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- Remove excessive bold formatting and structured sections - Simplify language to be more conversational - Remove 'Answer:' and 'Pros:' patterns - Make it sound more like developer-written documentation - Remove 'Questions Addressed' section - Simplify testing checklist format
- Created pyproject.toml with build system configuration and project metadata - Migrated all metadata from setup.py to pyproject.toml - Updated Dockerfile to install package from pyproject.toml during build - Updated documentation (README.md, QUICKSTART.md, DEPLOYMENT_REQUIREMENTS.md) - Maintained backward compatibility with setup.py Fixes #45
- Created credential masking utility (app/utils/credential_masking.py) - mask_credential(): Masks individual credentials (shows last 4 chars) - mask_string(): Masks credentials in text strings - mask_dict(): Masks credentials in dictionaries - safe_log_message(): Creates safe log messages - mask_exception_message(): Masks exception messages - Fixed all logging statements to mask credentials: - app/utils/config.py: Fixed error logging - app/models/llm_provider.py: Fixed all error logging - app/models/unified_qa.py: Fixed all error logging - app/models/gemini_qa.py: Fixed all error logging - app/services/data_retrieval.py: Fixed 12 error logging instances - app/api/routers/system.py: Fixed 10 error logging instances - app/api/routers/bugsigdb_analysis.py: Fixed error logging - app/api/routers/bugsigdb_analysis_v2.py: Fixed 5 error logging instances - app/api/routers/study_analysis.py: Fixed error logging - app/api/utils/api_utils.py: Fixed error logging - app/api/app.py: Fixed global exception handler - Fixed error messages to not expose credentials - Added comprehensive test suite (tests/test_credential_masking.py) - Security audit completed for all critical files Fixes #46
- Created .github/workflows/ci.yml with comprehensive CI/CD pipeline - Test job: Runs tests on Python 3.8, 3.9, 3.10, 3.11 - Lint job: Code quality checks with black and flake8 - Type-check job: Type checking with mypy - Security job: Security scanning with bandit and safety - Docker-build job: Builds and tests Docker image - All-checks job: Summary of all checks - Features: - Tests run on all supported Python versions (3.8-3.11) - Automated linting (black, flake8) - Automated type checking (mypy) - Security scanning (bandit, safety) - Docker image build and test - Code coverage reporting - Workflow runs on PR and push to main/develop - Added status badges to README: - CI/CD Pipeline status badge - Code Quality (Black) badge Fixes #49
- Add PYTHONPATH environment variable for tests - Add verification step before running tests - Increase maxfail to 10 to see more test failures - Add E501 to flake8 ignore list (line length) - Add better diagnostic output for debugging
- Update pyproject.toml to use paper-qa>=4.9.0 (compatible with Python 3.8-3.11) - Add conditional paper-qa installation in CI workflow: - Python 3.11: Install from GitHub (latest) or fallback to 4.9.0 - Python 3.8-3.10: Install paper-qa>=4.9.0,<5.0.0 (stable version) - Fixes CI failures: paper-qa>=5.0.0 doesn't exist on PyPI yet This resolves the 'No matching distribution found for paper-qa>=5.0.0' error
- Remove Python version matrix (3.8, 3.9, 3.10, 3.11) - Use only Python 3.11 for all tests (matches Docker and production) - Simplify paper-qa installation (no conditional logic needed) - Fixes pandas>=2.1.1 compatibility issues with older Python versions This makes CI faster and avoids dependency conflicts with Python 3.8-3.10
- Fix missing commas in dictionaries (gemini_qa.py) - Fix unterminated docstring in data_retrieval.py - Fix indentation errors in test files (test_api_utils.py, test_integration.py, test_cache_manager.py, test_text_processing.py, test_api_endpoints.py, test_integration_workflow.py) - Update CI lint job to use Docker for black and flake8 (avoids venv setup) All files now pass Python syntax validation and should format correctly with black.
- Add 'load: true' to docker/build-push-action to make image available locally - This fixes the 'Unable to find image' error in the Docker test step - Image is now properly loaded into Docker daemon for testing
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Created .github/workflows/ci.yml with comprehensive CI/CD pipeline
Features:
Added status badges to README:
Fixes #49