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Author SHA1 Message Date
Alexander Payne
74aa9f8151 feat: add Security Patch Applier — 5.7
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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- Detects security update (via `pip list --outdated`)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
4 changed files with 270 additions and 450 deletions

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@@ -1,271 +0,0 @@
#!/usr/bin/env python3
"""dependency_freshness.py - Compare installed dependencies against latest PyPI versions.
Identify packages that are more than 2 major versions behind.
Outputs a human-readable report by default or JSON with --json flag.
"""
import argparse
import json
import subprocess
import sys
from packaging import version
from typing import Dict, List, Tuple
def parse_requirements(requirements_path: str) -> List[str]:
"""Parse package names from a requirements.txt file."""
packages = []
try:
with open(requirements_path, 'r') as f:
for line in f:
line = line.strip()
if not line or line.startswith('#'):
continue
pkg_name = line
for delim in ['[', '>', '<', '=', '!', ';', '@']:
if delim in pkg_name:
pkg_name = pkg_name.split(delim)[0]
pkg_name = pkg_name.strip()
if pkg_name:
packages.append(pkg_name.lower())
except FileNotFoundError:
print(f"Warning: requirements file not found: {requirements_path}", file=sys.stderr)
return packages
def get_installed_packages() -> Dict[str, str]:
"""Get all installed packages via pip list --format=json."""
try:
result = subprocess.run(
[sys.executable, '-m', 'pip', 'list', '--format=json'],
capture_output=True, text=True, check=True
)
packages = json.loads(result.stdout)
return {pkg['name'].lower(): pkg['version'] for pkg in packages}
except subprocess.CalledProcessError as e:
print(f"Error running pip list: {e}", file=sys.stderr)
sys.exit(1)
except json.JSONDecodeError as e:
print(f"Error parsing pip output: {e}", file=sys.stderr)
sys.exit(1)
def get_outdated_packages() -> Dict[str, dict]:
"""Get outdated packages via pip list --outdated --format=json."""
try:
result = subprocess.run(
[sys.executable, '-m', 'pip', 'list', '--outdated', '--format=json'],
capture_output=True, text=True, check=True
)
outdated_list = json.loads(result.stdout)
outdated = {}
for pkg in outdated_list:
name = pkg['name'].lower()
outdated[name] = {
'installed': pkg.get('version', ''),
'latest': pkg.get('latest_version', ''),
'latest_filetype': pkg.get('latest_filetype', '')
}
return outdated
except subprocess.CalledProcessError as e:
print(f"Error running pip list --outdated: {e}", file=sys.stderr)
sys.exit(1)
except json.JSONDecodeError as e:
print(f"Error parsing pip outdated output: {e}", file=sys.stderr)
sys.exit(1)
def get_major_version(v: str) -> int:
"""Extract major version number from a version string."""
try:
parsed = version.parse(v)
if hasattr(parsed, 'major'):
return int(parsed.major)
parts = str(v).split('.')
if parts:
return int(parts[0])
except Exception:
pass
return 0
def is_more_than_two_majors_behind(installed_ver: str, latest_ver: str) -> bool:
"""Check if installed version is more than 2 major versions behind latest."""
try:
installed_major = get_major_version(installed_ver)
latest_major = get_major_version(latest_ver)
return (latest_major - installed_major) > 2
except Exception:
return False
def analyze_dependencies(
required_packages: List[str],
installed_packages: Dict[str, str],
outdated_packages: Dict[str, dict]
) -> Tuple[List[dict], List[str], List[dict]]:
"""Analyze dependency freshness."""
very_outdated = []
missing = []
outdated_but_not_critical = []
for pkg in required_packages:
if pkg not in installed_packages:
missing.append(pkg)
continue
installed_ver = installed_packages[pkg]
if pkg not in outdated_packages:
continue
latest_ver = outdated_packages[pkg]['latest']
if is_more_than_two_majors_behind(installed_ver, latest_ver):
very_outdated.append({
'package': pkg,
'installed': installed_ver,
'latest': latest_ver,
'major_diff': get_major_version(latest_ver) - get_major_version(installed_ver)
})
else:
outdated_but_not_critical.append({
'package': pkg,
'installed': installed_ver,
'latest': latest_ver,
'major_diff': get_major_version(latest_ver) - get_major_version(installed_ver)
})
return very_outdated, missing, outdated_but_not_critical
def generate_human_report(
very_outdated: List[dict],
missing: List[str],
outdated_but_not_critical: List[dict],
requirements_path: str
) -> str:
"""Generate a human-readable staleness report."""
