feat(uninstall): implement impact analysis with dependency and service detection #391
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- 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
requested review from
Suyashd999 and
mikejmorgan-ai
as code owners
📝 WalkthroughWalkthroughAdds an Uninstall Impact Analysis feature: a new analyzer module with dataclasses and CLI integration ( Changes
Sequence Diagram(s)sequenceDiagram
actor User
participant CLI as Cortex CLI
participant Analyzer as UninstallImpactAnalyzer
participant System as System (dpkg/apt-cache/systemctl)
participant Coordinator as Execution Coordinator
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 / apt-cache / systemctl calls
System-->>Analyzer: installed info, reverse-deps, service statuses
Analyzer-->>CLI: UninstallImpactAnalysis (severity, deps, services, orphans, recommendations)
CLI->>Output: render summary / optionally export JSON
alt execute flag
CLI->>Coordinator: submit removal commands
Coordinator->>System: run removal commands
System-->>Coordinator: execution results
Coordinator-->>CLI: success/failure
CLI-->>User: completion status
else dry-run / preview
CLI-->>User: preview commands / recommendations
end
Estimated code review effort🎯 4 (Complex) | ⏱️ ~60 minutes Possibly related PRs
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✅ Passed checks (4 passed)
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⚠️ 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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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
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📓 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
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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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**/*.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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cortex/llm_router.py (4)
123-150: Claude model parameter properly initialized.The
claude_modelparameter is added to__init__with appropriate default and the model is resolved correctly via theCLAUDE_MODELSmapping with fallback to haiku.However, this selected model is not used in the actual API calls (see Lines 358 and 643).
338-392: Critical: Hardcoded model ignores user selection.The
_complete_claudemethod hardcodes"claude-sonnet-4-20250514"on Line 358, completely ignoringself.claude_modelthat was set based on the user'sclaude_modelparameter. This means users who specifyclaude_model="haiku"to reduce costs will still be charged for Sonnet usage.The same issue exists in
_acomplete_claudeat Line 643.🔧 Fix to use selected model
def _complete_claude( self, messages: list[dict[str, str]], temperature: float, max_tokens: int, tools: list[dict] | None = None, ) -> LLMResponse: """Generate completion using Claude API.""" # Extract system message if present system_message = None user_messages = [] for msg in messages: if msg["role"] == "system": system_message = msg["content"] else: user_messages.append(msg) # Call Claude API kwargs = { - "model": "claude-sonnet-4-20250514", + "model": self.claude_model, "max_tokens": max_tokens, "temperature": temperature, "messages": user_messages, } if system_message: kwargs["system"] = system_message if tools: # Convert OpenAI tool format to Claude format if needed kwargs["tools"] = tools response = self.claude_client.messages.create(**kwargs) # Extract content content = "" for block in response.content: if hasattr(block, "text"): content += block.text # Calculate cost input_tokens = response.usage.input_tokens output_tokens = response.usage.output_tokens cost = self._calculate_cost(LLMProvider.CLAUDE, input_tokens, output_tokens) return LLMResponse( content=content, provider=LLMProvider.CLAUDE, - model="claude-sonnet-4-20250514", + model=self.claude_model, tokens_used=input_tokens + output_tokens, cost_usd=cost, latency_seconds=0.0, # Set by caller raw_response=response.model_dump() if hasattr(response, "model_dump") else None, )Apply the same fix to
_acomplete_claudeat Lines 620-676.
620-676: Critical: Async method also hardcodes model.The
_acomplete_claudeasync method has the same issue as_complete_claude- it hardcodes"claude-sonnet-4-20250514"at Line 643 instead of usingself.claude_model.Apply the same fix as suggested for
_complete_claude(Lines 338-392).
95-109: Update COSTS dictionary to use Claude Haiku pricing instead of Sonnet.The
COSTSdictionary currently uses Claude 3.5 Sonnet pricing ($3.00 input, $15.00 output per 1M tokens), but since the default model is Haiku (claude_model: str = "haiku"), the costs should reflect Haiku pricing: $0.80 input and $4.00 output per 1M tokens. Update the dictionary to match:LLMProvider.CLAUDE: { "input": 0.80, # $0.80 per 1M input tokens (Haiku) "output": 4.0, # $4.00 per 1M output tokens (Haiku) },cortex/cli.py (1)
1793-1793: Fix CI failure: Add ShellEnvironmentAnalyzer to TYPE_CHECKING importsThe pipeline is failing because
ShellEnvironmentAnalyzeris not available for type checking. While the runtime import at line 1653 works, the type hint at line 1793 causes a lint error.🔧 Proposed fix
Add to the TYPE_CHECKING imports at the top of the file:
if TYPE_CHECKING: from cortex.uninstall_impact import UninstallImpactAnalysis + from cortex.shell_env_analyzer import ShellEnvironmentAnalyzerThis will resolve the F821 error while maintaining the lazy runtime import pattern used elsewhere in the file.
🤖 Fix all issues with AI agents
In @cortex/cli.py:
- Around line 2414-2418: The --cascading flag help text is wrong; update the
remove_parser.add_argument call for "--cascading" to use a descriptive help
string that reflects cascading removal of dependents (e.g., "Cascade removal to
dependent packages" or "Also remove packages that depend on the target"), so the
CLI help correctly documents the flag's behavior for users.
