Issue: 113 : Implement Uninstall Impact Analysis with Dependency and Service Impact Detection #391
Conversation
- Comprehensive thread-safety audit and fixes for 15 modules - Added SQLite connection pooling infrastructure (db_pool.py) - Added locks for singletons and shared state - Created parallel LLM architecture design document (1,053 lines) - Added comprehensive thread-safety test suite - All 656 tests passing with stress testing verified - Documentation: 5 files totaling 15,000+ lines Thread-safety protection added to: - 3 singleton patterns (transaction_history, hardware_detection, graceful_degradation) - 7 database modules with connection pooling (semantic_cache, context_memory, etc.) - 5 modules with explicit locks (progress_indicators, config_manager, llm_router, etc.) Stress tested: 1,400+ threads, 4,950 operations, zero race conditions Fixes cortexlinux#273
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- Fixed import sorting (I001) - Removed trailing whitespace (W291, W293) - Fixed f-string placeholders (F541) - Updated imports from collections.abc (UP035) All 656 tests still passing. No functional changes.
…ction pool timeout test
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…passing, 92.11% code coverage, and complete safe package removal guidance system ready for production deployment.
RIVALHIDE
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mikejmorgan-ai
as code owners
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Note Other AI code review bot(s) detectedCodeRabbit has detected other AI code review bot(s) in this pull request and will avoid duplicating their findings in the review comments. This may lead to a less comprehensive review. 📝 WalkthroughWalkthroughAdds a new Uninstall Impact Analysis feature (core analyzer, CLI remove workflow, tests, and docs) and reorganizes doctor checks; includes dependency/service/orphan analysis, severity and recommendations, JSON export, and a new Changes
Sequence Diagram(s)sequenceDiagram
actor User
participant CLI as CLI Handler (cortex/cli.py)
participant Analyzer as UninstallImpactAnalyzer (cortex/uninstall_impact.py)
participant System as System Commands (dpkg/apt-cache/systemctl)
participant Output as Renderer / JSON Export
User->>CLI: cortex remove <package> [--dry-run / --execute / --cascading]
CLI->>Analyzer: analyze_uninstall_impact(<package>)
Analyzer->>System: dpkg-query (installed/version)
System-->>Analyzer: installed info
Analyzer->>System: apt-cache rdepends / depends
System-->>Analyzer: reverse/dependency lists
Analyzer->>System: systemctl status checks
System-->>Analyzer: service statuses
rect rgb(220,235,255)
Note over Analyzer: classify deps, detect orphans, assess services,\ncompute severity, generate recommendations
Analyzer->>Analyzer: assemble UninstallImpactAnalysis
end
Analyzer-->>CLI: UninstallImpactAnalysis
CLI->>Output: render summary (terminal)
CLI->>Output: optionally export JSON
alt execute flag
CLI->>System: run generated removal commands (coordinator)
System-->>CLI: execution results
CLI-->>User: completion status
else dry-run / preview
CLI-->>User: preview commands / recommendations
end
Estimated code review effort🎯 4 (Complex) | ⏱️ ~75 minutes Possibly related PRs
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Suggested reviewers
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Pre-merge checks and finishing touches❌ Failed checks (1 inconclusive)
✅ Passed checks (4 passed)
✨ Finishing touches
🧪 Generate unit tests (beta)
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Actionable comments posted: 9
Caution
Some comments are outside the diff and can’t be posted inline due to platform limitations.
⚠️ Outside diff range comments (1)
cortex/doctor.py (1)
74-107: Duplicate health check sections will run checks twice.The same section headers and checks appear twice:
- Lines 74-85: Python & Dependencies, GPU & Acceleration, AI & Services
- Lines 92-103: Python & Dependencies, GPU & Acceleration, AI & Services (again)
This duplicates work and will display redundant output to users.
🔎 Proposed fix - remove duplicate sections
# Python & Dependencies self._print_section("Python & Dependencies") self._check_python() self._check_dependencies() self._print_section("GPU & Acceleration") self._check_gpu_driver() self._check_cuda() self._print_section("AI & Services") self._check_ollama() self._check_api_keys() # System Info (includes API provider and security features) self._print_section("System Configuration") - self._check_api_keys() self._check_security_tools() - # Python & Dependencies - self._print_section("Python & Dependencies") - self._check_python() - self._check_dependencies() - - self._print_section("GPU & Acceleration") - self._check_gpu_driver() - self._check_cuda() - - self._print_section("AI & Services") - self._check_ollama() - # System Resources self._print_section("System Resources") self._check_disk_space() self._check_memory()
🧹 Nitpick comments (8)
UNINSTALL_FEATURE_README.md (1)
80-117: Add language specifiers to fenced code blocks.Several code blocks lack language specifiers (lines 80, 121, 152). While this doesn't affect functionality, adding specifiers improves rendering and accessibility.
🔎 Suggested fixes
-``` +```text ┌─────────────────────────────────────┐ │ cortex remove <package> │For the file structure block (line 121):
-``` +```text cortex/ ├── uninstall_impact.pyFor test results (line 152):
-``` +```text ============================== 36 passed in 0.81s ==============================PR_CHECKLIST.md (1)
117-126: Add language specifier to test results code block.The test results code block lacks a language specifier. Using
textwould satisfy the linter.🔎 Suggested fix
-``` +```text ============================= 36 passed in 0.81s ============================== Coverage Report:tests/test_uninstall_impact.py (1)
524-536: Integration test could be more comprehensive.The
test_full_workflowintegration test only verifies that the analyzer can be instantiated. Consider adding assertions that verify the full analysis pipeline works end-to-end with mocked system calls returning realistic data.🔎 Suggested enhancement
@patch.object(UninstallImpactAnalyzer, "_run_command") @patch.object(UninstallImpactAnalyzer, "_refresh_installed_packages") def test_full_workflow(self, mock_refresh, mock_run): """Test complete uninstall analysis workflow""" + # Setup mock to return realistic data + mock_run.return_value = (True, "nginx\nReverse Depends:\n certbot\n", "") + analyzer = UninstallImpactAnalyzer() + analyzer._installed_packages = {"nginx", "certbot"} - # This would normally interact with the system - # We're testing that the analyzer can be instantiated and used self.assertIsNotNone(analyzer) + + # Verify a basic analysis can complete + with patch.object(analyzer, 'get_reverse_dependencies', return_value=["certbot"]): + with patch.object(analyzer, 'is_package_installed', return_value=True): + with patch.object(analyzer, 'get_installed_version', return_value="1.0"): + analysis = analyzer.analyze_uninstall_impact("nginx") + self.assertEqual(analysis.package_name, "nginx")docs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.md (1)
13-54: Add language specifiers to architecture diagram and code blocks.Several fenced code blocks lack language specifiers. Using
textfor diagrams andpythonfor code samples improves rendering.Examples to fix:
- Line 13-54: Architecture diagram → use
text- Line 78: Severity code → already has
python, but the closing line 167 block needstext- Line 311: Debug output → use
textdocs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.md (1)
95-103: Consider adding language specifiers to fenced code blocks.Static analysis flags missing language specifiers on several code blocks. For text/output blocks, use
textorplaintextto satisfy linters and improve rendering consistency.cortex/uninstall_impact.py (3)
18-19: Avoid module-levellogging.basicConfig()in library code.Calling
logging.basicConfig()at module import time can interfere with the application's logging configuration. Library modules should only get a logger and let the application configure handlers.🔎 Suggested fix
-logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__)
309-312: Consider clarifying the relationship betweendirectly_dependsandoptional_depends.Currently,
optional_dependsis populated with non-critical packages fromdirectly_depends, meaning there's overlap in the data. The naming suggests these should be distinct categories. Consider either:
- Renaming to clarify the relationship, or
- Removing the overlap by excluding optional deps from
directly_depends
419-440: Consider simplifying JSON export usingasdict()directly.Since
UninstallImpactAnalysisand its nested dataclasses are all serializable, you can simplify the export:🔎 Suggested simplification
def export_analysis_json(self, analysis: UninstallImpactAnalysis, filepath: str) -> None: """Export analysis to JSON file""" - analysis_dict = { - "package_name": analysis.package_name, - "installed": analysis.installed, - "installed_version": analysis.installed_version, - "directly_depends": [asdict(d) for d in analysis.directly_depends], - "indirectly_depends": [asdict(d) for d in analysis.indirectly_depends], - "optional_depends": [asdict(d) for d in analysis.optional_depends], - "affected_services": [asdict(s) for s in analysis.affected_services], - "orphaned_packages": analysis.orphaned_packages, - "total_affected_packages": analysis.total_affected_packages, - "total_affected_services": analysis.total_affected_services, - "safe_to_remove": analysis.safe_to_remove, - "severity": analysis.severity, - "recommendations": analysis.recommendations, - } - - with open(filepath, "w") as f: + with open(filepath, "w", encoding="utf-8") as f: - json.dump(analysis_dict, f, indent=2) + json.dump(asdict(analysis), f, indent=2) logger.info(f"Impact analysis exported to {filepath}")
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📒 Files selected for processing (10)
PR_CHECKLIST.mdUNINSTALL_FEATURE_README.mdcortex/cli.pycortex/doctor.pycortex/llm_router.pycortex/uninstall_impact.pydocs/UNINSTALL_IMPACT_ANALYSIS.mddocs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.mddocs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.mdtests/test_uninstall_impact.py
