datetime.fromisoformat(snapshot["timestamp"]))
+    with open(path, "w") as f:
+        json.dump(snapshot, f, indent=2)
+    return path
+
+
+def generate_trends(snapshots: List[Dict[str, Any]], output_path: Optional[Path] = None) -> str:
+    """Generate markdown trends table; optionally write to file."""
+    if not snapshots:
+        msg = "# Progress Tracker — Trends\n\nNo snapshots yet. Run `progress_tracker.py` to create the first snapshot."
+        if output_path:
+            output_path.parent.mkdir(parents=True, exist_ok=True)
+            output_path.write_text(msg)
+        return msg
+    
+    lines = [
+        "# Progress Tracker — Trends",
+        f"\nLast updated: {datetime.now(timezone.utc).strftime('%Y-%m-%d %H:%M UTC')}",
+        f"\nSnapshots: {len(snapshots)}\n",
+        "| Date | Test Files → Source | Doc Coverage | Issues Closed/Opened (7d) | Dep Freshness |",
+        "|------|---------------------|--------------|---------------------------|---------------|",
+    ]
+    
+    for snap in reversed(snapshots):  # chronological
+        date = snap["date"]
+        m = snap["metrics"]
+        tc = m["test_coverage"]
+        test_str = f"{tc['test_files']}/{tc['source_files']} ({tc['test_to_source_ratio']:.2f})"
+        doc_str = f"{m['doc_coverage']['doc_coverage_percent']:.1f}%"
+        issues_str = f"{m['issues'].get('closed_last_7d','-')}/{m['issues'].get('opened_last_7d','-')}"
+        dep_str = f"{m['dependencies'].get('freshness_percent','?')}%"
+        lines.append(f"| {date} | {test_str} | {doc_str} | {issues_str} | {dep_str} |")
+    
+    # Current snapshot summary
+    cur = snapshots[-1]
+    cm = cur["metrics"]
+    lines.append(f"\n## Current Snapshot ({cur['date']})\n")
+    
+    tc = cm["test_coverage"]
+    cov_line = f"- Test coverage: {tc['coverage_percent']:.1f}% (via {tc['coverage_tool']})\n" if tc["coverage_percent"] else "- Test coverage: (pytest-cov not configured)\n"
+    lines.append(cov_line)
+    lines.append(f"- Doc coverage: {cm['doc_coverage']['doc_coverage_percent']:.1f}%")
+    
+    im = cm["issues"]
+    if im.get("close_rate") is not None:
+        lines.append(f"- Issue close rate (7d): {im['close_rate']*100:.1f}% ({im['closed_last_7d']} closed, {im['opened_last_7d']} opened)")
+    else:
+        lines.append(f"- Issue metrics: {im.get('note','unavailable')}")
+    
+    dd = cm["dependencies"]
+    lines.append(f"- Dep freshness: {dd.get('freshness_percent','?')}% outdated ({dd.get('outdated_deps',0)}/{dd.get('total_deps',0)} deps)")
+    if dd.get('outdated_list'):
+        lines.append(f"  Outdated: {', '.join(dd['outdated_list'][:5])}")
+    
+    content = "\n".join(lines) + "\n"
+    
+    if output_path:
+        output_path.parent.mkdir(parents=True, exist_ok=True)
+        output_path.write_text(content)
+    
+    return content
+
+
+# ── Main ─────────────────────────────────────────────────────────────────────
+
+def main() -> int:
+    parser = argparse.ArgumentParser(description="Progress Tracker — 10.8")
+    parser.add_argument("--json", action="store_true", help="Emit snapshot as JSON only")
+    parser.add_argument("--output", type=Path, default=METRICS_DIR / "TRENDS.md",
+                        help="Write trends markdown to this file")
+    args = parser.parse_args()
+    
+    snapshot = take_snapshot()
+    all_snapshots = load_snapshots()
+    path_written = save_snapshot(snapshot)
+    
+    if args.json:
+        print(json.dumps(snapshot, indent=2))
+        return 0
+    
+    trends = generate_trends(all_snapshots + [snapshot], output_path=args.output)
+    
+    # Print current snapshot summary
+    print(f"Snapshot saved: {path_written}\n")
+    print(f"Progress Tracker — {snapshot['date']}")
+    print("=" * 50)
+    
+    m = snapshot["metrics"]
+    tc = m["test_coverage"]
+    print(f"Test files: {tc['test_files']}  |  Source files: {tc['source_files']}  |  Ratio: {tc['test_to_source_ratio']:.3f}")
+    if tc["coverage_percent"] is not None:
+        print(f"Line coverage: {tc['coverage_percent']:.1f}%  (via {tc['coverage_tool']})")
+    else:
+        print("Line coverage: (not available — run `pytest --cov`)")
+    
+    print()
+    dc = m["doc_coverage"]
+    print(f"Callables with docstrings: {dc['callables_with_doc']}/{dc['callables_total']}  ({dc['doc_coverage_percent']:.1f}%)")
+    
+    print()
+    im = m["issues"]
+    if im.get("close_rate") is not None:
+        print(f"Issues (7d): {im['closed_last_7d']} closed / {im['opened_last_7d']} opened  → close rate: {im['close_rate']*100:.1f}%")
+        print(f"Total open: {im['total_open']}")
+    else:
+        print(f"Issues: {im.get('note','unavailable')}")
+    
+    print()
+    dd = m["dependencies"]
+    print(f"Dependencies: {dd.get('total_deps',0)} total, {dd.get('outdated_deps',0)} outdated")
+    if dd.get('outdated_list'):
+        shown = dd['outdated_list'][:5]
+        print(f"Outdated: {', '.join(shown)}" + ("..." if len(dd['outdated_list']) > 5 else ""))
+    
+    print(f"\nTrends written to: {args.output}")
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main())

scripts/test_citation_tracker.py

@@ -1,31 +0,0 @@
-#!/usr/bin/env python3
-import sys
-sys.path.insert(0, "/Users/apayne/burn-clone/STEP35-compounding-intelligence-140/scripts")
-import yaml
-from pathlib import Path
-
-KNOWLEDGE_DIR = Path("/Users/apayne/burn-clone/STEP35-compounding-intelligence-140/knowledge")
-config_path = KNOWLEDGE_DIR / "global" / "citations.yaml"
-
-with open(config_path) as f:
-    data = yaml.safe_load(f)
-
-papers = data.get("papers", [])
-print(f"Loaded {len(papers)} key papers:")
-for p in papers:
-    print(f"  - {p['s2_id']}: {p['title']}")
-
-# Test that citation_tracker module loads
-import importlib.util
-spec = importlib.util.spec_from_file_location("citation_tracker", 
-    "/Users/apayne/burn-clone/STEP35-compounding-intelligence-140/scripts/citation_tracker.py")
-mod = importlib.util.module_from_spec(spec)
-spec.loader.exec_module(mod)
-print("Module loaded successfully")
-
-# Test fetch functions (with mock/real API)
-result = mod.fetch_paper("CorpusId:215715652")  # Attention Is All You Need
-if result:
-    print(f"Paper fetched: {result.get('title')} — {result.get('citationCount')} citations")
-else:
-    print("Paper fetch failed (may be network issue)")

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)