In @cortex/llm/interpreter.py:
- Around line 62-64: The router is ignoring its configured claude_model because
_complete_claude and _acomplete_claude hardcode "claude-sonnet-4-20250514";
replace those hardcoded model strings in the four occurrences with
self.claude_model so the router's claude_model parameter is used (update the
methods _complete_claude and _acomplete_claude to reference self.claude_model),
and ensure self.claude_model is initialized from the CLAUDE_MODELS mapping or
the same CORTEX_USE_HAIKU env-based mechanism the interpreter uses so both
components select models consistently.
🧹 Nitpick comments (10)
tests/test_llm_router.py (1)
38-59: Test coverage gap: Tests verify initialization but not runtime behavior.These tests validate that
router.claude_modelis set correctly during initialization, but they don't verify that the selected model is actually used when making API calls to Claude. Since_complete_claude(line 358 in cortex/llm_router.py) hardcodes"claude-sonnet-4-20250514"instead of usingself.claude_model, these tests would pass even though the model selection doesn't work at runtime.🧪 Proposed enhancement to verify runtime model usage
Add a test that mocks the Claude API call and verifies the correct model is passed:
@patch("cortex.llm_router.Anthropic") def test_haiku_model_used_in_api_call(self, mock_anthropic): """Test that Haiku model is actually used in API calls.""" mock_content = Mock() mock_content.text = "Response" mock_response = Mock() mock_response.content = [mock_content] mock_response.usage = Mock(input_tokens=100, output_tokens=50) mock_response.model_dump = lambda: {} mock_client = Mock() mock_client.messages.create.return_value = mock_response mock_anthropic.return_value = mock_client router = LLMRouter(claude_api_key="test-key", claude_model="haiku") router.claude_client = mock_client router._complete_claude( messages=[{"role": "user", "content": "Hello"}], temperature=0.7, max_tokens=1024 ) # Verify the correct model was used call_args = mock_client.messages.create.call_args self.assertEqual(call_args.kwargs["model"], "claude-3-5-haiku-20241022")tests/test_uninstall_impact.py (3)
489-512: Thread safety test doesn't verify concurrent write safety.This test creates threads that all perform read operations (
is_package_installed), but it doesn't verify that concurrent writes to_installed_packagesor_reverse_deps_cacheare thread-safe. The test would pass even without proper locking, as it only checks that threads complete without errors.♻️ Enhanced thread safety test
To properly test thread safety, simulate concurrent cache updates:
def test_thread_safe_cache_updates(self): """Test that cache updates are thread-safe""" analyzer = UninstallImpactAnalyzer() results = [] errors = [] def update_cache(pkg_name): try: # Simulate concurrent cache writes analyzer._reverse_deps_cache[pkg_name] = [f"dep-{pkg_name}"] # Small delay to increase chance of race condition import time time.sleep(0.001) # Read back to verify result = analyzer._reverse_deps_cache.get(pkg_name) results.append((pkg_name, result)) except Exception as e: errors.append(e) threads = [ threading.Thread(target=update_cache, args=(f"pkg{i}",)) for i in range(10) ] for thread in threads: thread.start() for thread in threads: thread.join() # Verify no errors and all updates succeeded self.assertEqual(len(errors), 0) self.assertEqual(len(results), 10)
152-161: Tests directly access private attributes instead of using public API.The test directly sets
self.analyzer._installed_packagesinstead of mocking the_refresh_installed_packages()method or using a public interface. While this works for unit testing, it couples tests to implementation details.Consider mocking
_refresh_installed_packages()to populate the cache through the intended code path:@patch.object(UninstallImpactAnalyzer, "_refresh_installed_packages") def test_is_package_installed(self, mock_refresh): """Test checking if package is installed""" # Set up cache via the refresh method def setup_cache(): self.analyzer._installed_packages = {"nginx", "python3", "git"} mock_refresh.side_effect = setup_cache self.analyzer._refresh_installed_packages() self.assertTrue(self.analyzer.is_package_installed("nginx")) self.assertTrue(self.analyzer.is_package_installed("python3")) self.assertFalse(self.analyzer.is_package_installed("nonexistent"))Note: If the current approach is intentional for testing internal state, you can safely ignore this suggestion.
517-526: Integration test is minimal.The integration test only verifies that the analyzer can be instantiated and doesn't test any actual workflow. While this is acceptable for a unit test suite, consider adding more comprehensive integration tests that exercise the full analysis workflow with realistic mocked data.
Example of a more comprehensive integration test:
@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""" analyzer = UninstallImpactAnalyzer() analyzer._installed_packages = {"nginx", "openssl", "certbot"} # Mock apt-cache rdepends output def run_command_side_effect(cmd): if "rdepends" in cmd: return (True, "nginx\nReverse Depends:\n certbot\n", "") elif "is-active" in cmd: return (True, "active\n", "") elif "dpkg-query" in cmd: return (True, "1.18.0", "") return (False, "", "command not found") mock_run.side_effect = run_command_side_effect # Run full analysis result = analyzer.analyze_uninstall_impact("nginx") # Verify comprehensive results self.assertTrue(result.installed) self.assertEqual(result.package_name, "nginx") self.assertGreater(len(result.directly_depends), 0)docs/CLAUDE_HAIKU_4.5_COMPLETE_GUIDE.md (2)
53-53: Add language specification to unmarked code blocks.Seven code blocks lack language identifiers (lines 53, 99, 401, 425, 455, 475, 712). Add language tags for proper syntax highlighting and linting compliance.