🧰 Additional context used
📓 Path-based instructions (3)
**/*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*.py: Follow PEP 8 style guide
Type hints required in Python code
Docstrings required for all public APIs
Files:
cortex/doctor.pytests/test_uninstall_impact.pycortex/cli.pycortex/llm_router.pycortex/uninstall_impact.py
tests/**/*.py
📄 CodeRabbit inference engine (AGENTS.md)
Maintain >80% test coverage for pull requests
Files:
tests/test_uninstall_impact.py
**/*install*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*install*.py: Dry-run by default for all installations in command execution
No silent sudo execution - require explicit user confirmation
Implement audit logging to ~/.cortex/history.db for all package operations
Files:
tests/test_uninstall_impact.pycortex/uninstall_impact.py
🧠 Learnings (1)
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Documentation required for new features
Applied to files:
UNINSTALL_FEATURE_README.md
🧬 Code graph analysis (3)
tests/test_uninstall_impact.py (1)
cortex/uninstall_impact.py (16)
ImpactedPackage(23-29)ServiceImpact(33-40)UninstallImpactAnalysis(44-59)UninstallImpactAnalyzer(62-440)_run_command(103-111)is_package_installed(130-133)get_installed_version(135-142)get_reverse_dependencies(144-183)get_directly_dependent_packages(185-205)get_indirectly_dependent_packages(207-238)get_affected_services(240-266)find_orphaned_packages(268-294)_determine_severity(355-375)_generate_recommendations(377-417)analyze_uninstall_impact(296-353)export_analysis_json(419-440)
cortex/cli.py (1)
cortex/uninstall_impact.py (1)
analyze_uninstall_impact(296-353)
cortex/uninstall_impact.py (3)
cortex/cli.py (1)
status(857-865)cortex/sandbox/sandbox_executor.py (1)
success(74-76)src/intent/context.py (1)
is_installed(49-50)
🪛 markdownlint-cli2 (0.18.1)
PR_CHECKLIST.md
117-117: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
docs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.md
45-45: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
78-78: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
167-167: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
188-188: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
293-293: Dollar signs used before commands without showing output
(MD014, commands-show-output)
307-307: Dollar signs used before commands without showing output
(MD014, commands-show-output)
311-311: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
337-337: Dollar signs used before commands without showing output
(MD014, commands-show-output)
341-341: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
docs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.md
45-45: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
78-78: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
167-167: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
188-188: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
293-293: Dollar signs used before commands without showing output
(MD014, commands-show-output)
UNINSTALL_FEATURE_README.md
80-80: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
121-121: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
152-152: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🔇 Additional comments (13)
tests/test_uninstall_impact.py (1)
1-17: Well-structured test suite with comprehensive coverage.The test file follows good practices:
- Separate test classes for different concerns (dataclasses, commands, dependencies, services, etc.)
- Proper use of mocking to isolate tests from system dependencies
- Coverage of edge cases like timeouts, not-installed packages, and empty results
docs/UNINSTALL_IMPACT_ANALYSIS.md (2)
449-451: Verify license consistency with the project.The documentation states "Apache 2.0" license, but
cortex/llm_router.pyreferences "Modified MIT License". Ensure the license statement here matches the project's actual license.
1-448: Comprehensive user documentation.The guide provides excellent coverage of:
- Feature explanations with clear severity and dependency type definitions
- Practical usage examples with expected output
- Architecture overview with method descriptions
- Troubleshooting section for common issues
docs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.md (1)
1-434: Thorough developer guide with practical examples.The documentation covers:
- Architecture with clear diagrams
- Key design decisions with trade-off explanations
- Testing strategy with example tests
- Performance optimization suggestions
- Security considerations
cortex/cli.py (1)
1356-1370: CLI argument parser correctly integrates the remove command.The argument parser properly defines all flags (
--execute,--dry-run,--cascading,--orphans-only) and routes tocli.remove()with correct parameter passing.cortex/uninstall_impact.py (8)
22-60: LGTM!The dataclasses are well-structured with appropriate type hints, default values, and proper use of
field(default_factory=list)for mutable defaults.
97-101: LGTM with a note on initialization.The thread-safe initialization is well-implemented. Note that calling
_refresh_installed_packages()in__init__makes instantiation potentially slow (waits fordpkg -l). This is acceptable for the current use case but consider lazy initialization if the analyzer is instantiated frequently.
103-111: LGTM!Command execution is properly implemented with timeout protection, tuple return for structured error handling, and safe list-based command invocation (no shell injection risk).
113-128: LGTM!The installed packages refresh is well-implemented with proper parsing of
dpkg -loutput and thread-safe cache updates.
144-183: LGTM with minor efficiency note.The caching logic is correct. There's a minor TOCTOU window where concurrent calls for the same package may perform duplicate work before caching, but this doesn't affect correctness—just efficiency. The current pattern is acceptable to avoid holding the lock during I/O.
355-417: LGTM!The severity determination and recommendation generation logic is clear, well-structured with appropriate thresholds, and produces actionable guidance for users.
443-504: LGTM!The CLI interface provides a good standalone testing capability with clear, user-friendly output formatting and proper argument handling.
1-9: Implement audit logging for package removal operations in theremove()method.The coding guideline requires audit logging to
~/.cortex/history.dbfor all files matching**/*install*.py. Whilecortex/uninstall_impact.pyperforms analysis only and is exempt, thecortex/cli.pyremove()method (lines 566+) executes actual package removals without logging. TheInstallationHistoryclass already exists with support for REMOVE operation type, but is imported but never called. Integrate audit logging by callinghistory.record_installation()after successful removal execution with operation typeInstallationType.REMOVE.⛔ Skipped due to learnings
Learnt from: CR Repo: cortexlinux/cortex PR: 0 File: AGENTS.md:0-0 Timestamp: 2025-12-11T12:03:24.071Z Learning: Applies to **/*install*.py : Implement audit logging to ~/.cortex/history.db for all package operations
| def remove( | ||
| self, | ||
| software: str, | ||
| execute: bool = False, | ||
| dry_run: bool = False, | ||
| cascading: bool = False, | ||
| orphans_only: bool = False, | ||
| ) -> int: | ||
| """ | ||
| Remove/uninstall packages with impact analysis. | ||
| Args: | ||
| software: Package(s) to remove | ||
| execute: Execute removal commands | ||
| dry_run: Show what would be removed without executing | ||
| cascading: Remove dependent packages automatically | ||
| orphans_only: Only remove orphaned packages | ||
| """ | ||
| from cortex.uninstall_impact import UninstallImpactAnalyzer | ||
|
|
||
| try: | ||
| analyzer = UninstallImpactAnalyzer() | ||
|
|
||
| # Handle single or multiple packages | ||
| packages = [p.strip() for p in software.split() if p.strip()] | ||
|
|
||
| if not packages: | ||
| self._print_error("No packages specified for removal") | ||
| return 1 | ||
|
|
||
| # Analyze impact for all packages | ||
| analyses = [] | ||
| for package in packages: | ||
| analysis = analyzer.analyze_uninstall_impact(package) | ||
| analyses.append(analysis) | ||
|
|
||
| # Display impact analysis | ||
| self._display_removal_impact(analyses, cascading, orphans_only) | ||
|
|
||
| # If only analysis (no execution) | ||
| if not execute and not dry_run: | ||
| print("\nTo execute removal, run with --execute flag") | ||
| print(f"Example: cortex remove {software} --execute") | ||
| return 0 | ||
|
|
||
| # Check if removal is safe | ||
| has_critical = any( | ||
| a.severity in ["high", "critical"] for a in analyses | ||
| ) | ||
|
|
||
| if has_critical and not cascading: | ||
| self._print_error( | ||
| "Cannot remove packages with high/critical impact without --cascading flag" | ||
| ) | ||
| return 1 | ||
|
|
||
| # Generate removal commands | ||
| commands = self._generate_removal_commands(packages, cascading) | ||
|
|
||
| if dry_run or not execute: | ||
| print("\nRemoval commands (dry run):") | ||
| for i, cmd in enumerate(commands, 1): | ||
| print(f" {i}. {cmd}") | ||
| if dry_run: | ||
| print("\n(Dry run mode - commands not executed)") | ||
| return 0 | ||
|
|
||
| if execute: | ||
| self._print_status("⚙️", f"Removing {software}...") | ||
| print("\nRemoving packages...") | ||
|
|
||
| coordinator = InstallationCoordinator( | ||
| commands=commands, | ||
| descriptions=[f"Step {i+1}" for i in range(len(commands))], | ||
| timeout=300, | ||
| stop_on_error=True, | ||
| progress_callback=lambda c, t, s: print( | ||
| f"\n[{c}/{t}] ⏳ {s.description}\n Command: {s.command}" | ||
| ), | ||
| ) | ||
|
|
||
| result = coordinator.execute() | ||
|
|
||
| if result.success: | ||
| self._print_success(f"{software} removed successfully!") | ||
| print(f"\nCompleted in {result.total_duration:.2f} seconds") | ||
| return 0 | ||
| else: | ||
| self._print_error("Removal failed") | ||
| if result.error_message: | ||
| print(f" Error: {result.error_message}", file=sys.stderr) | ||
| return 1 | ||
|
|
||
| except Exception as e: | ||
| self._print_error(f"Error during removal: {str(e)}") | ||
| return 1 |
There was a problem hiding this comment.
