feat: AI-powered dependency conflict prediction (#428) #633
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Implements cortexlinux#428 - AI-powered dependency conflict prediction Features: - Parse /var/lib/dpkg/status for current system state - Build dependency graph from apt-cache - Predict conflicts BEFORE installation starts - Check version constraints and known package conflicts - Detect transitive dependency conflicts - Suggest resolution strategies ranked by safety: 1. Install compatible version (SAFE) 2. Upgrade/downgrade conflicting package (LOW_RISK) 3. Use virtual environment for Python (SAFE) 4. Remove conflicting package (MEDIUM_RISK) 5. Use alternative package (LOW_RISK) - Support pip package conflict detection Usage: cortex deps predict <package> cortex deps predict mysql-server Integration: - Automatically runs before `cortex install <package>` - Blocks installation if conflicts detected (use --execute to override) Example output: $ cortex deps predict mysql-server⚠️ Conflict predicted: mysql-server vs mariadb-server Suggested Resolutions: 1. Remove mariadb-server (MEDIUM_RISK) [Recommended] 2. Use alternative: postgresql (LOW_RISK)
bimakw
requested review from
Anshgrover23,
Suyashd999 and
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. 📝 WalkthroughWalkthroughA new ConflictPredictor module is added and integrated into the CLI: installs now run a pre-install conflict prediction step and a new "deps predict" action is available. Comprehensive tests for prediction logic and parsing are included. Changes
Sequence DiagramsequenceDiagram
participant User as User/CLI
participant CLI as cortex CLI
participant Predictor as ConflictPredictor
participant DpkgApt as dpkg/apt System
participant PkgMgr as Package Manager
User->>CLI: cortex install <package> [--execute]
CLI->>Predictor: predict_conflicts(package_name)
Predictor->>DpkgApt: read /var/lib/dpkg/status & apt-cache & pip list
DpkgApt-->>Predictor: metadata, versions, deps
Predictor->>Predictor: analyze declared/version/transitive conflicts
Predictor-->>CLI: ConflictPrediction (conflicts, resolutions, can_install)
alt Conflicts Detected
CLI->>User: show conflicts & resolutions
alt --execute provided
User-->>CLI: confirm proceed
CLI->>PkgMgr: install package
PkgMgr-->>User: installation result
else
CLI->>User: block install, suggest resolutions
end
else No Conflicts
CLI->>PkgMgr: install package
PkgMgr-->>User: installation result
end
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Summary of ChangesHello @bimakw, I'm Gemini Code Assist1! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed! This pull request significantly enhances the Highlights
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Code Review
This pull request introduces an impressive new feature for AI-powered dependency conflict prediction. The implementation is comprehensive, covering both apt and pip packages, analyzing transitive dependencies, and suggesting resolution strategies. The code is well-structured with dataclasses and enums, and the inclusion of unit tests is commendable. However, I've identified a few critical issues in the logic for parsing package information and checking conflicts that could lead to incorrect predictions. There are also several opportunities for refactoring to improve the code's robustness and maintainability. Addressing these points will significantly enhance the reliability and quality of this new feature.
| package_name = software.split()[0].strip() | ||
| for prefix in ["apt-get", "apt", "install", "pip", "pip3", "-y"]: | ||
| if package_name == prefix: | ||
| parts = software.split() | ||
| for p in parts: | ||
| if p not in ["apt-get", "apt", "install", "pip", "pip3", "-y", "sudo"]: | ||
| package_name = p | ||
| break |
There was a problem hiding this comment.