Example fixes for lines 53 and 401
-``` +``` Latency Comparison:For line 401, specify
bashor appropriate language. Similar fixes needed for all unmarked blocks.Also applies to: 99-99, 401-401, 425-425, 455-455, 475-475, 712-712
6-6: Wrap bare URLs in markdown link format.Lines 6, 693-695 contain bare URLs (e.g.,
https://github.com/...). Per markdown standards, wrap in[link](url)format or use<url>for automatic linking.Example fixes
-**Repository**: https://github.com/cortexlinux/cortex +**Repository**: [cortexlinux/cortex](https://github.com/cortexlinux/cortex)Apply similar formatting to lines 693-695.
Also applies to: 693-695
HAIKU_4.5_ENABLEMENT_SUMMARY.md (1)
187-187: Style: Add comma after year in date.Line 187: "December 29, 2025" should be "December 29, 2025," per some style guides when used in month-day-year format.
docs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.md (1)
95-95: Add language specification to fenced code blocks.Four code blocks (lines 95, 106, 173, 201) lack language identifiers. Add language tags (e.g.,
bash,python,text) for proper syntax highlighting.Example fix
-``` +```bash cortex remove python --dry-runAlso applies to: 106-106, 173-173, 201-201
cortex/uninstall_impact.py (2)
18-19: Consider removing module-level logging.basicConfigThe
logging.basicConfig()call at module level can interfere with the application's logging configuration. Since this module is imported bycortex/cli.py, which may have its own logging setup, this could override or conflict with that configuration.♻️ Recommended approach
-logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__)Let the application configure logging centrally, and this module will inherit the configuration through the logger hierarchy.
303-360: Comprehensive impact analysis with minor dataclass inconsistencyThe method provides thorough analysis covering all aspects: dependencies, services, orphans, severity, and recommendations.
Note: The
safe_to_removelogic (line 340) correctly sets it to False for non-installed packages, but the dataclass default is True (line 57). While not causing bugs (since this method always sets the value), the inconsistent default could be confusing.Consider aligning the dataclass default:
- safe_to_remove: bool = True + safe_to_remove: bool = FalseThis better reflects that packages should not be assumed safe to remove by default.
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**/*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*.py: Follow PEP 8 style guide
Type hints required in Python code
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Files:
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**/*install*.py
📄 CodeRabbit inference engine (AGENTS.md)
**/*install*.py: Dry-run by default for all installations in command execution
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Files:
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🧠 Learnings (3)
📚 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
📚 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 **/*.py : Type hints required in Python code
Applied to files:
cortex/cli.py
🧬 Code graph analysis (2)
tests/test_uninstall_impact.py (1)
cortex/uninstall_impact.py (16)
ImpactedPackage(23-29)ServiceImpact(33-40)UninstallImpactAnalysis(44-59)UninstallImpactAnalyzer(62-451)_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(240-264)find_orphaned_packages(266-301)_determine_severity(362-382)_generate_recommendations(384-428)analyze_uninstall_impact(303-360)export_analysis_json(430-451)
cortex/uninstall_impact.py (5)
cortex/logging_system.py (3)
critical(212-214)info(200-202)warning(204-206)cortex/cli.py (1)
status(1265-1273)cortex/sandbox/sandbox_executor.py (1)
success(74-76)src/intent/context.py (1)
is_installed(49-50)tests/test_shell_env_analyzer.py (2)
parser(94-96)analyzer(106-108)
🪛 GitHub Actions: CI
cortex/cli.py
[error] 1793-1793: ruff check failed. F821 Undefined name 'ShellEnvironmentAnalyzer' at cortex/cli.py:1793:41.
🪛 LanguageTool
docs/CLAUDE_HAIKU_4.5_COMPLETE_GUIDE.md
[style] ~3-~3: Some style guides suggest that commas should set off the year in a month-day-year date.
Context: ...mentation Guide Date: December 29, 2025 Status: ✅ Production Ready **Ve...
(MISSING_COMMA_AFTER_YEAR)
[uncategorized] ~4-~4: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...te**: December 29, 2025 Status: ✅ Production Ready Version: 1.0 Repository: ht...
(EN_COMPOUND_ADJECTIVE_INTERNAL)
[uncategorized] ~746-~746: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...ions for Cortex Linux while maintaining high quality and backward compatibility. The 5x spee...
(EN_COMPOUND_ADJECTIVE_INTERNAL)
[uncategorized] ~748-~748: If this is a compound adjective that modifies the following noun, use a hyphen.
Context: ...kage management tasks. Status: ✅ Production Ready Testing: ✅ **All 59 tests passi...
(EN_COMPOUND_ADJECTIVE_INTERNAL)
[style] ~758-~758: Some style guides suggest that commas should set off the year in a month-day-year date.
Context: ...*: 1.0 Last Updated: December 29, 2025 Maintained By: Cortex Linux Team ...
(MISSING_COMMA_AFTER_YEAR)
HAIKU_4.5_ENABLEMENT_SUMMARY.md
[style] ~187-~187: Some style guides suggest that commas should set off the year in a month-day-year date.
Context: ... (Claude Sonnet 4.5) Date: December 29, 2025 Repository: https://github.com/cortexli...
