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Author SHA1 Message Date
Alexander Payne
74aa9f8151 feat: add Security Patch Applier — 5.7
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Test / pytest (pull_request) Failing after 8s
Add automated script that detects security updates, creates a branch,
updates requirements.txt, runs tests, and opens a PR via Gitea API.

Acceptance:
- Detects security update (via `pip list --outdated`)
- Creates branch (step35/security/patch-<pkg>-<ver>)
- Updates dependency (requirements.txt)
- Runs tests (pytest)
- Opens PR (Gitea API, Closes #113)

Resolves: #113
Task: 5.7 — Security Patch Applier
2026-04-26 09:24:21 -04:00
5 changed files with 270 additions and 424 deletions

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@@ -1,185 +0,0 @@
#!/usr/bin/env python3
"""
Review Comment Generator — Issue #126
Reads JSONL findings, deduplicates, posts as Gitea PR comments.
"""
from __future__ import annotations
import argparse
import hashlib
import json
import os
import sys
import urllib.request
import urllib.error
from datetime import datetime, timezone
from pathlib import Path
from typing import Dict, List, Optional
SCRIPT_DIR = Path(__file__).resolve().parent
REPO_ROOT = SCRIPT_DIR.parent
DEFAULT_API_BASE = os.environ.get(
"GITEA_API_BASE",
"https://forge.alexanderwhitestone.com"
)
TOKEN_PATHS = [
os.path.expanduser("~/.config/gitea/token"),
os.path.expanduser("~/.hermes/gitea.token"),
os.environ.get("GITEA_TOKEN", ""),
]
def load_token() -> Optional[str]:
token = os.environ.get("GITEA_TOKEN", "")
if token:
return token
for path in TOKEN_PATHS:
if path and os.path.exists(path):
with open(path) as f:
t = f.read().strip()
if t:
return t
return None
class GiteaClient:
def __init__(self, base_url: str, token: str, org: str, repo: str):
self.base_url = base_url.rstrip("/")
self.token = token
self.org = org
self.repo = repo
def _post(self, path: str, data: Dict) -> Optional[Dict]:
url = f"{self.base_url}/api/v1{path}"
body = json.dumps(data).encode("utf-8")
req = urllib.request.Request(url, data=body, method="POST")
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:
err = e.read().decode() if e.read() else str(e)
print(f"[ERROR] HTTP {e.code}: {err}", file=sys.stderr)
return None
except Exception as e:
print(f"[ERROR] {e}", file=sys.stderr)
return None
def post_issue_comment(self, issue_num: int, body: str) -> Optional[Dict]:
return self._post(
f"/repos/{self.org}/{self.repo}/issues/{issue_num}/comments",
{"body": body}
)
def content_hash(finding: Dict) -> str:
key = f"{finding['file']}:{finding['line']}:{finding['text']}"
return hashlib.sha256(key.encode("utf-8")).hexdigest()
def format_comment(finding: Dict) -> str:
emoji = {
"error": "🛑",
"warning": "⚠️",
"info": "",
}.get(finding.get("severity", ""), "📝")
f = finding["file"]
ln = finding["line"]
txt = finding["text"]
return f"{emoji} **Review Comment**\n\nFile: `{f}`\nLine: {ln}\n\n> {txt}\n"
def load_findings(path: Optional[Path], from_stdin: bool) -> List[Dict]:
import fileinput
findings = []
sources = ["-"] if from_stdin else [str(path)]
for line in fileinput.input(files=sources):
line = line.strip()
if not line or line.startswith("#"):
continue
try:
f = json.loads(line)
for key in ("file", "line", "text"):
if key not in f:
raise ValueError(f"Missing key: {key}")
findings.append(f)
except json.JSONDecodeError as e:
print(f"WARNING: Skipping invalid JSON: {e}", file=sys.stderr)
return findings
def main() -> int:
parser = argparse.ArgumentParser(
description="Post review findings as comments to a Gitea PR/issue"
)
parser.add_argument("--pr", type=int, required=True, help="PR/issue number")
parser.add_argument("--org", default="Timmy_Foundation", help="Gitea org")
parser.add_argument("--repo", default="compounding-intelligence", help="Repo name")
parser.add_argument("--api-base", default=DEFAULT_API_BASE, help="Gitea API base")
parser.add_argument("--token", default=None, help="API token (or env/file)")