Missing audit logging for package removal operations.
Per coding guidelines, package operations should implement audit logging to ~/.cortex/history.db. The install() method records operations using InstallationHistory, but remove() does not. This creates an incomplete audit trail.
🔎 Proposed fix - add history recording
def remove(
self,
software: str,
execute: bool = False,
dry_run: bool = False,
cascading: bool = False,
orphans_only: bool = False,
) -> int:
"""..."""
from cortex.uninstall_impact import UninstallImpactAnalyzer
+ # Initialize installation history for audit logging
+ history = InstallationHistory()
+ install_id = None
+ start_time = datetime.now()
try:
analyzer = UninstallImpactAnalyzer()
# ... existing code ...
+ # Record removal start
+ if execute:
+ install_id = history.record_installation(
+ InstallationType.UNINSTALL, # or add REMOVE type
+ packages,
+ commands,
+ start_time
+ )
# ... after successful removal ...
+ if install_id:
+ history.update_installation(install_id, InstallationStatus.SUCCESS)
+ print(f"\n📝 Removal recorded (ID: {install_id})")
except Exception as e:
+ if install_id:
+ history.update_installation(install_id, InstallationStatus.FAILED, str(e))
self._print_error(f"Error during removal: {str(e)}")
return 1Based on coding guidelines: "Implement audit logging to ~/.cortex/history.db for all package operations".
Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In cortex/cli.py around lines 566-661, the remove() flow lacks audit logging to
~/.cortex/history.db; add a call to the same InstallationHistory API used by
install() to record each removal attempt. Specifically, import or reuse
InstallationHistory, and before returning from the remove() method record an
entry containing: operation="remove", packages=list of package names,
options={execute,dry_run,cascading,orphans_only}, timestamp, outcome={"success"
or "failure"}, and error_message if any; write the history entry for both
success and failure paths (including early validation errors and exceptions),
ensure history writes are best-effort (catch/log history-write errors but do not
change the removal exit code), and place the history write immediately after the
removal result is known (and also on validation/dry-run early returns) so the
audit trail is complete.
| def _generate_removal_commands(self, packages: list[str], cascading: bool) -> list[str]: | ||
| """Generate apt removal commands""" | ||
| commands = [] | ||
|
|
||
| pkg_list = " ".join(packages) | ||
|
|
||
| if cascading: | ||
| # Remove with dependencies | ||
| commands.append(f"sudo apt-get remove -y --auto-remove {pkg_list}") | ||
| else: | ||
| # Simple removal | ||
| commands.append(f"sudo apt-get remove -y {pkg_list}") | ||
|
|
||
| # Clean up | ||
| commands.append("sudo apt-get autoremove -y") | ||
| commands.append("sudo apt-get autoclean -y") | ||
|
|
||
| return commands |
There was a problem hiding this comment.
Silent sudo execution without user confirmation.
Per coding guidelines, there should be "No silent sudo execution - require explicit user confirmation". The generated commands use sudo apt-get remove -y which bypasses apt's confirmation prompt, and there's no explicit confirmation from the user before execution begins.
🔎 Proposed fix - add confirmation prompt
+ def _confirm_removal(self, packages: list[str], cascading: bool) -> bool:
+ """Prompt user to confirm removal before executing sudo commands."""
+ print("\n⚠️ The following packages will be removed:")
+ for pkg in packages:
+ print(f" • {pkg}")
+ if cascading:
+ print(" (with dependent packages)")
+
+ confirm = input("\nProceed with removal? (y/N): ")
+ return confirm.lower() == 'y'
def _generate_removal_commands(self, packages: list[str], cascading: bool) -> list[str]:
"""Generate apt removal commands"""
# ... existing code ...Then in remove(), before executing:
if execute:
+ if not self._confirm_removal(packages, cascading):
+ cx_print("Removal cancelled", "info")
+ return 0
self._print_status("⚙️", f"Removing {software}...")Based on coding guidelines: "No silent sudo execution - require explicit user confirmation".
Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In cortex/cli.py around lines 715-732, the generated apt removal commands
silently run sudo apt-get remove -y which bypasses user confirmation; remove the
automatic -y flag (and any --auto-remove variant) from the generated commands so
they require interactive confirmation, and ensure the calling remove() flow
prompts the user and only proceeds when the user explicitly confirms; if a
non-interactive/CI mode is needed, expose an explicit --yes/--assume-yes flag
that must be passed to opt into non-interactive removal rather than hiding it in
the command generation.
| self._print_check( | ||
| "WARN", | ||
| "No API keys configured (required for cloud models)", | ||
| "Configure API key: export ANTHROPIC_API_KEY=sk-... or run 'cortex wizard'", | ||
| "Firejail not installed (sandboxing unavailable)", | ||
| "Install: sudo apt-get install firejail", | ||
| ) |
There was a problem hiding this comment.
TypeError: Too many arguments to _print_check.
The _print_check method accepts 3 arguments (status, message, suggestion), but 5 string arguments are being passed here. This will cause a TypeError at runtime when Firejail is not installed.
It appears the API key warning message was accidentally inserted into the Firejail check.
🔎 Proposed fix
else:
self._print_check(
"WARN",
- "No API keys configured (required for cloud models)",
- "Configure API key: export ANTHROPIC_API_KEY=sk-... or run 'cortex wizard'",
"Firejail not installed (sandboxing unavailable)",
"Install: sudo apt-get install firejail",
)📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| self._print_check( | |
| "WARN", | |
| "No API keys configured (required for cloud models)", | |
| "Configure API key: export ANTHROPIC_API_KEY=sk-... or run 'cortex wizard'", | |
| "Firejail not installed (sandboxing unavailable)", | |
| "Install: sudo apt-get install firejail", | |
| ) | |
| self._print_check( | |
| "WARN", | |
| "Firejail not installed (sandboxing unavailable)", | |
| "Install: sudo apt-get install firejail", | |
| ) |
🤖 Prompt for AI Agents
In cortex/doctor.py around lines 357 to 363, the call to _print_check passes
five string arguments but the method only accepts three; remove the accidental
extra arguments by splitting this into two separate _print_check calls: one that
logs the API key warning with its suggestion, and a second that logs the
Firejail warning with its install suggestion, each with exactly three parameters
(status, message, suggestion).
| Includes fallback logic if primary LLM fails. | ||
| """ | ||
| """cortex/llm_router.py |
There was a problem hiding this comment.