(MISSING_COMMA_AFTER_YEAR)
🪛 markdownlint-cli2 (0.18.1)
docs/CLAUDE_HAIKU_4.5_COMPLETE_GUIDE.md
6-6: Bare URL used
(MD034, no-bare-urls)
53-53: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
99-99: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
401-401: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
425-425: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
455-455: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
475-475: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
693-693: Bare URL used
(MD034, no-bare-urls)
694-694: Bare URL used
(MD034, no-bare-urls)
695-695: Bare URL used
(MD034, no-bare-urls)
712-712: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
docs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.md
95-95: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
106-106: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
173-173: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
201-201: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
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🔇 Additional comments (11)
cortex/llm_router.py (1)
89-93: Well-structured model mapping.The
CLAUDE_MODELSdictionary provides a clean abstraction for model selection. Good use of constants for maintainability.docs/CLAUDE_HAIKU_4.5_COMPLETE_GUIDE.md (1)
1-760:⚠️ CRITICAL: Scope mismatch — file appears unrelated to PR objectives.This comprehensive guide documents Claude Haiku 4.5 LLM implementation, but PR objectives focus on "Uninstall Impact Analysis (Issue #113)". The Haiku feature is not mentioned in the linked issue or PR objectives at all.
Clarification needed: Is this file intended for this PR, or was it included in error? If Haiku enablement is part of this PR, please update PR description and objectives to reflect all features being delivered.
HAIKU_4.5_ENABLEMENT_SUMMARY.md (1)
1-188:⚠️ CRITICAL: Scope mismatch — file documents unrelated Haiku LLM feature.This summary documents Claude Haiku 4.5 enablement changes (LLM model selection), which is unrelated to the stated PR objective of "Uninstall Impact Analysis (Issue #113)". The feature is not mentioned in PR objectives or acceptance criteria.
Same clarification needed: Is this intended for this PR? If so, PR objectives require updating. If not, this file should be removed from this PR.
docs/UNINSTALL_IMPACT_ANALYSIS_SUMMARY.md (1)
1-305:⚠️ CRITICAL: Implementation files are missing from review.This is a summary document, not the actual implementation code. To properly review the Uninstall Impact Analysis feature, the following files must be provided:
- cortex/uninstall_impact.py (claimed 506 lines) — Core analyzer implementation
- tests/test_uninstall_impact.py (claimed 530 lines) — Test suite with 36 tests
- cortex/cli.py (modifications) — CLI command integration
- Any other modified/new files related to the feature
The summary makes specific claims about code quality, test coverage (92.11%), and functionality that cannot be verified without seeing the actual implementation code. Please provide the source files for proper code review.
cortex/cli.py (3)
29-29: LGTM: Proper TYPE_CHECKING importCorrectly uses TYPE_CHECKING to avoid circular imports while providing type hints.
882-970: Good implementation of remove workflow with proper safety measuresThe method correctly implements:
- Audit logging to installation history (lines 898, 916-918)
- Type hints for all parameters and return type
- Comprehensive docstring
- Error handling with best-effort history recording
- Safety checks before execution
Based on learnings, the audit logging to ~/.cortex/history.db is properly implemented through InstallationHistory.
1119-1141: Excellent safety design: Commands require user confirmationThe removal commands correctly omit the
-yflag, requiring interactive user confirmation for all sudo operations. The explicit comment documenting this design decision is helpful.Based on learnings, this properly implements "No silent sudo execution - require explicit user confirmation."
cortex/uninstall_impact.py (4)
22-60: Well-designed dataclasses with proper type hintsThe dataclasses correctly use:
- Type hints for all fields (per coding guidelines)
field(default_factory=list)for mutable defaults- Modern union syntax (
str | None)- Class-level docstrings
As per coding guidelines, type hints are properly implemented.
97-134: Excellent thread-safety and secure command executionThe implementation correctly uses:
- Threading lock for cache synchronization (lines 98, 126-128, 132-133)
- Subprocess with timeout to prevent hanging (line 106)
- No
shell=True, preventing shell injection vulnerabilities- Proper exception handling for timeouts and errors
266-301: LGTM: Clear orphan detection logicThe method correctly identifies orphaned packages by checking if the target package is their only dependency. The docstring clearly explains the logic, and the implementation properly filters out critical packages.
144-183: Add type hint for package_name parameterThe parameter
package_nameis missing a type hint. Per coding guidelines, type hints are required in Python code.📝 Proposed fix
- def get_reverse_dependencies(self, package_name: str) -> list[str]: + def get_reverse_dependencies(self, package_name: str) -> list[str]:Actually, checking the code again, the type hint IS present on line 144. This is correct as-is.
Looking at line 144 more carefully, the type hint is already present. Let me reconsider this.
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Actionable comments posted: 1
🤖 Fix all issues with AI agents
In @cortex/cli.py:
- Around line 1121-1142: The removal commands currently omit the -y flag and
will hang when run non-interactively; update _generate_removal_commands to
include the -y flag on apt-get remove and apt-get autoremove (leave autoclean
as-is or add -y if it may prompt) so apt will not prompt, and add a CLI-level
confirmation prompt in _execute_removal (before calling
_run_removal_coordinator) that asks the user to confirm the package removal
(handle EOFError/KeyboardInterrupt and respect dry_run/execute flow), returning
early if the user declines; keep printing commands in dry-run mode as before.
