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- Added comprehensive test suite with 238 tests (70% increase) - Fixed all previously failing tests - Added 4 new test modules: advanced functionality, numerical methods, performance, workflow integration - Enhanced pytest configuration with proper markers - Updated .gitignore to exclude large files (.mgf, .ckpt) - Improved code quality and test coverage dramatically
- Add main CI workflow with multi-Python version testing - Include performance and memory testing jobs - Add code quality checks (black, isort, mypy, flake8) - Set up coverage reporting with Codecov - Add release workflow for package publishing - Include dependency update testing with automated issue creation - Add status badge workflow for quick test feedback - Update README with status badges - Enhanced pyproject.toml with proper build configuration and dependencies Features: - Tests run on push/PR to main and develop branches - Multi-Python version matrix (3.11, 3.12) - Comprehensive test categorization (fast, unit, integration, performance) - Automatic dependency caching - Optional RustyMS dependency handling - Code quality enforcement - Weekly dependency compatibility checks
- Corrected license field in pyproject.toml from MIT to Apache-2.0 - Updated license badge in README.md to reflect Apache-2.0 license - Updated PyPI classifier to use correct Apache Software License
- Update license format from deprecated table to SPDX string - Remove deprecated license classifier - Add explicit package discovery configuration - Include main py-modules to resolve build configuration errors - Fix CI build pipeline setuptools compatibility
- Add numba>=0.57.0 for feature generators - Add psutil>=5.9.0 for performance tests - Add rich>=13.0.0 for utilities logging - Add mokapot>=0.8.0 for main module - Resolve ModuleNotFoundError in CI test collection
- Add tensorflow>=2.13.0 for keras modules - Add scikeras>=0.12.0 for KerasClassifier wrapper - Add tqdm>=4.65.0 for progress bars - Resolve ModuleNotFoundError for keras in workflow integration tests
- Rename config_new.py → config.py (new simplified system becomes primary) - Backup old config system as config_old.py for reference - Update all import statements: * run.py: from config_new import → from config import * test_config_compatibility.py: updated import * demo_new_config.py: updated import (also added to git) - Benefits of replacement: * Clean primary config.py with simplified flat structure * Full backwards compatibility maintained * All existing functionality preserved * Users can now import from 'config' instead of 'config_new' * Old complex system preserved as config_old.py for reference All tests pass: ✅ New config.py works correctly ✅ Backwards compatibility maintained ✅ Demo script works ✅ Compatibility test passes ✅ Main workflow accepts both config formats The new simplified config system is now the primary configuration system.
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Add retention time margins & directLFQ quant
…eractive input from pickling
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