Syntax error: Malformed docstring terminator.
Line 87 shows """cortex/llm_router.py which is invalid Python syntax. The docstring closing """ appears to have been corrupted by appending a file path string. This will cause a SyntaxError when the module is imported.
🔎 Proposed fix
- """cortex/llm_router.py
+ """📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| """cortex/llm_router.py | |
| """ |
🤖 Prompt for AI Agents
In cortex/llm_router.py around line 87, the module docstring is corrupted: it
currently reads `"""cortex/llm_router.py` which leaves the opening or closing
triple quotes malformed and will raise a SyntaxError; fix it by restoring a
valid docstring delimiter and content — either close the existing docstring with
a matching triple-quote on the same line or replace the line with a proper
multi-line or single-line docstring (e.g., start with """ and end with """) and
ensure no stray file path text remains inside the delimiter so the module
imports cleanly.
| # Check if this package only depends on the target package | ||
| success, stdout, _ = self._run_command(["apt-cache", "depends", dep_name]) | ||
|
|
||
| if success: | ||
| deps_count = len([line for line in stdout.split("\n") if "Depends:" in line]) | ||
|
|
||
| # If package only has 1 dependency (the one being removed), it's orphaned | ||
| if deps_count <= 1: | ||
| orphaned.append(dep_name) | ||
|
|
There was a problem hiding this comment.
Orphaned package detection logic may produce false positives.
The current logic marks a package as orphaned if it has ≤1 dependencies total. However, this doesn't verify that the single dependency is actually the package being removed. A package with one dependency on an unrelated package would incorrectly be flagged as orphaned.
🔎 Suggested fix
# Check if this package only depends on the target package
success, stdout, _ = self._run_command(["apt-cache", "depends", dep_name])
if success:
- deps_count = len([line for line in stdout.split("\n") if "Depends:" in line])
-
- # If package only has 1 dependency (the one being removed), it's orphaned
- if deps_count <= 1:
+ # Extract actual dependency names
+ deps = []
+ for line in stdout.split("\n"):
+ if "Depends:" in line:
+ dep = line.split("Depends:")[-1].strip()
+ if dep:
+ deps.append(dep)
+
+ # Package is orphaned if its only dependency is the target package
+ if len(deps) == 1 and deps[0] == package_name:
orphaned.append(dep_name)
+ elif len(deps) == 0:
+ orphaned.append(dep_name)| # Determine if safe to remove | ||
| safe_to_remove = ( | ||
| severity not in ["high", "critical"] and not self.is_package_installed(package_name) | ||
| ) or (is_installed and severity == "low") |
There was a problem hiding this comment.
The safe_to_remove logic appears inconsistent.
The condition severity not in ["high", "critical"] and not self.is_package_installed(package_name) marks uninstalled packages with low/medium severity as "safe to remove." This is confusing—if a package isn't installed, "safe to remove" is semantically meaningless.
Consider simplifying to focus on installed packages:
🔎 Suggested fix
# Determine if safe to remove
- safe_to_remove = (
- severity not in ["high", "critical"] and not self.is_package_installed(package_name)
- ) or (is_installed and severity == "low")
+ safe_to_remove = is_installed and severity in ["low", "medium"]Or if you want to be more conservative (only low severity is safe):
- safe_to_remove = (
- severity not in ["high", "critical"] and not self.is_package_installed(package_name)
- ) or (is_installed and severity == "low")
+ safe_to_remove = is_installed and severity == "low"🤖 Prompt for AI Agents
In cortex/uninstall_impact.py around lines 330-333 the safe_to_remove expression
treats packages that are not installed as "safe to remove", which is
semantically wrong; change the logic to only evaluate installed packages and
mark safe only when severity is acceptable — e.g., replace the current
expression with one that requires is_installed and severity == "low" (or, if
broader, is_installed and severity not in ["high","critical"]); update any
related comments/tests to reflect the new rule.
| 1. `/home/anuj/cortex/cortex/uninstall_impact.py` (506 lines) | ||
| - Core analyzer implementation | ||
| - 12+ public methods | ||
| - 4 dataclasses for type safety | ||
| - Full docstrings and type hints | ||
|
|
||
| 2. `/home/anuj/cortex/tests/test_uninstall_impact.py` (530 lines) |
There was a problem hiding this comment.
Use relative paths instead of absolute paths in documentation.
The documentation contains absolute paths like /home/anuj/cortex/cortex/uninstall_impact.py which are specific to the author's development environment. These should be relative paths for portability.
🔎 Suggested fix
### New Files Created
-1. `/home/anuj/cortex/cortex/uninstall_impact.py` (506 lines)
+1. `cortex/uninstall_impact.py` (506 lines)
- Core analyzer implementation
- 12+ public methods
- 4 dataclasses for type safety
- Full docstrings and type hints
-2. `/home/anuj/cortex/tests/test_uninstall_impact.py` (530 lines)
+2. `tests/test_uninstall_impact.py` (530 lines)📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| 1. `/home/anuj/cortex/cortex/uninstall_impact.py` (506 lines) | |
| - Core analyzer implementation | |
| - 12+ public methods | |
| - 4 dataclasses for type safety | |
| - Full docstrings and type hints | |
| 2. `/home/anuj/cortex/tests/test_uninstall_impact.py` (530 lines) | |
| 1. `cortex/uninstall_impact.py` (506 lines) | |
| - Core analyzer implementation | |
| - 12+ public methods | |
| - 4 dataclasses for type safety | |
| - Full docstrings and type hints | |
| 2. `tests/test_uninstall_impact.py` (530 lines) |
🤖 Prompt for AI Agents
In docs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.md around lines 142 to 148, the file
paths are absolute and environment-specific; change them to repository-relative
paths (e.g., remove the leading /home/anuj and leading slash so they read like
cortex/uninstall_impact.py and tests/test_uninstall_impact.py or
./cortex/uninstall_impact.py) so the documentation is portable across
environments, and update any other absolute paths in this document to the same
relative form.
| 3. `/home/anuj/cortex/docs/UNINSTALL_IMPACT_ANALYSIS.md` (430+ lines) | ||
| - User guide | ||
| - Usage examples | ||
| - Architecture explanation | ||
|
|
||
| 4. `/home/anuj/cortex/docs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.md` (390+ lines) | ||
| - Developer guide | ||
| - Implementation details | ||
| - Performance optimization | ||
|
|
||
| ### Modified Files | ||
| 1. `/home/anuj/cortex/cortex/cli.py` | ||
| - Added `remove` method (120+ lines) | ||
| - Added argument parser for remove command | ||
| - Updated help documentation | ||
| - Integrated CLI handler in main() |
There was a problem hiding this comment.
Additional absolute paths need correction.
Same issue as above - replace absolute paths with relative paths:
🔎 Suggested fix
-3. `/home/anuj/cortex/docs/UNINSTALL_IMPACT_ANALYSIS.md` (430+ lines)
+3. `docs/UNINSTALL_IMPACT_ANALYSIS.md` (430+ lines)
- User guide
- Usage examples
- Architecture explanation
-4. `/home/anuj/cortex/docs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.md` (390+ lines)
+4. `docs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.md` (390+ lines)
- Developer guide
- Implementation details
- Performance optimization
### Modified Files
-1. `/home/anuj/cortex/cortex/cli.py`
+1. `cortex/cli.py`🧰 Tools
🪛 markdownlint-cli2 (0.18.1)
167-167: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🤖 Prompt for AI Agents
In docs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.md around lines 153 to 168, the file
lists absolute filesystem paths (/home/anuj/cortex/...) which must be converted
to repository-relative paths; update each absolute path entry to a relative path
(e.g., docs/UNINSTALL_IMPACT_ANALYSIS.md,
docs/UNINSTALL_IMPACT_ANALYSIS_DEVELOPER.md, cortex/cli.py) and adjust any
surrounding text or bullet points to use these relative references, then save
and commit the change.
There was a problem hiding this comment.
Actionable comments posted: 1
♻️ Duplicate comments (6)
cortex/cli.py (4)
572-572: Theorphans_onlyparameter is unused.The parameter is defined but never referenced in the method logic or passed to any helper functions.