🧹 Nitpick comments (2)
cortex/cli.py (2)
999-1009: Consider allowing user override for high/critical severity removals.The current logic blocks removals with high/critical severity unless
--cascadingis provided. While this is a good safety measure, it's inflexible - users who understand the risk cannot proceed without also enabling cascading removal (which might remove more packages than intended).Consider prompting for explicit confirmation instead of blocking entirely, similar to the pattern in
docker_permissions(lines 80-99). This would allow expert users to proceed while maintaining safety.♻️ Alternative approach with confirmation prompt
def _validate_removal_safety( self, analyses: list["UninstallImpactAnalysis"], cascading: bool ) -> bool: """Validate that removal is safe given constraints""" 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 False + cx_print( + "⚠️ Warning: Removing packages with high/critical impact may break your system!", + "warning" + ) + try: + response = console.input( + "[bold yellow]Proceed with removal anyway? (y/N): [/bold yellow]" + ) + if response.lower() not in ("y", "yes"): + cx_print("Removal cancelled for safety", "info") + return False + except (EOFError, KeyboardInterrupt): + console.print() + cx_print("Removal cancelled", "info") + return False return True
1137-1141: Verify autoremove behavior aligns with impact analysis.The removal workflow automatically runs
sudo apt-get autoremoveandautocleanafter the main removal. While this is standard practice, consider whether:
- The orphaned packages identified by
UninstallImpactAnalyzermatch whatautoremovewill actually remove- Users should be shown which additional packages
autoremovewill remove before executionThe current approach is acceptable but could be enhanced by showing a preview of autoremove's planned actions, especially since the impact analysis already identifies orphaned packages.
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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:
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🧠 Learnings (3)
📚 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
📚 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 **/*.py : Type hints required in Python code
Applied to files:
cortex/cli.py
🧬 Code graph analysis (1)
cortex/cli.py (3)
cortex/uninstall_impact.py (3)
UninstallImpactAnalysis(44-59)UninstallImpactAnalyzer(62-451)analyze_uninstall_impact(303-360)cortex/coordinator.py (2)
execute(230-279)InstallationCoordinator(51-324)cortex/installation_history.py (3)
InstallationHistory(74-632)record_installation(258-316)update_installation(318-367)
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🔇 Additional comments (4)
cortex/cli.py (4)
31-31: LGTM - Proper use of TYPE_CHECKING for forward reference.The TYPE_CHECKING import of
UninstallImpactAnalysiscorrectly avoids runtime circular dependencies while enabling type hints in the removal flow.
884-972: Approve overall structure with integration of history logging.The
removemethod follows the established pattern frominstalland correctly integrates audit logging as required. The workflow is clear: parse → analyze → validate → execute → record outcome.The nested
_record_historyhelper uses best-effort recording (catching exceptions) to prevent history failures from blocking removal operations, which is appropriate.Based on learnings, this correctly implements audit logging to
~/.cortex/history.dbfor package removal operations.
2409-2420: LGTM - CLI argument parsing is well-structured.The
removesubcommand argument parsing follows the established pattern from theinstallcommand and provides clear help text. The flags (--execute,--dry-run,--cascading) are appropriate for the removal workflow with impact analysis.
973-1142: Add docstrings to helper methods.The helper methods implementing the removal flow lack docstrings, which violates the coding guideline "Docstrings required for all public APIs." While these are private methods, they implement non-trivial logic and would benefit from documentation.
As per coding guidelines: "Docstrings required for all public APIs" - consider this applies to substantial internal methods as well.
📝 Example docstring for _generate_removal_commands
def _generate_removal_commands(self, packages: list[str], cascading: bool) -> list[str]: - """Generate apt removal commands. - - Note: Commands do NOT include -y flag to require interactive confirmation. - Users must explicitly confirm removals for safety. - """ + """Generate apt removal commands for the given packages. + + Args: + packages: List of package names to remove + cascading: If True, include --auto-remove flag to remove dependencies + + Returns: + List of shell commands to execute the removal + + Note: + Commands do NOT include -y flag to require interactive confirmation. + Users must explicitly confirm removals for safety. + """Likely an incorrect or invalid review comment.
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Actionable comments posted: 1
🤖 Fix all issues with AI agents
In @cortex/cli.py:
- Around line 909-929: The except block in _record_history currently swallows
all exceptions and only logs at DEBUG; change it to surface failures by logging
a WARNING with a clear message including the exception (hist_err) so
users/admins see that history write failed, while still logging full debug
details (stack trace) for diagnostics; update the except handler in
_record_history (the try/except around history.record_installation and
history.update_installation) to call logging.warning(...) with context and the
exception and also log.debug(...) or logging.exception(...) for the full
traceback.
🧹 Nitpick comments (2)
cortex/cli.py (2)
956-965: Consider adding explicit user confirmation before removal.While the generated commands don't include the
-yflag (ensuring interactive confirmation at the sudo level), users might benefit from an explicit confirmation prompt before the removal process begins—similar to the pattern used in_sandbox_promote(lines 529-539).💡 Example confirmation pattern
Add before line 957:
# Prompt user before executing removal if execute and not getattr(args, 'yes', False): pkg_list = ', '.join(packages) try: response = console.input( f"[bold yellow]⚠️ Remove {pkg_list}? (y/n): [/bold yellow]" ) if response.lower() not in ('y', 'yes'): cx_print("Removal cancelled", "info") _record_history("success", "User cancelled removal", packages) return 0 except (EOFError, KeyboardInterrupt): console.print() cx_print("Removal cancelled", "info") _record_history("success", "User cancelled removal", packages) return 0This would require adding a
--yesflag to the remove parser (similar to sandbox promote).Based on learnings, no silent sudo execution is allowed without explicit user confirmation.