The logic to extract the package name from the software string is not robust. It fails for commands that start with sudo, as "sudo" is not in the list of prefixes to be skipped. For example, if the input is "sudo apt-get install nginx", the extracted package_name will incorrectly be "sudo". This should be refactored for more reliable package name extraction.
| package_name = software.split()[0].strip() | |
| for prefix in ["apt-get", "apt", "install", "pip", "pip3", "-y"]: | |
| if package_name == prefix: | |
| parts = software.split() | |
| for p in parts: | |
| if p not in ["apt-get", "apt", "install", "pip", "pip3", "-y", "sudo"]: | |
| package_name = p | |
| break | |
| # Extract package name by filtering out known command parts | |
| parts = software.split() | |
| known_command_parts = {"sudo", "apt-get", "apt", "install", "pip", "pip3", "-y"} | |
| package_name = next((p for p in parts if p not in known_command_parts), None) | |
| if not package_name: | |
| # Let the outer except block handle this by raising an error. | |
| raise ValueError(f"Could not determine package_name from '{software}'") |
| def _parse_dependency_list(self, dep_str: str) -> list[str]: | ||
| """Parse dependency string including version constraints.""" | ||
| return self._parse_package_list(dep_str) |
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The _parse_dependency_list method, which is used to parse the Depends field for installed packages, calls _parse_package_list. This strips out version constraint information. As a result, the depends attribute of InstalledPackage only contains package names, not their required versions. This is a significant limitation as it prevents the conflict predictor from checking if a new package would break the dependency requirements of an already installed package.
The dependency parsing for installed packages should be enhanced to capture version constraints. You should update the InstalledPackage dataclass to store VersionConstraint objects and implement _parse_dependency_list to correctly parse them, similar to how it's done for PackageCandidate.
| def _check_pip_conflicts(self, package_name: str, prediction: ConflictPrediction) -> None: | ||
| """Check for pip package conflicts.""" |
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The _check_pip_conflicts method is incomplete. It only checks for version constraints that start with <, such as numpy<2.0. It completely ignores other operators. For example, the PIP_CONFLICTS dictionary defines pandas: {"numpy": ">=1.20"}, but this >= constraint will never be evaluated by the current logic. The implementation needs to be extended to handle other common pip version specifiers like >=, ==, etc.
Additionally, simple string comparison for versions is unreliable (e.g., '1.10' > '1.2'). For robust Python package version and specifier handling, it's highly recommended to use the packaging library.
| except Exception as e: | ||
| # Don't block installation if prediction fails | ||
| self._debug(f"Conflict prediction skipped: {e}") |
There was a problem hiding this comment.
Catching a broad Exception and logging it only at the debug level can hide important errors from the user. If an unexpected error occurs during conflict prediction, it would be helpful for the user to be aware of it, even if the installation is not blocked. Consider logging these errors at a warning level so the user knows why the prediction was skipped.
| except Exception as e: | |
| # Don't block installation if prediction fails | |
| self._debug(f"Conflict prediction skipped: {e}") | |
| except Exception as e: | |
| # Don't block installation if prediction fails, but warn the user. | |
| console.print(f"[yellow]Warning: Conflict prediction skipped due to an error: {e}[/yellow]") | |
| self._debug(f"Full error during conflict prediction: {e}") |
| "openjdk-8-jdk": [], | ||
| "openjdk-11-jdk": [], | ||
| "openjdk-17-jdk": [], |
There was a problem hiding this comment.
The KNOWN_CONFLICTS dictionary contains entries for Java JDKs with empty conflict lists (e.g., "openjdk-8-jdk": []). These entries serve no purpose and can be removed to reduce clutter. If they are intended as placeholders for future logic, a TODO comment would be more appropriate.
