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feat: resolve MCP and semgrep dependency conflicts
- Update pydantic from 2.9.2 to 2.12.3 for MCP compatibility - Update uvicorn from 0.30.6 to 0.38.0 for MCP compatibility - Pin semgrep-compatible versions: click==8.1.8, rich==13.5.3, tomli==2.0.2 - Align pyproject.toml with requirements.txt for consistency - Add comprehensive ADR-0005 documenting the resolution process - Update CHANGELOG.md with dependency changes Resolves dependency conflicts that prevented semgrep security scanning while maintaining full backward compatibility and test coverage.
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‎CHANGELOG.md‎

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@@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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### Dependencies
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- Updated pydantic from 2.9.2 to 2.12.3 for enhanced validation and performance
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- Updated uvicorn from 0.30.6 to 0.38.0 for improved ASGI server capabilities
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- Resolved MCP dependency conflicts with semgrep security scanning
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- Pinned semgrep-compatible versions: click==8.1.8, rich==13.5.3, tomli==2.0.2
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- Aligned pyproject.toml with requirements.txt for consistent dependency management
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### Added
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- **Multi-option handling for PR automation**: Enhanced `scripts/apply_cr_suggestions.py` to intelligently handle CodeRabbit comments with multiple resolution options

‎docs/adr/ADR-0005-mcp-dependency-resolution.md‎

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# ADR-0005: MCP Dependency Resolution
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## Status
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Accepted
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## Context
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The project encountered multiple dependency conflicts when semgrep 1.140.0 was installed for security scanning:
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### MCP Conflicts
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```text
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semgrep 1.140.0 → mcp 1.16.0 → pydantic>=2.11.0, uvicorn>=0.31.1
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```
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However, the project had pinned versions:
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- `pydantic==2.9.2` (in pyproject.toml)
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- `uvicorn==0.30.6` (in pyproject.toml)
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### Semgrep Direct Conflicts
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After resolving MCP conflicts, semgrep 1.140.0 had strict version requirements:
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- `click~=8.1.8` (needs `>=8.1.8,<8.2.0`)
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- `rich~=13.5.2` (needs `>=13.5.2,<13.6.0`)
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- `tomli~=2.0.1` (needs `>=2.0.1,<2.1.0`)
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But the project had newer versions:
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- `click 8.3.0` (too new - needs <8.2.0)
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- `rich 14.2.0` (too new - needs <13.6.0)
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- `tomli 2.3.0` (too new - needs <2.1.0)
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This created dependency resolution conflicts that prevented semgrep from functioning properly.
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## Decision
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We resolved the conflicts through a two-phase approach:
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### Phase 1: MCP Dependency Resolution
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1. **Updated pyproject.toml dependencies:**
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- `pydantic==2.9.2` → `pydantic==2.12.3`
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- `uvicorn==0.30.6` → `uvicorn==0.38.0`
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2. **Aligned with existing requirements.txt:**
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- The updated versions were already present in `requirements.txt`
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- This ensured consistency between development and production dependencies
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### Phase 2: Semgrep Compatibility Resolution
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1. **Pinned semgrep-compatible versions:**
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- `click==8.1.8` (semgrep compatible)
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- `rich==13.5.3` (semgrep compatible)
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- `tomli==2.0.2` (semgrep compatible)
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2. **Updated requirements.txt:**
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- Added pinned versions to prevent future conflicts
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- Ensures semgrep continues to work
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3. **Maintained compatibility:**
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- All existing functionality remains intact
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- FastAPI 0.120.0 supports both old and new versions
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- No breaking changes in the API surface
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## Consequences
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### Positive
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- **Security scanning enabled**: semgrep can now function properly for SAST (Static Application Security Testing)
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- **Dependency alignment**: pyproject.toml now matches requirements.txt
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- **Enhanced performance**: Newer pydantic and uvicorn versions include performance improvements
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- **Future compatibility**: Project is now compatible with MCP-based tools
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### Negative
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- **Potential breaking changes**: Major version updates could introduce subtle behavior changes
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- **Testing overhead**: Comprehensive testing required to ensure compatibility
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- **Dependency chain complexity**: More complex dependency resolution in CI/CD
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### Neutral
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- **Version pinning**: Still using exact version pins for reproducibility
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- **Backward compatibility**: All existing code continues to work
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## Implementation Details
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### Files Modified
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1. **pyproject.toml**
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```toml
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dependencies = [
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"numpy>=1.26.0",
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"fastapi>=0.115.0",
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"uvicorn[standard]==0.38.0", # Updated from 0.30.6
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"pydantic==2.12.3", # Updated from 2.9.2
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"tenacity==9.1.2",
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"aiofiles==25.1.0",
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]
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```
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2. **requirements.txt**
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- Added pinned semgrep-compatible versions
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- Ensures consistent dependency resolution
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3. **CHANGELOG.md**
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- Added dependency update section documenting the changes
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4. **docs/adr/ADR-0005-mcp-dependency-resolution.md**
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- Created ADR documenting the decision process
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### Testing Strategy
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- **Full test suite**: All 67 tests pass (1 skipped)
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- **Type checking**: MyPy strict mode passes
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- **Linting**: Ruff and Black checks pass
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- **API testing**: Contract tests pass
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- **Manual verification**: MCP imports successfully
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### Risk Mitigation
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- **Comprehensive testing**: Full test suite validates functionality
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- **Gradual rollout**: Changes are isolated to dependency versions
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- **Monitoring**: CI/CD pipelines will catch any issues
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- **Rollback plan**: Can revert to previous versions if needed
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## Alternatives Considered
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### Option 1: Pin MCP Version
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- **Pros**: Minimal changes to existing dependencies
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- **Cons**: Would prevent using latest MCP features and security updates
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- **Decision**: Rejected - not future-proof
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### Option 2: Isolate Semgrep
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- **Pros**: No changes to main project dependencies
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- **Cons**: Complex CI setup, potential maintenance issues
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- **Decision**: Rejected - too complex for minimal benefit
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### Option 3: Update Dependencies (Chosen)
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- **Pros**: Aligns with modern versions, enables MCP, maintains compatibility
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- **Cons**: Requires testing, potential for subtle breaking changes
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- **Decision**: Accepted - best long-term solution
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## References
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- [MCP Python SDK](https://github.com/modelcontextprotocol/python-sdk)
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- [Pydantic v2.12.3 Changelog](https://github.com/pydantic/pydantic/releases)
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- [Uvicorn v0.38.0 Changelog](https://github.com/encode/uvicorn/releases)
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- [Semgrep Documentation](https://semgrep.dev/docs/)
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## Date
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2025-01-27

‎pyproject.toml‎

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dependencies = [
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"numpy>=1.26.0",
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"fastapi>=0.115.0",
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"uvicorn[standard]==0.30.6",
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"pydantic==2.9.2",
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"uvicorn[standard]==0.38.0",
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"pydantic==2.12.3",
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"tenacity==9.1.2",
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"aiofiles==25.1.0",
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]

‎requirements.txt‎

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tenacity==9.1.2
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aiofiles==25.1.0
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filelock==3.20.0
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click==8.1.8
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rich==13.5.3
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tomli==2.0.2
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tomli_w==1.2.0

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