1121-1142: Cleanup commands always included.The method always appends
autoremoveandautocleancommands (lines 1139-1140), even for simple removals. While these are useful, they might confuse users who expect to see only the commands directly related to the specified package.Consider making these cleanup steps optional or clearly separating them in the display output.
♻️ Optional improvement
-def _generate_removal_commands(self, packages: list[str], cascading: bool) -> list[str]: +def _generate_removal_commands(self, packages: list[str], cascading: bool, cleanup: bool = True) -> list[str]: """Generate apt removal commands. Note: Commands do NOT include -y flag to require interactive confirmation. Users must explicitly confirm removals for safety. """ commands: list[str] = [] pkg_list = " ".join(packages) if cascading: # Remove with dependencies - requires user confirmation commands.append(f"sudo apt-get remove --auto-remove {pkg_list}") else: # Simple removal - requires user confirmation commands.append(f"sudo apt-get remove {pkg_list}") - # Clean up commands also require confirmation - commands.append("sudo apt-get autoremove") - commands.append("sudo apt-get autoclean") + if cleanup: + # Clean up commands also require confirmation + commands.append("sudo apt-get autoremove") + commands.append("sudo apt-get autoclean") return commands
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🧠 Learnings (3)
📚 Learning: 2025-12-11T12:03:24.071Z
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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 **/*.py : Type hints required in Python code
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
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🔇 Additional comments (6)
cortex/cli.py (6)
31-31: LGTM!The TYPE_CHECKING import for
UninstallImpactAnalysisfollows Python typing best practices for forward references without runtime overhead.
999-1009: Safety validation logic is clear.The method correctly gates high/critical severity removals behind the
--cascadingflag. However, users might find it confusing that--cascadingis required not just to remove dependencies, but to permit the removal at all.Consider clarifying this in help text or documentation.
1054-1120: Display methods are well-structured.The display logic is cleanly decomposed into focused helper methods with clear responsibilities. The code handles edge cases (empty lists, not installed packages) appropriately.
973-1052: Helper methods follow established patterns.The removal helpers correctly mirror the structure used in the
installmethod, promoting consistency across the codebase. Type hints are complete, and error handling is appropriate.
2409-2420: Argument parser properly configured.The remove command parser follows consistent patterns with other CLI commands and includes appropriate flags for the removal workflow.
2759-2765: LGTM!Command routing correctly passes all parsed arguments to the
removemethod.
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cortex/doctor.py:103
- The code contains duplicate check sections. Lines 74-85 are duplicated at lines 88-103, causing the same diagnostic checks to run twice. This creates unnecessary overhead and confusing output for users running system diagnostics.
# 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()
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Actionable comments posted: 2
🤖 Fix all issues with AI agents
In @cortex/uninstall_impact.py:
- Around line 134-142: Add a docstring to the public method
get_installed_version(package_name: str) describing the parameter
(package_name), the return value (str version or None), and the behavior
(returns None if package not installed or command fails; otherwise returns the
stripped version string retrieved via dpkg-query). Keep it concise, follow
project docstring style (one-line summary plus param/return details), and place
it directly above the method definition.
- Around line 61-62: The class UninstallImpactAnalyzer is missing a class-level
docstring; add a comprehensive docstring to the UninstallImpactAnalyzer class
that briefly describes its purpose (analyzing the impact of uninstalling
packages), intended usage, main responsibilities, and the key public methods
(e.g., analyze, summarize_impact, get_affected_packages or whatever public APIs
exist) including expected inputs and return types and any raised exceptions;
place this docstring immediately below the class declaration so tools and users
of the public API see it.
🧹 Nitpick comments (4)
cortex/uninstall_impact.py (4)
17-18: Remove root logger configuration from library code.Library modules should not configure the root logger with
logging.basicConfig(). This overrides any logging configuration set by the application using this module. Remove these lines and let the application (CLI) configure logging as needed.♻️ Proposed fix
-logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__)
239-263: Consider extracting critical services as a class constant.The
critical_servicesset on line 251 is hardcoded within the method. For consistency with the class design (which usesCRITICAL_PACKAGESas a class constant), consider moving this to a class-level constant likeCRITICAL_SERVICES. This improves maintainability and makes it easier for users to customize the list.♻️ Proposed refactor
Add at class level (after CRITICAL_PACKAGES):
# Critical services that should not be disrupted CRITICAL_SERVICES = {"ssh", "docker", "postgresql", "mysql"}Then update the method:
def get_affected_services(self, package_name: str) -> list[ServiceImpact]: """Get system services that depend on this package""" affected = [] for service_name, packages in self.SERVICE_PACKAGE_MAP.items(): if package_name in packages: # Try to get service status success, status_out, _ = self._run_command(["systemctl", "is-active", service_name]) status = "active" if success and "active" in status_out else "inactive" # Check if service is critical - critical_services = {"ssh", "docker", "postgresql", "mysql"} - is_critical = service_name in critical_services + is_critical = service_name in self.CRITICAL_SERVICES
265-300: Orphan detection heuristic may have false positives.The current orphan detection (lines 297-298) considers a package orphaned if its only dependency is the package being removed. However, this doesn't account for packages that were explicitly installed by the user (as opposed to auto-installed as dependencies). Consider enhancing this logic to check if packages were auto-installed.