| "openjdk-8-jdk": [], | |
| "openjdk-11-jdk": [], | |
| "openjdk-17-jdk": [], | |
| # Java conflicts can be added here if any are identified. |
| current_pkg: dict = {} | ||
| for line in content.split("\n"): | ||
| if line.startswith("Package:"): | ||
| if current_pkg.get("Package") and current_pkg.get("Status", "").startswith( | ||
| "install ok" | ||
| ): | ||
| self._add_installed_package(current_pkg) | ||
| current_pkg = {"Package": line.split(":", 1)[1].strip()} | ||
| elif line.startswith("Version:"): | ||
| current_pkg["Version"] = line.split(":", 1)[1].strip() | ||
| elif line.startswith("Status:"): | ||
| current_pkg["Status"] = line.split(":", 1)[1].strip() | ||
| elif line.startswith("Depends:"): | ||
| current_pkg["Depends"] = line.split(":", 1)[1].strip() | ||
| elif line.startswith("Conflicts:"): | ||
| current_pkg["Conflicts"] = line.split(":", 1)[1].strip() | ||
| elif line.startswith("Breaks:"): | ||
| current_pkg["Breaks"] = line.split(":", 1)[1].strip() | ||
| elif line.startswith("Provides:"): | ||
| current_pkg["Provides"] = line.split(":", 1)[1].strip() | ||
|
|
||
| # Don't forget the last package | ||
| if current_pkg.get("Package") and current_pkg.get("Status", "").startswith("install ok"): | ||
| self._add_installed_package(current_pkg) | ||
|
|
There was a problem hiding this comment.
The logic for parsing the dpkg/status file uses a long if/elif chain to process each line. This approach is a bit fragile and can be hard to maintain. A more robust and readable approach would be to parse the file in blocks (separated by blank lines) and then process each block as a dictionary of key-value pairs.
| current_pkg: dict = {} | |
| for line in content.split("\n"): | |
| if line.startswith("Package:"): | |
| if current_pkg.get("Package") and current_pkg.get("Status", "").startswith( | |
| "install ok" | |
| ): | |
| self._add_installed_package(current_pkg) | |
| current_pkg = {"Package": line.split(":", 1)[1].strip()} | |
| elif line.startswith("Version:"): | |
| current_pkg["Version"] = line.split(":", 1)[1].strip() | |
| elif line.startswith("Status:"): | |
| current_pkg["Status"] = line.split(":", 1)[1].strip() | |
| elif line.startswith("Depends:"): | |
| current_pkg["Depends"] = line.split(":", 1)[1].strip() | |
| elif line.startswith("Conflicts:"): | |
| current_pkg["Conflicts"] = line.split(":", 1)[1].strip() | |
| elif line.startswith("Breaks:"): | |
| current_pkg["Breaks"] = line.split(":", 1)[1].strip() | |
| elif line.startswith("Provides:"): | |
| current_pkg["Provides"] = line.split(":", 1)[1].strip() | |
| # Don't forget the last package | |
| if current_pkg.get("Package") and current_pkg.get("Status", "").startswith("install ok"): | |
| self._add_installed_package(current_pkg) | |
| # Split content into package blocks | |
| package_blocks = content.strip().split("\n\n") | |
| for block in package_blocks: | |
| pkg_dict = {} | |
| for line in block.split("\n"): | |
| if ":" in line: | |
| key, value = line.split(":", 1) | |
| pkg_dict[key.strip()] = value.strip() | |
| if pkg_dict.get("Package") and pkg_dict.get("Status", "").startswith("install ok"): | |
| self._add_installed_package(pkg_dict) |
| depth: int = 0, | ||
| ) -> None: | ||
| """Recursively check transitive dependency conflicts.""" | ||
| if depth > 5: # Limit recursion depth |
There was a problem hiding this comment.
The recursion depth limit is hardcoded as a magic number 5. This should be defined as a class-level constant to improve readability and make it easier to configure if needed.