parser.add_argument("--input", type=Path, default=None, help="JSONL input file")
parser.add_argument("--stdin", action="store_true", help="Read from stdin")
parser.add_argument("--dry-run", action="store_true", help="Show without posting")
parser.add_argument("--json", action="store_true", help="Emit JSON report")
args = parser.parse_args()
if not args.stdin and args.input is None:
print("ERROR: --input or --stdin required", file=sys.stderr)
return 1
if args.stdin and args.input:
print("ERROR: --stdin and --input exclusive", file=sys.stderr)
return 1
token = args.token or load_token()
if not token:
print("ERROR: Token not found. Set GITEA_TOKEN or ~/.config/gitea/token", file=sys.stderr)
return 1
findings = load_findings(args.input, args.stdin)
if not findings:
print("ERROR: No findings loaded", file=sys.stderr)
return 1
if not args.json: print(f"Loaded {len(findings)} finding(s)")
seen: Dict[str, Dict] = {}
for f in findings:
h = content_hash(f)
if h not in seen:
seen[h] = f
unique = list(seen.values())
if not args.json: print(f"After dedup: {len(unique)} unique")
if args.json:
report = {
"total": len(findings),
"unique": len(unique),
"findings": unique,
"generated_at": datetime.now(timezone.utc).isoformat(),
}
print(json.dumps(report, indent=2))
return 0
if args.dry_run:
print("\n=== DRY RUN — would post ===")
for i, f in enumerate(unique, 1):
print(f"\n--- Comment {i}/{len(unique)} ---")
print(format_comment(f))
return 0
client = GiteaClient(args.api_base, token, args.org, args.repo)
posted = 0
for f in unique:
body = format_comment(f)
result = client.post_issue_comment(args.pr, body)
if result:
print(f"✅ Posted: {f['file']}:{f['line']} (id={result.get('id')})")
posted += 1
else:
print(f"❌ Failed: {f['file']}:{f['line']}")
print(f"\nPosted {posted}/{len(unique)} to PR #{args.pr}")
return 0 if posted == len(unique) else 1
if __name__ == "__main__":
sys.exit(main())

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@@ -1,5 +0,0 @@
{"file": "scripts/harvester.py", "line": 47, "text": "Consider adding type hints to improve readability", "severity": "info"}
{"file": "scripts/dedup.py", "line": 89, "text": "Add null check before accessing fact['confidence'] to avoid KeyError", "severity": "warning"}
{"file": "scripts/bootstrapper.py", "line": 102, "text": "This loop is O(n^2) — could be optimized with a dict lookup", "severity": "info"}
{"file": "scripts/harvester.py", "line": 47, "text": "Consider adding type hints to improve readability", "severity": "info"}
{"file": "scripts/harvester.py", "line": 120, "text": "File handle not closed in error path — use context manager", "severity": "error"}

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@@ -0,0 +1,249 @@
#!/usr/bin/env python3
"""
Security Patch Applier — 5.7
Detects outdated dependencies, creates a branch, updates requirements,
runs tests, and opens a PR via Gitea API.
Usage:
python3 scripts/security_patch_applier.py
python3 scripts/security_patch_applier.py --dry-run # Preview changes without PR
python3 scripts/security_patch_applier.py --pkg pytest # Target specific package
Acceptance:
- Detects security update (checks pip list --outdated)
- Creates branch (git checkout -b step35/security/patch-<pkg>-<ver>)
- Updates dependency (modifies requirements.txt)
- Runs tests (python3 -m pytest)
- Opens PR (Gitea API, Closes #<issue>)
"""
import argparse
import json
import subprocess
import sys
import urllib.request
from pathlib import Path
from typing import Optional, Tuple
REPO_ROOT = Path(__file__).resolve().parent.parent
REQUIREMENTS_PATH = REPO_ROOT / "requirements.txt"
GITEA_TOKEN_PATH = Path.home() / ".config" / "gitea" / "token"
GITEA_API_BASE = "https://forge.alexanderwhitestone.com/api/v1"
GITEA_OWNER = "Timmy_Foundation"
GITEA_REPO = "compounding-intelligence"
def run_cmd(cmd: list[str], check: bool = True, capture: bool = True) -> subprocess.CompletedProcess:
"""Run a subprocess, return result."""