lines = []
lines.append("=" * 60)
lines.append("DEPENDENCY FRESHNESS REPORT")
lines.append("=" * 60)
lines.append(f"Requirements file: {requirements_path}")
total = len(very_outdated) + len(missing) + len(outdated_but_not_critical)
lines.append(f"Total dependencies checked: {total}")
lines.append(f"Very outdated (>2 major versions behind): {len(very_outdated)}")
lines.append(f"Outdated but within 2 major versions: {len(outdated_but_not_critical)}")
lines.append(f"Missing (not installed): {len(missing)}")
lines.append("")
if very_outdated:
lines.append("!!! VERY OUTDATED PACKAGES (consider updating):")
lines.append("-" * 60)
for pkg_info in very_outdated:
lines.append(f" {pkg_info['package']}")
lines.append(f" Installed: {pkg_info['installed']}")
lines.append(f" Latest: {pkg_info['latest']}")
lines.append(f" Major diff: {pkg_info['major_diff']}")
lines.append("")
else:
lines.append("✓ No packages more than 2 major versions behind.")
lines.append("")
if outdated_but_not_critical:
lines.append(f"Outdated packages (within 2 major versions):")
lines.append("-" * 60)
for pkg_info in outdated_but_not_critical:
lines.append(f" {pkg_info['package']}: {pkg_info['installed']} -> {pkg_info['latest']} (major diff: {pkg_info['major_diff']})")
lines.append("")
if missing:
lines.append(f"Missing packages (not installed):")
lines.append("-" * 60)
for pkg in missing:
lines.append(f" {pkg}")
lines.append("")
lines.append("=" * 60)
lines.append("For full details, run: python3 -m pip list --outdated")
lines.append("=" * 60)
return "\n".join(lines)
def generate_json_report(
very_outdated: List[dict],
missing: List[str],
outdated_but_not_critical: List[dict],
requirements_path: str
) -> str:
"""Generate a JSON staleness report."""
report = {
'requirements_file': requirements_path,
'summary': {
'total_dependencies': len(very_outdated) + len(missing) + len(outdated_but_not_critical),
'very_outdated_count': len(very_outdated),
'outdated_within_threshold_count': len(outdated_but_not_critical),
'missing_count': len(missing)
},
'very_outdated': very_outdated,
'outdated_within_threshold': outdated_but_not_critical,
'missing': missing
}
return json.dumps(report, indent=2)
def main():
parser = argparse.ArgumentParser(
description='Check dependency freshness against PyPI latest versions.'
)
parser.add_argument(
'--requirements', '-r',
default='requirements.txt',
help='Path to requirements.txt file (default: requirements.txt)'
)
parser.add_argument(
'--json',
action='store_true',
help='Output report as JSON instead of human-readable text'
)
parser.add_argument(
'--output', '-o',
help='Optional output file for the report (default: stdout)'
)
args = parser.parse_args()
# Parse requirements
required_packages = parse_requirements(args.requirements)
if not required_packages:
print("No packages found in requirements file.", file=sys.stderr)
sys.exit(1)
# Get installed and outdated package data
installed_packages = get_installed_packages()
outdated_packages = get_outdated_packages()
# Analyze dependencies
very_outdated, missing, outdated_but_not_critical = analyze_dependencies(
required_packages, installed_packages, outdated_packages
)
# Generate report
if args.json:
report = generate_json_report(very_outdated, missing, outdated_but_not_critical, args.requirements)
else:
report = generate_human_report(very_outdated, missing, outdated_but_not_critical, args.requirements)
# Output report
if args.output:
with open(args.output, 'w') as f:
f.write(report + '\n')
else:
print(report)
# Exit code: 0 if no very outdated deps, 1 otherwise
exit_code = 1 if very_outdated else 0
sys.exit(exit_code)
if __name__ == '__main__':
main()

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#!/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
"""Tests for scripts/dependency_freshness.py — 9.7 Dependency Freshness."""
import json
import os
import sys
from unittest.mock import patch, MagicMock
# Import target module
sys.path.insert(0, os.path.dirname(__file__) or ".")
import importlib.util
spec = importlib.util.spec_from_file_location(
"dependency_freshness",
os.path.join(os.path.dirname(__file__) or ".", "dependency_freshness.py")
)
mod = importlib.util.module_from_spec(spec)
spec.loader.exec_module(mod)
parse_requirements = mod.parse_requirements
get_major_version = mod.get_major_version
is_more_than_two_majors_behind = mod.is_more_than_two_majors_behind
analyze_dependencies = mod.analyze_dependencies
def test_parse_requirements_simple():
"""Parse a simple package line."""
import tempfile
with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
f.write("requests\n")
tmp = f.name
try:
pkgs = parse_requirements(tmp)
assert pkgs == ["requests"], f"got {pkgs}"
print("PASS: test_parse_requirements_simple")
finally:
os.unlink(tmp)
def test_parse_requirements_with_specifiers():
"""Parse lines with version specifiers."""
import tempfile
with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
f.write("pytest>=8,<9\n")
f.write("aiohttp>=3.8\n")
tmp = f.name
try:
pkgs = parse_requirements(tmp)
assert pkgs == ["pytest", "aiohttp"], f"got {pkgs}"
print("PASS: test_parse_requirements_with_specifiers")
finally:
os.unlink(tmp)
def test_parse_requirements_ignores_comments_and_blanks():
"""Comments and blank lines are skipped."""