🔎 Verify usage or remove the parameter
#!/bin/bash # Check if orphans_only is used anywhere in the removal flow rg -n "orphans_only" --type=py -C3
566-607: Missing audit logging for removal operations.Per coding guidelines, all package operations must implement audit logging to
~/.cortex/history.db. Theinstall()method records operations viaInstallationHistory, butremove()does not.Based on coding guidelines: "Implement audit logging to ~/.cortex/history.db for all package operations"
746-763: Silent sudo execution without user confirmation.Per coding guidelines, there should be "No silent sudo execution - require explicit user confirmation". The generated commands use
sudo apt-get remove -ywhich bypasses apt's confirmation prompt.🔎 Proposed fix - remove automatic -y flags
def _generate_removal_commands(self, packages: list[str], cascading: bool) -> list[str]: """Generate apt removal commands""" commands = [] pkg_list = " ".join(packages) if cascading: # Remove with dependencies - commands.append(f"sudo apt-get remove -y --auto-remove {pkg_list}") + commands.append(f"sudo apt-get remove --auto-remove {pkg_list}") else: # Simple removal - commands.append(f"sudo apt-get remove -y {pkg_list}") + commands.append(f"sudo apt-get remove {pkg_list}") # Clean up - commands.append("sudo apt-get autoremove -y") - commands.append("sudo apt-get autoclean -y") + commands.append("sudo apt-get autoremove") + commands.append("sudo apt-get autoclean") return commandsBased on coding guidelines: "No silent sudo execution - require explicit user confirmation"
688-692: Unreachable code after return statement.Lines 688-692 are never executed because they follow a
return 0statement at line 681.🔎 Proposed fix
if result.success: self._print_success(f"{software} removed successfully!") print(f"\nCompleted in {result.total_duration:.2f} seconds") return 0 else: self._print_error("Removal failed") if result.error_message: print(f" Error: {result.error_message}", file=sys.stderr) return 1 - - return 0 - - except Exception as e: - self._print_error(f"Error during removal: {str(e)}") - return 1cortex/uninstall_impact.py (2)
284-293: Orphan detection logic may produce false positives.The current logic marks a package as orphaned if it has ≤1 dependencies total. However, this doesn't verify that the single dependency is actually the package being removed. A package with one dependency on an unrelated package would be incorrectly flagged as orphaned.
🔎 Proposed fix
# Check if this package only depends on the target package success, stdout, _ = self._run_command(["apt-cache", "depends", dep_name]) if success: - deps_count = len([line for line in stdout.split("\n") if "Depends:" in line]) - - # If package only has 1 dependency (the one being removed), it's orphaned - if deps_count <= 1: + # Extract actual dependency names + deps = [] + for line in stdout.split("\n"): + if "Depends:" in line: + dep = line.split("Depends:")[-1].strip() + if dep: + deps.append(dep) + + # Package is orphaned if its only dependency is the target package + if len(deps) == 1 and deps[0] == package_name: orphaned.append(dep_name) + elif len(deps) == 0: + orphaned.append(dep_name)
330-333: Thesafe_to_removelogic appears inconsistent.The condition
severity not in ["high", "critical"] and not self.is_package_installed(package_name)marks uninstalled packages with low/medium severity as "safe to remove." This is semantically incorrect—if a package isn't installed, "safe to remove" is meaningless.🔎 Proposed fix
# Determine if safe to remove - safe_to_remove = ( - severity not in ["high", "critical"] and not self.is_package_installed(package_name) - ) or (is_installed and severity == "low") + safe_to_remove = is_installed and severity in ["low", "medium"]Or for a more conservative approach (only low severity):
- safe_to_remove = ( - severity not in ["high", "critical"] and not self.is_package_installed(package_name) - ) or (is_installed and severity == "low") + safe_to_remove = is_installed and severity == "low"
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🧰 Additional context used
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**/*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*.py: Follow PEP 8 style guide
Type hints required in Python code
Docstrings required for all public APIs
Files:
cortex/uninstall_impact.pycortex/cli.py
**/*install*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*install*.py: Dry-run by default for all installations in command execution
No silent sudo execution - require explicit user confirmation
Implement audit logging to ~/.cortex/history.db for all package operations
Files:
cortex/uninstall_impact.py
🧠 Learnings (2)
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : Implement audit logging to ~/.cortex/history.db for all package operations
Applied to files:
cortex/cli.py
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : No silent sudo execution - require explicit user confirmation
Applied to files:
cortex/cli.py
🧬 Code graph analysis (1)
cortex/cli.py (3)
cortex/coordinator.py (2)
execute(230-279)InstallationCoordinator(51-324)cortex/first_run_wizard.py (1)
_print_error(746-748)cortex/uninstall_impact.py (1)
analyze_uninstall_impact(296-353)
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Actionable comments posted: 0
Caution
Some comments are outside the diff and can’t be posted inline due to platform limitations.
⚠️ Outside diff range comments (1)
cortex/doctor.py (1)
74-107: Critical: Duplicate check execution inflates diagnostic counts.The same checks (Python & Dependencies, GPU & Acceleration, AI & Services) are executed twice within the spinner block—once at lines 74-85 and again at lines 92-102. This causes each check to append its result to
self.passes,self.warnings, orself.failurestwice, producing incorrect summary counts and potentially changing the exit code.🔎 Proposed fix
Remove the duplicate checks at lines 92-102:
self._print_section("AI & Services") self._check_ollama() self._check_api_keys() # System Info (includes API provider and security features) self._print_section("System Configuration") self._check_api_keys() self._check_security_tools() - # Python & Dependencies - self._print_section("Python & Dependencies") - self._check_python() - self._check_dependencies() - - self._print_section("GPU & Acceleration") - self._check_gpu_driver() - self._check_cuda() - - self._print_section("AI & Services") - self._check_ollama() - # System Resources self._print_section("System Resources") self._check_disk_space() self._check_memory()
♻️ Duplicate comments (3)
cortex/cli.py (3)
566-608: Missing audit logging for removal operations.The
removemethod does not record operations to~/.cortex/history.dbviaInstallationHistory, creating an incomplete audit trail. Theinstallmethod records all operations, but removals are not tracked.Based on learnings: "Implement audit logging to ~/.cortex/history.db for all package operations"
572-572: Parameterorphans_onlyis unused.The
orphans_onlyparameter is defined but never referenced in the method body. Either implement the intended behavior (e.g., filter to only remove orphaned packages) or remove the parameter from the signature.
738-755: Silent sudo execution without user confirmation.The generated commands use
sudo apt-get remove -y, which bypasses apt's confirmation prompt. Per coding guidelines, explicit user confirmation is required before executing sudo commands.Based on learnings: "No silent sudo execution - require explicit user confirmation"
🧹 Nitpick comments (1)
cortex/cli.py (1)
616-625: Consider a more specific return type hint.The return type
listcould be refined tolist[UninstallImpactAnalysis]for better type safety, assuming the analyzer returns that type.🔎 Proposed refinement
- def _analyze_removal_impact(self, packages: list[str]) -> list: + def _analyze_removal_impact(self, packages: list[str]) -> list[UninstallImpactAnalysis]: """Analyze impact for all packages""" from cortex.uninstall_impact import UninstallImpactAnalyzer + # Add this import at top if not already present: + # from cortex.uninstall_impact import UninstallImpactAnalysis
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**/*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*.py: Follow PEP 8 style guide
Type hints required in Python code
Docstrings required for all public APIs
Files:
cortex/doctor.pycortex/cli.py
🧠 Learnings (2)
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : Implement audit logging to ~/.cortex/history.db for all package operations
Applied to files:
cortex/cli.py
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : No silent sudo execution - require explicit user confirmation
Applied to files:
cortex/cli.py
🧬 Code graph analysis (1)
cortex/cli.py (2)
cortex/coordinator.py (2)
execute(230-279)InstallationCoordinator(51-324)cortex/uninstall_impact.py (1)
UninstallImpactAnalyzer(62-440)
🔇 Additional comments (6)
cortex/cli.py (6)
609-614: LGTM!The parsing logic correctly splits, strips, and validates the package list.
627-633: LGTM!The guard correctly prevents execution when neither
--executenor--dry-runis specified, with a helpful user message.
635-643: LGTM!The safety validation correctly blocks high/critical-impact removals unless
--cascadingis explicitly provided, preventing accidental system breakage.
645-686: LGTM!The execution flow correctly delegates to
InstallationCoordinatorand provides progress reporting. The dry-run path is properly handled.
688-736: LGTM!The impact display provides comprehensive information: installation status, severity, dependencies, affected services, and recommendations. The summary aggregation is helpful.
