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PyProphet v3.0.4

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@singjc singjc released this 21 Oct 00:58
· 177 commits to master since this release
v3.0.4
7224251

[3.0.4] - 2025-10-21

🚀 Features

  • Enhance PyInstaller scripts for macOS and Windows with metadata collection and binary inclusion
  • Expand GitHub Actions workflow to include comprehensive testing for all commands across platforms
  • Add concurrency control to GitHub Actions workflows for improved efficiency
  • Add concurrency control to multiple GitHub Actions workflows for improved efficiency
  • Add PyInstaller hook for pyprophet package to ensure proper module collection

🐛 Bug Fixes

  • (build) Fix archiving of windows build release to use zip instead of tar

💼 Other

  • Pyinstaller build scripts
  • Gha's for package building
  • Create launcher for PyInstaller bundles with threading support
  • Windows dist script
  • Create PyInstaller hooks for duckdb and xgboost packages
  • Implement PyInstaller hook for pyopenms package with dynamic library collection
  • Move build scripts to a dedicated directory and update paths
  • Update build script paths to reflect new directory structure

🚜 Refactor

  • Remove tabulate dependency and update related code in main.py
  • Remove numexpr dependency from project configuration
  • Remove seaborn dependency from project configuration
  • Reorganize imports and clean up unused code in report.py
  • Remove statsmodels dependency and update related code in stats.py
  • Reduce decimal precision in lfdr tests for consistency
  • Update expected output values in lfdr tests for consistency
  • Add Gaussian kernel density estimation comparison script
  • Update expected output values in pyprophet score tests for consistency with change of kernel density estimate
  • Filter script
  • Reorganize imports and optimize database query in split.py
  • Update expected output values in pyprophet IPF scoring tests for consistency
  • Implement statsmodels KDEUnivariate method
  • Update expected output values in pyprophet score tests for consistency
  • Add comparison script for FFT-based KDE and statsmodels KDEUnivariate
  • Replace DCT-based KDE with FFT-based KDE implementation
  • Update expected output values in pyprophet IPF scoring tests for consistency
  • Update expected output values in test_stats for consistency
  • Update expected output values in pyprophet export test for consistency
  • Update build and test workflows for improved clarity and manual trigger

📚 Documentation

  • Update installation instructions and add options for pre-built executables and Docker
  • Add contributing guidelines and commit message conventions

⚙️ Miscellaneous Tasks

  • Remove feature branch from GitHub Actions workflow triggers
  • Update Python version support and refine package discovery settings
  • Add GitHub Actions workflow for automatic changelog generation
  • Remove concurrency settings from GitHub Actions workflow
  • Update CHANGELOG.md
  • Refactor GitHub Actions workflow for improved build and artifact handling
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