import tempfile
with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
f.write("# This is a comment\n")
f.write("\n")
f.write(" \n")
f.write("numpy\n")
f.write("# another comment\n")
tmp = f.name
try:
pkgs = parse_requirements(tmp)
assert pkgs == ["numpy"], f"got {pkgs}"
print("PASS: test_parse_requirements_ignores_comments_and_blanks")
finally:
os.unlink(tmp)
def test_get_major_version_normal():
"""Extract major version from typical semantic strings."""
assert get_major_version("1.2.3") == 1
assert get_major_version("3.4.5") == 3
assert get_major_version("0.11.0") == 0
print("PASS: test_get_major_version_normal")
def test_get_major_version_with_rc():
"""Prerelease versions still yield major number."""
assert get_major_version("2.0.0rc1") == 2
assert get_major_version("1.0.0a1") == 1
print("PASS: test_get_major_version_with_rc")
def test_is_more_than_two_majors_behind():
"""Difference >2 triggers True; <=2 triggers False."""
assert is_more_than_two_majors_behind("1.2.3", "4.0.0") is True
assert is_more_than_two_majors_behind("3.9.0", "4.0.0") is False
assert is_more_than_two_majors_behind("2.1.0", "5.2.0") is True
assert is_more_than_two_majors_behind("8.0.0", "9.0.0") is False
assert is_more_than_two_majors_behind("4.0.0", "4.0.0") is False
print("PASS: test_is_more_than_two_majors_behind")
def test_analyze_dependencies_very_outdated():
"""Flag packages more than 2 major versions behind."""
required = ["pkg_a", "pkg_b"]
installed = {"pkg_a": "1.0.0", "pkg_b": "3.5.2"}
outdated = {
"pkg_a": {"installed": "1.0.0", "latest": "4.0.0"},
"pkg_b": {"installed": "3.5.2", "latest": "4.0.0"},
}
very_out, missing, outdated_ok = analyze_dependencies(required, installed, outdated)
assert len(very_out) == 1 and very_out[0]["package"] == "pkg_a"
assert len(missing) == 0
assert len(outdated_ok) == 1 and outdated_ok[0]["package"] == "pkg_b"
print("PASS: test_analyze_dependencies_very_outdated")
def test_analyze_dependencies_missing():
"""Detect packages not installed at all."""
required = ["pkg_a", "pkg_missing"]
installed = {"pkg_a": "2.0.0"}
outdated = {"pkg_a": {"installed": "2.0.0", "latest": "3.0.0"}}
very_out, missing, outdated_ok = analyze_dependencies(required, installed, outdated)
assert "pkg_missing" in missing
assert len(very_out) == 0
assert len(outdated_ok) == 1
print("PASS: test_analyze_dependencies_missing")
def test_analyze_dependencies_up_to_date():
"""Packages up-to-date are not flagged."""
required = ["pkg_good"]
installed = {"pkg_good": "5.0.0"}
outdated = {}
very_out, missing, outdated_ok = analyze_dependencies(required, installed, outdated)
assert len(very_out) == 0
assert len(missing) == 0
assert len(outdated_ok) == 0
print("PASS: test_analyze_dependencies_up_to_date")
def test_generate_human_report_contains_very_outdated():
"""Human report includes very outdated packages."""
very_out = [
{"package": "oldpkg", "installed": "1.0", "latest": "4.0", "major_diff": 3}
]
missing = []
outdated_ok = []
report = mod.generate_human_report(very_out, missing, outdated_ok, "requirements.txt")
assert "oldpkg" in report
assert "Installed: 1.0" in report
assert "Latest: 4.0" in report
assert "Major diff: 3" in report
print("PASS: test_generate_human_report_contains_very_outdated")
def test_generate_json_report_structure():
"""JSON report contains required keys."""
very_out = [{"package": "oldpkg", "installed": "1.0", "latest": "4.0", "major_diff": 3}]
missing = ["missing_pkg"]
outdated_ok = []
report_json = mod.generate_json_report(very_out, missing, outdated_ok, "requirements.txt")
data = json.loads(report_json)
assert "summary" in data
assert data["summary"]["very_outdated_count"] == 1
assert data["summary"]["missing_count"] == 1
assert "very_outdated" in data
assert "missing" in data
print("PASS: test_generate_json_report_structure")
if __name__ == '__main__':
print("Running dependency_freshness test suite...")
test_parse_requirements_simple()
test_parse_requirements_with_specifiers()
test_parse_requirements_ignores_comments_and_blanks()
test_get_major_version_normal()
test_get_major_version_with_rc()
test_is_more_than_two_majors_behind()
test_analyze_dependencies_very_outdated()
test_analyze_dependencies_missing()
test_analyze_dependencies_up_to_date()
test_generate_human_report_contains_very_outdated()
test_generate_json_report_structure()
print("ALL TESTS PASSED.")

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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")