For example, add MAX_RECURSION_DEPTH = 5 to the ConflictPredictor class and use self.MAX_RECURSION_DEPTH here.
| if depth > 5: # Limit recursion depth | |
| if depth > 5: # TODO: Use a class constant for max recursion depth |
| commands=[ | ||
| f"sudo apt-get install {conflict.conflicting_with}={conflict.required_version}" | ||
| if conflict.required_version | ||
| else f"sudo apt-get install --only-upgrade {conflict.conflicting_with}" | ||
| ], |
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The suggested command sudo apt-get install {conflict.conflicting_with}={conflict.required_version} might be incorrect or incomplete. The required_version field only contains the version number, not the comparison operator (e.g., >=, <). For apt-get, version constraints are not specified this way. This could mislead the user into running a command that doesn't work or doesn't resolve the conflict correctly. The command suggestion should be more robust or provide a more generic hint to guide the user.
| commands=[ | |
| f"sudo apt-get install {conflict.conflicting_with}={conflict.required_version}" | |
| if conflict.required_version | |
| else f"sudo apt-get install --only-upgrade {conflict.conflicting_with}" | |
| ], | |
| commands=[ | |
| f"apt-cache policy {conflict.conflicting_with}", | |
| f"# Find a version that satisfies '{conflict.required_version or 'compatible'}' and install it:", | |
| f"sudo apt-get install {conflict.conflicting_with}=<version>", | |
| ], |
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
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Actionable comments posted: 3
🤖 Fix all issues with AI agents
In `@cortex/cli.py`:
- Around line 832-845: The package-name extraction incorrectly treats a leading
"sudo" as the package (so ConflictPredictor gets "sudo"); update the extraction
logic in the block that builds package_name (the code around ConflictPredictor
and the variable software) to ignore common command prefixes including
"sudo"—either add "sudo" to the prefix list or explicitly strip a leading "sudo"
before splitting—and then continue scanning parts for the first token not in
["apt-get","apt","install","pip","pip3","-y","sudo"] so package_name becomes the
actual package (e.g., "nginx") before passing to ConflictPredictor.
In `@cortex/conflict_predictor.py`:
- Around line 370-387: predict_conflicts currently returns early when
_get_apt_package_info(package_name) yields no candidate, which skips pip-only
conflict checks; change the flow so that when candidate is falsy you still
normalize the input package_name (strip version specifiers like "==", ">=", "~="
or use packaging to parse names) and call _check_pip_conflicts(normalized_name,
prediction) to populate prediction.conflicts and prediction.resolutions, then
append the existing warning (prediction.warnings.append(...)) before returning;
keep existing behavior when candidate exists (i.e., run apt checks and also call
_check_pip_conflicts as appropriate) so both apt-absent pip-only installs and
version-pinned names are checked.
- Around line 552-574: The current lexicographic comparison in the pip conflict
check (involving PIP_CONFLICTS, _pip_cache and creating
PredictedConflict/ConflictType entries) must be replaced with semantic version
comparison using packaging.version.Version: import Version and InvalidVersion
(or use the project's conditional import/fallback pattern like in
config_manager.py), parse installed_ver and max_ver with Version and compare
(Version(installed_ver) >= Version(max_ver)); catch InvalidVersion and log/debug
a message instead of raising, and ensure packaging (e.g., "packaging>=21.0") is
added to dependencies in pyproject.toml or handled via the conditional import
fallback.
| # Predict conflicts before installation | ||
| try: | ||
| from cortex.conflict_predictor import ConflictPredictor | ||
|
|
||
| predictor = ConflictPredictor() | ||
| # Extract package name (first word, remove any pip/apt prefix) | ||
| package_name = software.split()[0].strip() | ||
| for prefix in ["apt-get", "apt", "install", "pip", "pip3", "-y"]: | ||
| if package_name == prefix: | ||
| parts = software.split() | ||
| for p in parts: | ||
| if p not in ["apt-get", "apt", "install", "pip", "pip3", "-y", "sudo"]: | ||
| package_name = p | ||
| break |
There was a problem hiding this comment.
Handle sudo prefix when extracting package name.
If the input starts with sudo (e.g., sudo apt-get install nginx), package_name remains "sudo" because it isn’t in the prefix list, so prediction targets the wrong package.