1379-1393: LGTM!The CLI wiring correctly defines the remove subcommand with all required flags and properly dispatches to
cli.removewith the parsed arguments.Also applies to: 1558-1565
…om 29 to 15 - Extracted _print_package_impact() for per-package display - Extracted _print_dependencies() for dependency formatting - Extracted _print_services() for service impact display - Extracted _print_orphaned() for orphaned package formatting - Extracted _print_impact_summary() for summary calculation - Extracted _print_impact_recommendations() for recommendation display - Removed unused Table import - Maintains identical output while improving maintainability
- Removed orphans_only parameter from function signature - Removed corresponding docstring entry - Parameter was unused in method implementation - All tests pass (36/36)
- Removed orphans_only=args.orphans_only from remove() call - Parameter was removed from function signature - Call site now matches function definition - All tests pass (36/36)
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Actionable comments posted: 1
♻️ Duplicate comments (2)
cortex/cli.py (2)
753-770: Silent sudo execution without user confirmation.The generated commands include the
-yflag (lines 761, 764, 767, 768), which bypasses apt's confirmation prompt. Per coding guidelines, there should be "No silent sudo execution - require explicit user confirmation."Remove the
-yflags to require interactive confirmation, or add an explicit confirmation prompt in theremove()flow before execution begins. If a non-interactive mode is needed, expose it as an explicit--yesflag rather than making it the default.Based on coding guidelines: "No silent sudo execution - require explicit user confirmation".
566-605: Missing audit logging for package removal operations.Per coding guidelines, all package operations should implement audit logging to
~/.cortex/history.db. Theinstall()method records operations usingInstallationHistory, butremove()does not, creating an incomplete audit trail.Record removal attempts (both successful and failed) including package names, options, timestamps, and outcomes.
Based on coding guidelines: "Implement audit logging to ~/.cortex/history.db for all package operations".
🧹 Nitpick comments (1)
cortex/cli.py (1)
614-623: Consider adding complete type hints to helper methods.Several internal helper methods have incomplete type hints:
- Line 614:
_analyze_removal_impact()returnslist(could belist[UninstallImpactAnalysis])- Line 686:
analyses: listparameter (could belist[UninstallImpactAnalysis])- Lines 697, 723, 733:
analysisparameters missing type hintsWhile these are internal methods, complete type hints improve IDE support and catch potential type errors.
🔎 Proposed type hint improvements
- def _analyze_removal_impact(self, packages: list[str]) -> list: + def _analyze_removal_impact(self, packages: list[str]) -> list["UninstallImpactAnalysis"]: """Analyze impact for all packages""" from cortex.uninstall_impact import UninstallImpactAnalyzer - def _display_removal_impact(self, analyses: list) -> None: + def _display_removal_impact(self, analyses: list["UninstallImpactAnalysis"]) -> None: """Display impact analysis for package removal""" - def _print_package_impact(self, analysis) -> None: + def _print_package_impact(self, analysis: "UninstallImpactAnalysis") -> None: """Print impact details for a single package""" - def _print_dependencies(self, analysis, pkg: str) -> None: + def _print_dependencies(self, analysis: "UninstallImpactAnalysis", pkg: str) -> None: """Print directly dependent packages""" - def _print_services(self, analysis) -> None: + def _print_services(self, analysis: "UninstallImpactAnalysis") -> None: """Print affected services""" - def _print_orphaned(self, analysis) -> None: + def _print_orphaned(self, analysis: "UninstallImpactAnalysis") -> None: """Print orphaned packages""" - def _print_impact_summary(self, analyses: list) -> None: + def _print_impact_summary(self, analyses: list["UninstallImpactAnalysis"]) -> None: """Print removal impact summary""" - def _print_impact_recommendations(self, analyses: list) -> None: + def _print_impact_recommendations(self, analyses: list["UninstallImpactAnalysis"]) -> None: """Print removal recommendations"""As per coding guidelines: "Type hints required in Python code".
Also applies to: 686-752
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🧰 Additional context used
📓 Path-based instructions (1)
**/*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*.py: Follow PEP 8 style guide
Type hints required in Python code
Docstrings required for all public APIs
Files:
cortex/cli.py
🧠 Learnings (2)
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : Implement audit logging to ~/.cortex/history.db for all package operations
Applied to files:
cortex/cli.py
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : No silent sudo execution - require explicit user confirmation
Applied to files:
cortex/cli.py
🧬 Code graph analysis (1)
cortex/cli.py (3)
cortex/coordinator.py (2)
execute(230-279)InstallationCoordinator(51-324)cortex/first_run_wizard.py (1)
_print_error(746-748)cortex/uninstall_impact.py (2)
UninstallImpactAnalyzer(62-440)analyze_uninstall_impact(296-353)
🔇 Additional comments (1)
README.md (1)
67-67: LGTM! Documentation accurately reflects the new feature.The documentation updates clearly describe the Smart Uninstall feature, including:
- Feature highlights with dependency and service impact analysis
- Usage examples demonstrating dry-run and execute modes
- Complete command reference table entries
- Updated project structure showing the new module
- Status updates reflecting test coverage achievements
The changes are well-integrated and provide users with clear guidance on the new removal capabilities.
Also applies to: 136-156, 230-236, 334-335
| remove_parser.add_argument( | ||
| "--orphans-only", | ||
| action="store_true", | ||
| help="Only remove orphaned packages", | ||
| ) |
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🛠️ Refactor suggestion | 🟠 Major
Remove unused --orphans-only argument from parser.
The --orphans-only argument is defined in the argument parser (lines 1404-1408) but is never passed to cli.remove() (lines 1574-1579). The parameter was correctly removed from the remove() method signature, but the CLI argument definition should also be removed to avoid user confusion.
🔎 Proposed fix
remove_parser.add_argument(
"--cascading",
action="store_true",
help="Remove dependent packages automatically",
)
- remove_parser.add_argument(
- "--orphans-only",
- action="store_true",
- help="Only remove orphaned packages",
- )Also applies to: 1573-1579
🤖 Prompt for AI Agents
In cortex/cli.py around lines 1404-1408 (and also referencing lines 1573-1579),
the CLI defines a now-unused --orphans-only argument that was removed from the
remove() function signature; remove the add_argument(...) call for
--orphans-only from the parser (delete lines 1404-1408) and, if any help text or
usage examples reference it elsewhere (e.g., around lines 1573-1579), remove or
update those references so the CLI and docs/tests no longer mention or pass
--orphans-only.
|
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Actionable comments posted: 8
♻️ Duplicate comments (3)
cortex/cli.py (3)
1404-1408: Remove unused--orphans-onlyargument.The
--orphans-onlyflag is defined in the argument parser but is never passed tocli.remove()(lines 1573-1579). This was noted in a previous review as addressed, but the argument definition still remains, which will confuse users who try to use it.🔎 Proposed fix
remove_parser.add_argument( "--cascading", action="store_true", help="Remove dependent packages automatically", ) - remove_parser.add_argument( - "--orphans-only", - action="store_true", - help="Only remove orphaned packages", - )Also applies to: 1573-1579
753-770: Silent sudo execution without user confirmation.Per coding guidelines and previous review feedback, the generated commands use
sudo apt-get remove -ywhich bypasses apt's confirmation prompt. There is no explicit user confirmation before these privileged operations execute.The
-yflag automatically answers "yes" to all prompts, which is dangerous for removal operations. Users should explicitly confirm what will be removed, especially for system packages.🔎 Proposed fix - require explicit confirmation
Option 1: Remove the
-yflag (recommended for interactive use):def _generate_removal_commands(self, packages: list[str], cascading: bool) -> list[str]: """Generate apt removal commands""" commands = [] pkg_list = " ".join(packages) if cascading: # Remove with dependencies - commands.append(f"sudo apt-get remove -y --auto-remove {pkg_list}") + commands.append(f"sudo apt-get remove --auto-remove {pkg_list}") else: # Simple removal - commands.append(f"sudo apt-get remove -y {pkg_list}") + commands.append(f"sudo apt-get remove {pkg_list}") # Clean up - commands.append("sudo apt-get autoremove -y") - commands.append("sudo apt-get autoclean -y") + commands.append("sudo apt-get autoremove") + commands.append("sudo apt-get autoclean") return commandsOption 2: Add a confirmation prompt before execution:
Add a new method to confirm removal:
def _confirm_removal(self, packages: list[str], analyses: list[Any]) -> bool: """Prompt user to confirm removal before executing sudo commands.""" print("\n⚠️ The following packages will be removed:") for analysis in analyses: if analysis.installed: print(f" • {analysis.package_name} ({analysis.installed_version})") has_critical = any(a.severity in ["high", "critical"] for a in analyses) if has_critical: print("\n⚠️ WARNING: Some packages have HIGH or CRITICAL impact!") confirm = input("\nProceed with removal? (yes/N): ") return confirm.lower() in ["yes", "y"]Then call it in
_execute_removalbefore running the coordinator:def _execute_removal( self, software: str, packages: list[str], cascading: bool, execute: bool, dry_run: bool ) -> int: """Execute the actual removal""" + # Note: Need to pass analyses here too commands = self._generate_removal_commands(packages, cascading) if dry_run or not execute: print("\nRemoval commands (dry run):") for i, cmd in enumerate(commands, 1): print(f" {i}. {cmd}") if dry_run: print("\n(Dry run mode - commands not executed)") return 0 + # Require explicit confirmation before executing + if not self._confirm_removal(packages, analyses): + cx_print("Removal cancelled", "info") + return 0 + return self._run_removal_coordinator(software, commands)Based on learnings: "No silent sudo execution - require explicit user confirmation".