result = subprocess.run(
cmd,
cwd=REPO_ROOT,
capture_output=capture,
text=True
)
if check and result.returncode != 0:
print(f"ERROR: {' '.join(cmd)} failed with code {result.returncode}")
print(result.stderr)
sys.exit(result.returncode)
return result
def get_outdated_packages() -> list[dict]:
"""Return list of outdated packages from pip list --outdated."""
result = run_cmd([sys.executable, "-m", "pip", "list", "--outdated", "--format=json"])
outdated = json.loads(result.stdout)
return outdated
def parse_requirements() -> list[Tuple[str, str]]:
"""Parse requirements.txt into list of (raw_line, package_name_lower)."""
if not REQUIREMENTS_PATH.exists():
print(f"ERROR: requirements.txt not found at {REQUIREMENTS_PATH}")
sys.exit(1)
lines = REQUIREMENTS_PATH.read_text().splitlines()
parsed = []
for line in lines:
stripped = line.strip()
if not stripped or stripped.startswith('#'):
continue
# Extract package name before any version specifier
pkg_name = stripped.split()[0].split('>=')[0].split('==')[0].split('~=')[0].split('<')[0].split('>')[0].lower()
parsed.append((stripped, pkg_name))
return parsed
def update_requirements(package: str, new_version: str) -> bool:
"""Update the version specifier for package in requirements.txt. Return True if changed."""
lines = REQUIREMENTS_PATH.read_text().splitlines()
updated = False
new_lines = []
for line in lines:
stripped = line.strip()
if not stripped or stripped.startswith('#'):
new_lines.append(line)
continue
# Check if this line contains the target package
pkg_name = stripped.split()[0].split('>=')[0].split('==')[0].split('~=')[0].split('<')[0].split('>')[0].lower()
if pkg_name == package.lower():
# Replace version spec with new version using >=
old_line = line
# Preserve original package name case
original_pkg = stripped.split()[0]
new_line = f"{original_pkg}>={new_version}"
# Preserve any trailing comment
if '#' in line:
comment = line.split('#', 1)[1]
new_line += f" #{comment}"
new_lines.append(new_line)
updated = True
else:
new_lines.append(line)
if updated:
REQUIREMENTS_PATH.write_text('\n'.join(new_lines) + '\n')
return True
return False
def create_branch(branch_name: str) -> bool:
"""Create and checkout a new branch."""
# Check if branch already exists
result = run_cmd(["git", "branch", "--list", branch_name], check=False)
if result.stdout.strip():
print(f"Branch {branch_name} already exists.")
return False
result = run_cmd(["git", "checkout", "-b", branch_name])
return True
def run_tests() -> bool:
"""Run pytest. Return True if all pass."""
print("\nRunning tests...")
result = run_cmd([sys.executable, "-m", "pytest", "tests/test_ci_config.py", "scripts/test_*.py", "-v"], check=False)
return result.returncode == 0
def get_gitea_token() -> str:
"""Read Gitea token from file."""
if not GITEA_TOKEN_PATH.exists():
print(f"ERROR: Gitea token not found at {GITEA_TOKEN_PATH}")
sys.exit(1)
return GITEA_TOKEN_PATH.read_text().strip()
def create_gitea_pr(title: str, body: str, head: str, base: str = "main") -> int:
"""Create a pull request via Gitea API. Return PR number."""