🛠️ Suggested fix
- package_name = software.split()[0].strip()
- for prefix in ["apt-get", "apt", "install", "pip", "pip3", "-y"]:
- if package_name == prefix:
- parts = software.split()
- for p in parts:
- if p not in ["apt-get", "apt", "install", "pip", "pip3", "-y", "sudo"]:
- package_name = p
- break
+ parts = software.split()
+ skip = {"sudo", "apt-get", "apt", "install", "pip", "pip3", "-y"}
+ package_name = next((p for p in parts if p not in skip), "")📝 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.
| # Predict conflicts before installation | |
| try: | |
| from cortex.conflict_predictor import ConflictPredictor | |
| predictor = ConflictPredictor() | |
| # Extract package name (first word, remove any pip/apt prefix) | |
| package_name = software.split()[0].strip() | |
| for prefix in ["apt-get", "apt", "install", "pip", "pip3", "-y"]: | |
| if package_name == prefix: | |
| parts = software.split() | |
| for p in parts: | |
| if p not in ["apt-get", "apt", "install", "pip", "pip3", "-y", "sudo"]: | |
| package_name = p | |
| break | |
| # Predict conflicts before installation | |
| try: | |
| from cortex.conflict_predictor import ConflictPredictor | |
| predictor = ConflictPredictor() | |
| # Extract package name (first word, remove any pip/apt prefix) | |
| parts = software.split() | |
| skip = {"sudo", "apt-get", "apt", "install", "pip", "pip3", "-y"} | |
| package_name = next((p for p in parts if p not in skip), "") |
🤖 Prompt for AI Agents
In `@cortex/cli.py` around lines 832 - 845, The package-name extraction
incorrectly treats a leading "sudo" as the package (so ConflictPredictor gets
"sudo"); update the extraction logic in the block that builds package_name (the
code around ConflictPredictor and the variable software) to ignore common
command prefixes including "sudo"—either add "sudo" to the prefix list or
explicitly strip a leading "sudo" before splitting—and then continue scanning
parts for the first token not in
["apt-get","apt","install","pip","pip3","-y","sudo"] so package_name becomes the
actual package (e.g., "nginx") before passing to ConflictPredictor.
| def predict_conflicts(self, package_name: str) -> ConflictPrediction: | ||
| """Predict conflicts before installing a package. | ||
| Args: | ||
| package_name: Name of package to install | ||
| Returns: | ||
| ConflictPrediction with all detected conflicts and resolutions | ||
| """ | ||
| logger.info(f"Predicting conflicts for {package_name}...") | ||
| prediction = ConflictPrediction(package=package_name) | ||
|
|
||
| # Get candidate package info | ||
| candidate = self._get_apt_package_info(package_name) | ||
| if not candidate: | ||
| prediction.warnings.append(f"Package {package_name} not found in apt cache") | ||
| return prediction | ||
|
|
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Pip conflicts are skipped when apt-cache lookup fails.
predict_conflicts returns early if the apt candidate is missing, so pip-only installs (or version‑pinned names not in apt) never hit _check_pip_conflicts, despite the advertised feature. Also, version‑pinned names like tensorflow==2.10 won’t match pip mappings. Consider normalizing the name and still running pip checks on apt-cache miss.
🛠️ Suggested fix
- prediction = ConflictPrediction(package=package_name)
+ normalized_name = re.split(r"[<>=!~]", package_name, 1)[0].split("[", 1)[0].strip()
+ prediction = ConflictPrediction(package=normalized_name)
+ package_name = normalized_name
@@
- candidate = self._get_apt_package_info(package_name)
+ candidate = self._get_apt_package_info(package_name)
if not candidate:
prediction.warnings.append(f"Package {package_name} not found in apt cache")
- return prediction
+ if self._is_python_related(package_name):
+ self._check_pip_conflicts(package_name, prediction)
+ if prediction.conflicts:
+ prediction.can_install = False
+ self._generate_resolutions(prediction)
+ return prediction🤖 Prompt for AI Agents
In `@cortex/conflict_predictor.py` around lines 370 - 387, predict_conflicts
currently returns early when _get_apt_package_info(package_name) yields no
candidate, which skips pip-only conflict checks; change the flow so that when
candidate is falsy you still normalize the input package_name (strip version
specifiers like "==", ">=", "~=" or use packaging to parse names) and call
_check_pip_conflicts(normalized_name, prediction) to populate
prediction.conflicts and prediction.resolutions, then append the existing
warning (prediction.warnings.append(...)) before returning; keep existing
behavior when candidate exists (i.e., run apt checks and also call
_check_pip_conflicts as appropriate) so both apt-absent pip-only installs and
version-pinned names are checked.