You can verify auto-installed status with:
apt-mark showauto <package>This would reduce false positives by only marking auto-installed packages as orphans.
♻️ Enhanced detection approach
# Package is only orphaned if its ONLY dependency is the one being removed + # AND it was auto-installed (not manually installed by user) if len(actual_deps) == 1 and actual_deps[0] == package_name: - orphaned.append(dep_name) + # Check if package was auto-installed + auto_check, stdout, _ = self._run_command(["apt-mark", "showauto", dep_name]) + if auto_check and dep_name in stdout: + orphaned.append(dep_name)
447-448: Specify file encoding explicitly.When opening files for writing, explicitly specify
encoding='utf-8'to ensure consistent behavior across different platforms and locale settings.♻️ Proposed fix
- with open(filepath, "w") as f: + with open(filepath, "w", encoding="utf-8") as f: json.dump(analysis_dict, f, indent=2)
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**/*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 (3)
📚 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 **/*.py : Type hints required in Python code
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 (1)
cortex/cli.py (1)
1116-1138: Good: Commands require explicit user confirmation.The removal commands correctly omit the
-yflag, ensuring users must interactively confirm each removal operation. This follows the coding guideline of "no silent sudo execution - require explicit user confirmation."Based on coding guidelines.
RIVALHIDE
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Actionable comments posted: 3
🤖 Fix all issues with AI agents
In @cortex/cli.py:
- Around line 937-940: The code currently records "_record_history('success',
...)" when _should_proceed_with_removal returns False, which incorrectly logs a
successful removal even though none occurred; change that call to record a
distinct status (e.g., "analyzed" or "preview") to reflect an
analysis-only/preview run — specifically update the branch that checks
_should_proceed_with_removal(execute, dry_run) to call
_record_history("analyzed", None, packages) (or skip recording entirely if you
prefer) before returning 0 so audit logs correctly reflect no removal was
performed.
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Docstrings required for all public APIs
Files:
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🧠 Learnings (3)
📚 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 **/*.py : Type hints required in Python code
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/uninstall_impact.py (3)
UninstallImpactAnalysis(43-58)UninstallImpactAnalyzer(61-450)analyze_uninstall_impact(302-359)cortex/installation_history.py (3)
InstallationHistory(74-632)record_installation(258-316)update_installation(318-367)
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🔇 Additional comments (11)
cortex/cli.py (11)
31-31: LGTM!The TYPE_CHECKING import for
UninstallImpactAnalysisis correctly guarded, enabling type hints without runtime circular import issues.
904-924: Nested function_record_historylacks type hints.Per coding guidelines, type hints are required. The nested function should have annotations.
Suggested fix
- def _record_history( - outcome: str, error_message: str | None = None, packages: list[str] | None = None - ) -> None: + def _record_history( + outcome: str, + error_message: str | None = None, + packages: list[str] | None = None, + ) -> None:Actually, the function already has type hints. Disregard this - the annotations are present.
968-973: LGTM!Clean package parsing with proper validation.
975-984: LGTM!Proper lazy import pattern and clean iteration over packages for impact analysis.
986-992: LGTM!Clear gate for determining whether to proceed with actual removal.
994-1004: LGTM!Safety validation correctly blocks high/critical impact removals unless cascading is explicitly enabled.
1022-1047: LGTM!Coordinator setup and execution handling is correct with proper success/failure reporting.
1049-1114: LGTM!Well-structured display helpers with appropriate output limiting for readability.
2404-2415: LGTM!Parser correctly defines the
removesubcommand with appropriate flags.
2754-2760: LGTM!Command routing correctly dispatches to
cli.remove()with all required arguments.
884-890: Missing--orphans-onlyflag from PR objectives.The PR description lists
--orphans-onlyas one of the CLI flags, but it's not implemented in the parser or method signature. If this is intentional deferral, consider documenting it; otherwise, it may need to be added.
| # Check safety and return early if just analyzing | ||
| if not self._should_proceed_with_removal(execute, dry_run): | ||
| _record_history("success", None, packages) | ||
| return 0 |
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Recording "success" when no removal occurs may confuse audit logs.
When execute=False and dry_run=False, the method returns early with _record_history("success"), but no actual removal was performed. This creates a misleading audit trail. Consider either:
- Not recording history for analysis-only invocations, or
- Using a distinct status like "analyzed" or "preview"
🤖 Prompt for AI Agents
In @cortex/cli.py around lines 937 - 940, The code currently records
"_record_history('success', ...)" when _should_proceed_with_removal returns
False, which incorrectly logs a successful removal even though none occurred;
change that call to record a distinct status (e.g., "analyzed" or "preview") to
reflect an analysis-only/preview run — specifically update the branch that
checks _should_proceed_with_removal(execute, dry_run) to call
_record_history("analyzed", None, packages) (or skip recording entirely if you
prefer) before returning 0 so audit logs correctly reflect no removal was
performed.
| 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) | ||
|
|
||
| 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 | ||
|
|
||
| return self._run_removal_coordinator(software, commands) |
There was a problem hiding this comment.
When both --execute and --dry-run are passed, --dry-run silently wins.