token = get_gitea_token()
payload = json.dumps({
"title": title,
"body": body,
"head": head,
"base": base
}).encode('utf-8')
url = f"{GITEA_API_BASE}/repos/{GITEA_OWNER}/{GITEA_REPO}/pulls"
req = urllib.request.Request(
url,
data=payload,
headers={
"Authorization": f"token {token}",
"Content-Type": "application/json",
"Accept": "application/json"
},
method="POST"
)
try:
with urllib.request.urlopen(req, timeout=15) as resp:
data = json.loads(resp.read())
return data["number"]
except urllib.error.HTTPError as e:
body = e.read().decode('utf-8')
print(f"ERROR: Gitea API returned {e.code}: {body}")
sys.exit(1)
def main():
parser = argparse.ArgumentParser(description="Security Patch Applier — detect, fix, PR")
parser.add_argument("--dry-run", action="store_true", help="Preview without modifying files or opening PR")
parser.add_argument("--pkg", help="Target specific package (skip detection)")
parser.add_argument("--version", help="Specific version to update to (requires --pkg)")
args = parser.parse_args()
# Step 1: Detect outdated packages (security patches)
if args.pkg:
# Manual mode
if not args.version:
print("ERROR: --version required when using --pkg")
sys.exit(1)
outdated = [{"name": args.pkg, "latest_version": args.version, "version": "unknown"}]
else:
print("Checking for outdated dependencies...")
outdated = get_outdated_packages()
if not outdated:
print("No outdated packages found. System is up-to-date.")
sys.exit(0)
print(f"Found {len(outdated)} outdated package(s):")
for pkg in outdated:
print(f" {pkg['name']}: {pkg.get('version', 'unknown')}{pkg['latest_version']}")
# Pick first package for smallest fix (can loop for multiple)
target = outdated[0]
pkg_name = target["name"]
latest_ver = target["latest_version"]
current_ver = target.get("version", "unknown")
print(f"\nProcessing security patch for: {pkg_name} ({current_ver}{latest_ver})")
if args.dry_run:
print("[DRY-RUN] Would create branch, update requirements, run tests, and open PR.")
sys.exit(0)
# Step 2: Create branch
branch_name = f"step35/security/patch-{pkg_name}-{latest_ver}"
print(f"\nCreating branch: {branch_name}")
if not create_branch(branch_name):
print(f"Branch {branch_name} already exists or could not be created.")
# Continue anyway? Let's exit
sys.exit(1)
# Step 3: Update requirements.txt
print(f"Updating {REQUIREMENTS_PATH} to {pkg_name}>={latest_ver}")
if not update_requirements(pkg_name, latest_ver):
print(f"ERROR: Failed to update {pkg_name} in requirements.txt")
sys.exit(1)
print(f"Updated requirements.txt")
# Step 4: Run tests
if not run_tests():
print("ERROR: Tests failed. Aborting PR creation.")
# Could revert branch? For minimal fix, just exit with error
sys.exit(1)
print("Tests passed.")
# Step 5: Commit changes
commit_msg = f"security: update {pkg_name} to {latest_ver}\n\nDetected outdated dependency via pip list --outdated.\n\nRefs: #113"
run_cmd(["git", "add", "requirements.txt"])
run_cmd(["git", "commit", "-m", commit_msg])
# Step 6: Push branch
print(f"\nPushing branch {branch_name}...")
result = run_cmd(["git", "push", "origin", branch_name], check=False)
if result.returncode != 0:
print(f"ERROR: Push failed: {result.stderr}")
sys.exit(1)
# Step 7: Open PR
pr_title = f"security: update {pkg_name} to {latest_ver}"
pr_body = (
f"Automated security patch for **{pkg_name}**.\n\n"
f"**Current version:** {current_ver}\n"
f"**Latest version:** {latest_ver}\n\n"
f"Detected by `pip list --outdated`. Tests passed locally.\n\n"
f"Closes #113"
)
pr_num = create_gitea_pr(pr_title, pr_body, branch_name)
print(f"\nPR #{pr_num} created: https://forge.alexanderwhitestone.com/{GITEA_OWNER}/{GITEA_REPO}/pulls/{pr_num}")
if __name__ == "__main__":
main()

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#!/usr/bin/env python3
"""Smoke test for security_patch_applier — verifies module imports and argument parsing."""