| if pip_name in self.PIP_CONFLICTS: | ||
| required_constraints = self.PIP_CONFLICTS[pip_name] | ||
|
|
||
| for dep_name, constraint in required_constraints.items(): | ||
| if dep_name in self._pip_cache: | ||
| installed_ver, _ = self._pip_cache[dep_name] | ||
| # Simple version check | ||
| if constraint.startswith("<"): | ||
| max_ver = constraint[1:] | ||
| if installed_ver >= max_ver: | ||
| prediction.conflicts.append( | ||
| PredictedConflict( | ||
| conflict_type=ConflictType.VERSION_MISMATCH, | ||
| package=pip_name, | ||
| conflicting_with=dep_name, | ||
| description=( | ||
| f"{pip_name} requires {dep_name}{constraint}, " | ||
| f"but {installed_ver} is installed via pip" | ||
| ), | ||
| installed_version=installed_ver, | ||
| required_version=constraint, | ||
| confidence=0.85, | ||
| ) |
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Fix version comparison to use semantic versioning instead of lexicographic comparison.
Line 561: installed_ver >= max_ver uses string comparison which produces incorrect results for version numbers (e.g., "1.10" < "1.9" lexicographically). This causes false positives/negatives in conflict detection.
Use packaging.version.Version for accurate semantic version comparison. However, note that packaging is not currently declared as a dependency in pyproject.toml. Either add it to the main dependencies list or use a conditional import with fallback (similar to the pattern in cortex/config_manager.py).
🛠️ Suggested approach
Add "packaging>=21.0" to dependencies in pyproject.toml, then update the comparison:
from packaging.version import Version, InvalidVersion
# At line 561:
try:
if Version(installed_ver) >= Version(max_ver):
prediction.conflicts.append(...)
except InvalidVersion:
logger.debug("Unable to parse pip versions for %s", dep_name)🤖 Prompt for AI Agents
In `@cortex/conflict_predictor.py` around lines 552 - 574, The current
lexicographic comparison in the pip conflict check (involving PIP_CONFLICTS,
_pip_cache and creating PredictedConflict/ConflictType entries) must be replaced
with semantic version comparison using packaging.version.Version: import Version
and InvalidVersion (or use the project's conditional import/fallback pattern
like in config_manager.py), parse installed_ver and max_ver with Version and
compare (Version(installed_ver) >= Version(max_ver)); catch InvalidVersion and
log/debug a message instead of raising, and ensure packaging (e.g.,
"packaging>=21.0") is added to dependencies in pyproject.toml or handled via the
conditional import fallback.
|
2 participants
Summary
Implements #428 - AI-powered dependency conflict prediction
Bounty: $150
Changes
New Module:
cortex/conflict_predictor.py/var/lib/dpkg/statusfor current system stateapt-cacheCLI Integration
cortex deps predict <package>cortex install <package>--executeto override)Test Coverage
tests/test_conflict_predictor.pyFeatures
Conflict Detection
Resolution Strategies (ranked by safety)
Example Usage
Acceptance Criteria from Issue
Test Plan
pytest tests/test_conflict_predictor.py -v(29 tests)/claim #428
Summary by CodeRabbit
New Features
Behavioral Changes
Tests
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