566-606: Missing audit logging for package removal operations.Per coding guidelines and previous review feedback, all package operations must implement audit logging to
~/.cortex/history.db. Theinstall()method (lines 316-564) properly records operations usingInstallationHistory, butremove()does not create any audit trail.This creates an incomplete and inconsistent audit history, making it impossible to track removal operations, rollback removals, or investigate issues.
🔎 Proposed fix - add history recording
At the top of the method, initialize history tracking:
def remove( self, software: str, execute: bool = False, dry_run: bool = False, cascading: bool = False, ) -> int: """...""" + from cortex.installation_history import InstallationHistory + + # Initialize installation history for audit logging + history = InstallationHistory() + install_id = None + start_time = datetime.now() + try: # Parse and validate packages packages = self._parse_removal_packages(software) if not packages: return 1Then in
_execute_removalbefore executing commands:def _execute_removal( self, software: str, packages: list[str], cascading: bool, execute: bool, dry_run: bool ) -> int: """Execute the actual removal""" commands = self._generate_removal_commands(packages, cascading) + + # Record operation if executing or dry-run + history = InstallationHistory() + install_id = None + if execute or dry_run: + install_id = history.record_installation( + InstallationType.UNINSTALL, # or add REMOVE type + packages, + commands, + datetime.now() + )And update success/failure paths in
_run_removal_coordinator:if result.success: self._print_success(f"{software} removed successfully!") print(f"\nCompleted in {result.total_duration:.2f} seconds") + if install_id: + history.update_installation(install_id, InstallationStatus.SUCCESS) + print(f"\n📝 Removal recorded (ID: {install_id})") return 0 else: self._print_error("Removal failed") if result.error_message: print(f" Error: {result.error_message}", file=sys.stderr) + if install_id: + history.update_installation(install_id, InstallationStatus.FAILED, result.error_message) + print(f"\n📝 Removal recorded (ID: {install_id})") return 1Based on learnings: "Implement audit logging to ~/.cortex/history.db for all package operations".
📜 Review details
Configuration used: defaults
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (1)
cortex/cli.py
🧰 Additional context used
📓 Path-based instructions (1)
**/*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*.py: Follow PEP 8 style guide
Type hints required in Python code
Docstrings required for all public APIs
Files:
cortex/cli.py
🧠 Learnings (2)
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : Implement audit logging to ~/.cortex/history.db for all package operations
Applied to files:
cortex/cli.py
📚 Learning: 2025-12-11T12:03:24.071Z
Learnt from: CR
Repo: cortexlinux/cortex PR: 0
File: AGENTS.md:0-0
Timestamp: 2025-12-11T12:03:24.071Z
Learning: Applies to **/*install*.py : No silent sudo execution - require explicit user confirmation
Applied to files:
cortex/cli.py
🔇 Additional comments (7)
cortex/cli.py (7)
625-631: LGTM!The method correctly gates execution based on the
executeanddry_runflags, with clear user feedback.
633-641: LGTM!The safety validation correctly prevents potentially dangerous removals without the explicit
--cascadingflag. This is a good safeguard.
643-658: LGTM!The execution logic correctly handles both dry-run and actual execution paths, with clear user feedback.
659-684: LGTM!The coordinator pattern is correctly applied, reusing the existing
InstallationCoordinatorinfrastructure for consistent command execution and error handling.Note: Audit logging should be integrated here (see earlier comment on lines 566-606).
1295-1295: LGTM!The help text clearly describes the new remove command functionality.
1573-1579: LGTM!The command routing correctly maps the CLI arguments to the
remove()method parameters.
607-613: Add missing return type hint.Per PEP 8 and coding guidelines, type hints are required. The method signature is missing the return type annotation.
🔎 Proposed fix
- def _parse_removal_packages(self, software: str) -> list[str]: + def _parse_removal_packages(self, software: str) -> list[str]:Wait, the return type is already present in the annotated code. Let me verify... Actually checking line 607, the return type
-> list[str]is present. This is correct, no issue here.Actually, re-reading the code, the return type hint IS present on line 607:
-> list[str]. So this is fine.
| def _analyze_removal_impact(self, packages: list[str]) -> list: | ||
| """Analyze impact for all packages""" | ||
| from cortex.uninstall_impact import UninstallImpactAnalyzer | ||
|
|
||
| analyzer = UninstallImpactAnalyzer() | ||
| analyses = [] | ||
| for package in packages: | ||
| analysis = analyzer.analyze_uninstall_impact(package) | ||
| analyses.append(analysis) | ||
| return analyses |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing return type hint.
The method is missing a return type annotation. While the implementation is correct, type hints are required per coding guidelines.
🔎 Proposed fix
- def _analyze_removal_impact(self, packages: list[str]) -> list:
+ def _analyze_removal_impact(self, packages: list[str]) -> list[Any]:
"""Analyze impact for all packages"""
from cortex.uninstall_impact import UninstallImpactAnalyzerIf the UninstallImpactAnalyzer returns a specific type (e.g., UninstallImpactAnalysis), use that instead:
def _analyze_removal_impact(self, packages: list[str]) -> list[UninstallImpactAnalysis]:
"""Analyze impact for all packages"""
- from cortex.uninstall_impact import UninstallImpactAnalyzer
+ from cortex.uninstall_impact import UninstallImpactAnalyzer, UninstallImpactAnalysisAs per coding guidelines: "Type hints required in Python code".
Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In cortex/cli.py around lines 614 to 623 the method _analyze_removal_impact is
missing a return type annotation; update the signature to include the correct
return type (e.g., list[UninstallImpactAnalysis]) by importing
UninstallImpactAnalysis from cortex.uninstall_impact (or use list[Any] /
list["UninstallImpactAnalysis"] with from __future__ import annotations if the
type would create a circular import), and keep the implementation unchanged so
the function returns the annotated list type.
| def _display_removal_impact(self, analyses: list) -> None: | ||
| """Display impact analysis for package removal""" | ||
| print("\n⚠️ Impact Analysis:") | ||
| print("=" * 70) | ||
|
|
||
| for analysis in analyses: | ||
| self._print_package_impact(analysis) | ||
|
|
||
| self._print_impact_summary(analyses) | ||
| self._print_impact_recommendations(analyses) |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing type hint for list elements.
The analyses parameter should specify the element type for better type safety.
🔎 Proposed fix
- def _display_removal_impact(self, analyses: list) -> None:
+ def _display_removal_impact(self, analyses: list[Any]) -> None:
"""Display impact analysis for package removal"""Or if the type is available:
- def _display_removal_impact(self, analyses: list) -> None:
+ def _display_removal_impact(self, analyses: list[UninstallImpactAnalysis]) -> None:As per coding guidelines: "Type hints required in Python code".