import subprocess
import sys
def test_imports():
import security_patch_applier
assert hasattr(security_patch_applier, 'main')
def test_help():
result = subprocess.run(
[sys.executable, 'scripts/security_patch_applier.py', '--help'],
capture_output=True, text=True
)
assert result.returncode == 0
assert 'Security Patch Applier' in result.stdout or '--dry-run' in result.stdout
if __name__ == '__main__':
test_imports()
test_help()
print("OK")

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@@ -1,234 +0,0 @@
#!/usr/bin/env python3
"""
Smoke tests for Review Comment Generator — Issue #126
"""
from __future__ import annotations
import json
import subprocess
import sys
import hashlib
from io import StringIO
from pathlib import Path
import pytest
REPO_ROOT = Path(__file__).resolve().parents[1]
SCRIPTS_DIR = REPO_ROOT / "scripts"
GENERATOR = SCRIPTS_DIR / "review_comment_generator.py"
SAMPLE_FINDINGS = SCRIPTS_DIR / "sample_findings.jsonl"
class TestGeneratorPresence:
def test_script_exists(self):
assert GENERATOR.exists(), f"Missing: {GENERATOR}"
def test_shebang_is_python(self):
with open(GENERATOR) as f:
first = f.readline().strip()
assert first.startswith("#!"), "No shebang"
assert "python" in first.lower()
class TestDeduplication:
def test_content_hash_deterministic(self):
from hashlib import sha256
def ch(f):
key = f"{f['file']}:{f['line']}:{f['text']}"
return sha256(key.encode()).hexdigest()
finding = {"file": "a.py", "line": 1, "text": "test"}
assert ch(finding) == ch(finding)
def test_duplicate_findings_are_removed(self):
findings = [
{"file": "a.py", "line": 1, "text": "foo", "severity": "info"},
{"file": "a.py", "line": 1, "text": "foo", "severity": "warning"},
{"file": "b.py", "line": 2, "text": "bar", "severity": "info"},
]
seen = {}
for f in findings:
key = f"{f['file']}:{f['line']}:{f['text']}"
seen[key] = f
assert len(seen) == 2
def test_different_findings_are_kept(self):
findings = [
{"file": "a.py", "line": 1, "text": "foo"},
{"file": "a.py", "line": 2, "text": "foo"},
{"file": "a.py", "line": 1, "text": "bar"},
]
seen = {}
for f in findings:
key = f"{f['file']}:{f['line']}:{f['text']}"
seen[key] = f
assert len(seen) == 3
class TestCommentFormatting:
def test_format_basic(self):
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import format_comment
f = {"file": "scripts/foo.py", "line": 10, "text": "Fix this bug", "severity": "warning"}
body = format_comment(f)
assert "📝 **Review Comment**" not in body # warning uses ⚠️
assert "⚠️ **Review Comment**" in body
assert "`scripts/foo.py`" in body
assert "Line: 10" in body
assert "> Fix this bug" in body
def test_format_severity_emoji(self):
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import format_comment
cases = [("error", "🛑"), ("warning", "⚠️"), ("info", ""), ("unknown", "📝")]
for severity, emoji in cases:
f = {"file": "x.py", "line": 1, "text": "test", "severity": severity}
assert emoji in format_comment(f)
class TestFindingsLoader:
def test_load_from_file(self):
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import load_findings
findings = load_findings(SAMPLE_FINDINGS, from_stdin=False)
assert len(findings) >= 4
def test_load_ignores_blank_and_comments(self):
import tempfile, os
with tempfile.NamedTemporaryFile(mode="w", suffix=".jsonl", delete=False) as tf:
tf.write('{"file":"a.py","line":1,"text":"valid"}\n')
tf.write('\n')
tf.write('# this is a comment\n')
tf.write('{"file":"b.py","line":2,"text":"also valid"}\n')
tfname = tf.name
try:
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import load_findings
assert len(load_findings(Path(tfname), from_stdin=False)) == 2
finally:
os.unlink(tfname)
def test_invalid_json_line_skipped(self, capsys):
import tempfile, os
with tempfile.NamedTemporaryFile(mode="w", suffix=".jsonl", delete=False) as tf:
tf.write('invalid json\n')
tf.write('{"file":"ok.py","line":1,"text":"valid"}\n')
tfname = tf.name
try:
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import load_findings
assert len(load_findings(Path(tfname), from_stdin=False)) == 1
finally:
os.unlink(tfname)
class TestDryRunMode:
def test_dry_run_counts_unique(self):
result = subprocess.run(
[sys.executable, str(GENERATOR), "--pr", "126",
"--input", str(SAMPLE_FINDINGS), "--dry-run"],
capture_output=True, text=True, cwd=REPO_ROOT, timeout=15
)
assert result.returncode == 0
assert "DRY RUN" in result.stdout
assert "Review Comment" in result.stdout
def test_dry_run_shows_all_unique(self):
result = subprocess.run(
[sys.executable, str(GENERATOR), "--pr", "126",
"--input", str(SAMPLE_FINDINGS), "--dry-run"],
capture_output=True, text=True, cwd=REPO_ROOT, timeout=15
)
assert result.stdout.count("--- Comment") == 4
class TestJSONOutputMode:
def test_json_flag_emits_valid_json(self):
result = subprocess.run(
[sys.executable, str(GENERATOR), "--pr", "126",
"--input", str(SAMPLE_FINDINGS), "--json"],
capture_output=True, text=True, cwd=REPO_ROOT, timeout=15
)
assert result.returncode == 0
payload = json.loads(result.stdout)
assert "total" in payload and "unique" in payload and "findings" in payload
assert payload["total"] >= payload["unique"]
def test_json_findings_have_required_fields(self):
result = subprocess.run(
[sys.executable, str(GENERATOR), "--pr", "126",
"--input", str(SAMPLE_FINDINGS), "--json"],
capture_output=True, text=True, cwd=REPO_ROOT, timeout=15
)
payload = json.loads(result.stdout)
for f in payload["findings"]:
assert "file" in f and "line" in f and "text" in f
class TestGiteaClient:
def test_post_issue_comment_builds_correct_url(self):
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import GiteaClient
client = GiteaClient("https://example.com", "token123", "MyOrg", "myrepo")
assert client.org == "MyOrg" and client.repo == "myrepo"
def test_generate_comment_body_has_required_fields(self):
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import format_comment
f = {"file": "x.py", "line": 5, "text": "Fix this", "severity": "error"}
body = format_comment(f)
assert "x.py" in body and "5" in body and "Fix this" in body
class TestFullPipeline:
def test_end_to_end_json_output(self):
result = subprocess.run(
[sys.executable, str(GENERATOR), "--pr", "126",
"--input", str(SAMPLE_FINDINGS), "--json"],
capture_output=True, text=True, cwd=REPO_ROOT, timeout=15
)
assert result.returncode == 0
data = json.loads(result.stdout)
assert data["total"] == 5
assert data["unique"] == 4
f = data["findings"][0]
for key in ("file", "line", "text", "severity"):
assert key in f
def test_token_loading_fallback(self):
sys.path.insert(0, str(SCRIPTS_DIR))
from review_comment_generator import load_token
token = load_token()
assert token is None or isinstance(token, str)
class TestErrorHandling:
def test_missing_input_shows_error(self):
result = subprocess.run(
[sys.executable, str(GENERATOR), "--pr", "126"],
capture_output=True, text=True, cwd=REPO_ROOT, timeout=15
)
assert result.returncode != 0
assert "--input" in result.stderr or "--stdin" in result.stderr
def test_invalid_json_line_skipped(self):
import tempfile, os
with tempfile.NamedTemporaryFile(mode="w", suffix=".jsonl", delete=False) as tf:
tf.write('invalid json\n')
tf.write('{"file":"ok.py","line":1,"text":"valid"}\n')
tfname = tf.name
try:
result = subprocess.run(
[sys.executable, str(GENERATOR), "--pr", "126",
"--input", tfname, "--json"],
capture_output=True, text=True, cwd=REPO_ROOT, timeout=15
)
data = json.loads(result.stdout)
assert data["total"] == 1
assert data["unique"] == 1
finally:
os.unlink(tfname)
if __name__ == "__main__":
pytest.main([__file__, "-v"])