If a user runs cortex remove pkg --execute --dry-run, the dry-run path is taken without indication that --execute was ignored. Consider either:
- Making them mutually exclusive at the parser level, or
- Printing a warning when both are specified
Option 1: Make flags mutually exclusive in parser
remove_parser.add_argument("--execute", action="store_true", help="Execute removal")
-remove_parser.add_argument("--dry-run", action="store_true", help="Show what would be removed")
+remove_group = remove_parser.add_mutually_exclusive_group()
+remove_group.add_argument("--execute", action="store_true", help="Execute removal")
+remove_group.add_argument("--dry-run", action="store_true", help="Show what would be removed")| def _generate_removal_commands(self, packages: list[str], cascading: bool) -> list[str]: | ||
| """Generate apt removal commands. | ||
| Note: Commands do NOT include -y flag to require interactive confirmation. | ||
| Users must explicitly confirm removals for safety. | ||
| """ | ||
| commands: list[str] = [] | ||
|
|
||
| pkg_list = " ".join(packages) | ||
|
|
||
| if cascading: | ||
| # Remove with dependencies - requires user confirmation | ||
| commands.append(f"sudo apt-get remove --auto-remove {pkg_list}") | ||
| else: | ||
| # Simple removal - requires user confirmation | ||
| commands.append(f"sudo apt-get remove {pkg_list}") | ||
|
|
||
| # Clean up commands also require confirmation | ||
| commands.append("sudo apt-get autoremove") | ||
| commands.append("sudo apt-get autoclean") | ||
|
|
||
| return commands |
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🧩 Analysis chain
🏁 Script executed:
# Find InstallationCoordinator class and its execute method
find . -type f -name "*.py" | xargs grep -l "class InstallationCoordinator"Repository: cortexlinux/cortex
Length of output: 85
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# Check the structure of cortex directory
git ls-files cortex/ | grep -E "\.(py)$" | head -20Repository: cortexlinux/cortex
Length of output: 521
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# Search for subprocess usage in coordinator-related files
rg "subprocess\." cortex/ -t py --max-count=10Repository: cortexlinux/cortex
Length of output: 9033
🏁 Script executed:
# Examine the InstallationCoordinator class in coordinator.py
cat cortex/coordinator.pyRepository: cortexlinux/cortex
Length of output: 13795
InstallationCoordinator executes commands with capture_output=True, preventing interactive prompts.
The _generate_removal_commands function correctly omits -y flags to require user confirmation, but InstallationCoordinator._execute_command() uses subprocess.run(..., capture_output=True, ...) which redirects stdin/stdout/stderr to pipes. This disables TTY interaction, causing apt-get remove commands to fail or hang when they attempt to prompt for confirmation.
Either:
- Remove
capture_output=Trueand usetext=Truealone to preserve TTY interaction for interactive commands, OR - Add a parameter to
InstallationCoordinatorto skip capture for specific commands requiring user interaction, OR - Have
_generate_removal_commandsadd-yflags and handle the requirement through a different UX mechanism (e.g., explicit confirmation dialog before generating commands)
This violates the "no silent sudo execution" requirement.
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@RIVALHIDE This is your last warning, Do not create low quality PRs, closing this one, create a fresh PR with all the required changes only.
Reason: Missing Contributing.md guidelines and Irrelevant changes.
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Why this file, remove it.
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@RIVALHIDE Does not need to be seperate file, there is only docs file for this feature.
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Remove this one as well, not related to PR.
5 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:
Demo
cd /home/anuj/Internship/cortex && source venv/bin/activate && echo "=== 1. Analyze LOW severity package (curl) ===" && python3 cortex/uninstall_impact.py curl 2>&1 | grep -v "^INFO"
cd /home/anuj/Internship/cortex && source venv/bin/activate && echo "" && echo "=== 2. Analyze HIGH severity package (python3) ===" && python3 cortex/uninstall_impact.py python3 2>&1 | grep -v "^INFO"
cd /home/anuj/Internship/cortex && source venv/bin/activate && echo "" && echo "=== 3. Analyze CRITICAL package (libc6) ===" && python3 cortex/uninstall_impact.py libc6 2>&1 | grep -v "^INFO"
cd /home/anuj/Internship/cortex && source venv/bin/activate && echo "" && echo "=== 4. CLI Usage - Dry Run ===" && python3 -m cortex.cli remove nginx --dry-run 2>&1 | grep -v "^INFO" | grep -v "WARNING:cortex" | grep -v "RuntimeWarning"
cd /home/anuj/Internship/cortex && source venv/bin/activate && echo "" && echo "=== 5. Safety Validation (blocks high-impact) ===" && python3 -m cortex.cli remove python3 --execute 2>&1 | grep -v "^INFO" | grep -v "WARNING:cortex" | grep -v "RuntimeWarning"
cd /home/anuj/Internship/cortex && source venv/bin/activate && echo "" && echo "=== 6. Export to JSON ===" && python3 cortex/uninstall_impact.py git --export /tmp/analysis.json 2>&1 | grep -v "^INFO" && echo "" && echo "JSON Output (first 25 lines):" && head -25 /tmp/analysis.json
cd /home/anuj/Internship/cortex && source venv/bin/activate && echo "" && echo "=== 7. Run Tests ===" && python3 -m pytest tests/test_uninstall_impact.py -v 2>&1 | tail -20