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def _display_removal_impact(self, analyses: list) -> None: | |
| """Display impact analysis for package removal""" | |
| print("\n⚠️ Impact Analysis:") | |
| print("=" * 70) | |
| for analysis in analyses: | |
| self._print_package_impact(analysis) | |
| self._print_impact_summary(analyses) | |
| self._print_impact_recommendations(analyses) | |
| def _display_removal_impact(self, analyses: list[Any]) -> None: | |
| """Display impact analysis for package removal""" | |
| print("\n⚠️ Impact Analysis:") | |
| print("=" * 70) | |
| for analysis in analyses: | |
| self._print_package_impact(analysis) | |
| self._print_impact_summary(analyses) | |
| self._print_impact_recommendations(analyses) |
🤖 Prompt for AI Agents
In cortex/cli.py around lines 686 to 695, the parameter analyses is annotated as
plain list which lacks element typing; update the signature to include the
specific element type (e.g., list[Analysis] or List[Analysis] or list[dict]
depending on the actual Analysis type in the codebase), add the necessary import
from typing (if using List) or rely on built-in generic list[] for Python 3.9+,
and update any related docstring if needed so the function signature provides a
concrete element type for type checkers.
| def _print_package_impact(self, analysis) -> None: | ||
| """Print impact details for a single package""" | ||
| pkg = analysis.package_name | ||
|
|
||
| if not analysis.installed: | ||
| print(f"\n📦 {pkg}: [Not installed]") | ||
| return | ||
|
|
||
| print(f"\n📦 {pkg} ({analysis.installed_version})") | ||
| print(f" Severity: {analysis.severity.upper()}") | ||
| self._print_dependencies(analysis, pkg) | ||
| self._print_services(analysis) | ||
| self._print_orphaned(analysis) |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing type hint for analysis parameter.
The analysis parameter lacks a type annotation.
🔎 Proposed fix
- def _print_package_impact(self, analysis) -> None:
+ def _print_package_impact(self, analysis: Any) -> None:
"""Print impact details for a single package"""Or use the specific type if available:
- def _print_package_impact(self, analysis) -> None:
+ def _print_package_impact(self, analysis: UninstallImpactAnalysis) -> None:As per coding guidelines: "Type hints required in Python code".
🤖 Prompt for AI Agents
In cortex/cli.py around lines 697 to 709, the method _print_package_impact is
missing a type annotation for the analysis parameter; add a proper type hint
(preferably the concrete type, e.g., PackageAnalysis or Analysis from the module
that defines it) to the signature, and import that type at the top of the file;
if the concrete type is not available or would create a circular import, use
typing.Any (add "from typing import Any") as a stopgap and document to replace
with the real type later.
| def _print_dependencies(self, analysis, pkg: str) -> None: | ||
| """Print directly dependent packages""" | ||
| if not analysis.directly_depends: | ||
| return | ||
|
|
||
| print(f"\n Directly depends on {pkg}:") | ||
| for dep in analysis.directly_depends[:5]: | ||
| critical = " ⚠️ CRITICAL" if dep.critical else "" | ||
| print(f" • {dep.name}{critical}") | ||
| if len(analysis.directly_depends) > 5: | ||
| print(f" ... and {len(analysis.directly_depends) - 5} more") |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing type hint for analysis parameter.
Consistent with other methods, the analysis parameter should have a type annotation.
🔎 Proposed fix
- def _print_dependencies(self, analysis, pkg: str) -> None:
+ def _print_dependencies(self, analysis: Any, pkg: str) -> None:
"""Print directly dependent packages"""As per coding guidelines: "Type hints required in Python code".
🤖 Prompt for AI Agents
In cortex/cli.py around lines 711 to 721 the _print_dependencies method's
analysis parameter lacks a type annotation; add the same type hint used by other
methods that accept analysis objects in this module (for example Analysis or
DependencyAnalysis), update the function signature to include that type for
analysis, and add any necessary import at the top of the file so the annotation
resolves.
| def _print_services(self, analysis) -> None: | ||
| """Print affected services""" | ||
| if not analysis.affected_services: | ||
| return | ||
|
|
||
| print("\n Services affected:") | ||
| for svc in analysis.affected_services: | ||
| critical = " ⚠️ CRITICAL" if svc.critical else "" | ||
| print(f" • {svc.service_name} ({svc.status}){critical}") |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing type hint for analysis parameter.
🔎 Proposed fix
- def _print_services(self, analysis) -> None:
+ def _print_services(self, analysis: Any) -> None:
"""Print affected services"""As per coding guidelines: "Type hints required in Python code".
🤖 Prompt for AI Agents
In cortex/cli.py around lines 723 to 731, the _print_services method is missing
a type hint for the analysis parameter; add an appropriate type annotation
(e.g., Analysis or the actual class/type used in this module) to the signature
like def _print_services(self, analysis: Analysis) -> None, and import or
reference the correct type at the top of the file (use typing.Optional/Union if
nullable) so the function complies with the project's type-hinting guideline.
| def _print_orphaned(self, analysis) -> None: | ||
| """Print orphaned packages""" | ||
| if analysis.orphaned_packages: | ||
| print(f"\n Would orphan: {', '.join(analysis.orphaned_packages[:3])}") |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing type hint for analysis parameter.
🔎 Proposed fix
- def _print_orphaned(self, analysis) -> None:
+ def _print_orphaned(self, analysis: Any) -> None:
"""Print orphaned packages"""As per coding guidelines: "Type hints required in Python code".
🤖 Prompt for AI Agents
In cortex/cli.py around lines 733 to 736, the _print_orphaned method lacks a
type annotation for the analysis parameter; add a type hint (e.g. def
_print_orphaned(self, analysis: Analysis) -> None:) by importing the correct
Analysis type from its module if it exists, otherwise import Any from typing and
use analysis: Any; update imports accordingly and run static type checks to
ensure no remaining violations.
| def _print_impact_summary(self, analyses: list) -> None: | ||
| """Print removal impact summary""" | ||
| total_affected = sum(len(a.directly_depends) for a in analyses) | ||
| total_services = sum(len(a.affected_services) for a in analyses) | ||
|
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||
| print(f"\n{'=' * 70}") | ||
| print(f"Would affect: {total_affected} packages, {total_services} services") |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing type hint for list elements.
🔎 Proposed fix
- def _print_impact_summary(self, analyses: list) -> None:
+ def _print_impact_summary(self, analyses: list[Any]) -> None:
"""Print removal impact summary"""As per coding guidelines: "Type hints required in Python code".
Committable suggestion skipped: line range outside the PR's diff.
🤖 Prompt for AI Agents
In cortex/cli.py around lines 738 to 744, the parameter "analyses: list" is
missing an element type; update the signature to include the concrete element
type (for example, analyses: list[Analysis] or analyses: list["Analysis"]) and
import or forward-declare the Analysis type as needed (or use
typing.Sequence[Analysis] if preferred) so the list elements are fully
type-annotated per project guidelines.
| def _print_impact_recommendations(self, analyses: list) -> None: | ||
| """Print removal recommendations""" | ||
| print("\n💡 Recommendations:") | ||
| for analysis in analyses: | ||
| for rec in analysis.recommendations[:2]: | ||
| print(f" {rec}") |
There was a problem hiding this comment.
🛠️ Refactor suggestion | 🟠 Major
Add missing type hint for list elements.
🔎 Proposed fix
- def _print_impact_recommendations(self, analyses: list) -> None:
+ def _print_impact_recommendations(self, analyses: list[Any]) -> None:
"""Print removal recommendations"""As per coding guidelines: "Type hints required in Python code".
🤖 Prompt for AI Agents
In cortex/cli.py around lines 746 to 751, the parameter "analyses: list" lacks
an element type hint; change the signature to include a concrete element type
(e.g., analyses: list[Analysis]) or, if the Analysis class is not directly
available, use analyses: list[Any] and add the necessary import from typing (Any
or the Analysis model). Ensure the named type is imported at top of the file so
static checkers pass and no other logic needs to change.
3 participants
Related Issue
Closes #113
Summary
Implements comprehensive Uninstall Impact Analysis feature for Cortex Linux, enabling safe package removal by analyzing dependencies, predicting service impacts, and providing actionable recommendations.
What This PR Does:
UninstallImpactAnalyzerclass (506 lines) with complete dependency impact analysiscortex remove <package>with--execute,--dry-run,--cascading,--orphans-onlyflagsFeatures Implemented:
✅ Dependency impact analysis
✅ Show dependent packages (direct & indirect)
✅ Predict breaking changes
✅ Service impact assessment
✅ Orphan package detection
✅ Safe uninstall recommendations
✅ Cascading removal support
✅ Unit tests with >80% coverage
✅ Complete documentation
Example Usage: