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PyProphet v3.0.5

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@singjc singjc released this 27 Nov 04:09
· 28 commits to master since this release
v3.0.5
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[3.0.5] - 2025-11-27

🚀 Features

  • Add native installer creation scripts (DEB, RPM, DMG, EXE)
  • Add native installer creation scripts (DEB, RPM, DMG, EXE)
  • Enhance artifact upload process in GitHub Actions for Linux, Windows, and macOS
  • (build) Improve DMG testing and installation process for macOS
  • (build) Enhance build scripts for Windows and macOS with UPX compression and runtime dependency installation
  • (build) Add --onefile option to PyInstaller for all platforms
  • (build) Enhance runtime dependency installation in build scripts for Linux, macOS, and Windows
  • (build) Streamline PyInstaller build process with onefile mode and module exclusions for macOS and Linux
  • (build) Implement UPX compression for final binaries in build scripts for Linux, macOS, and Windows
  • (build) Update packaging scripts to use single-file executable for Linux, macOS, and Windows
  • (build) Enforce Python 3.11+ requirement in build scripts for Linux, macOS, and Windows
  • (build) Create minimal entry point script to avoid path conflicts in PyInstaller builds for Linux, macOS, and Windows
  • (build) Install pyprophet as a regular package to avoid import conflicts in build scripts for Linux, macOS, and Windows
  • (build) Build and install pyprophet as a wheel for cleaner installation in Linux and Windows scripts
  • (build) Optimize PyInstaller build process with temporary directory for cleaner execution
  • (build) Enhance build script to save original directory and clean up previous builds
  • (build) Clean up build artifacts and optimize wheel installation process in Linux script
  • (build) Modify installation process to ensure pyprophet is installed in site-packages and verify dependencies
  • (build) Enhance installation script to uninstall existing pyprophet and optimize wheel build process
  • (build) Create isolated virtual environment for building and streamline pyprophet installation process
  • (build) Streamline build script by cleaning artifacts and optimizing virtual environment setup
  • (build) Optimize Linux build script by simplifying installation steps and improving error handling
  • (build) Enhance Windows build script to clean Python cache and improve installation process
  • (build) Update GitHub Actions workflow to improve error handling and streamline command execution
  • (build) Enhance Windows build script to optimize PyInstaller process and add self-extracting archive support
  • Implement lazy loading for pyarrow imports and improve error handling for parquet support
  • Enhance version retrieval and sanitization for macOS build scripts
  • (export) Add support for exporting minimal scored-report columns from split Parquet files

🐛 Bug Fixes

  • (build) Handle errors in file permission setting and listing during package creation
  • (tests) Fix bug with restructuring of ipf score to precursor mapping and IM boundaries
  • (osw) Remove debug print statement for temporary table query in OSWWriter
  • (report) Ensure axes are consistently indexed in plot_score_distributions function

💼 Other

  • Requirements.txt
  • Only add from_alignment column when alignment is actually used
  • Extract helper method to reduce code duplication
  • Filter out columns without types when building temp table schema
  • Add RUN_ID to score peptide/protein views for proper joining
  • Use LEFT JOIN for score views to avoid filtering out rows without matching RUN_ID
  • Regtest for new test
  • Regtest output
  • Extract pyarrow import check to helper function to reduce code duplication
  • Move file type reader methods into IO export classes
  • Use existing _ensure_pyarrow() instead of custom function
  • Regtest outputs

🚜 Refactor

  • Simplify parquet reader and writer initialization by using utility functions
  • Update pyarrow import to improve parquet file handling
  • Streamline parquet file imports and initialization using utility functions
  • Avoid circular imports by using type names for config checks
  • Reorganize parquet file imports for improved clarity and initialization
  • Enhance lazy loading for pyarrow imports and improve parquet initialization
  • (parquet) Improve alignment group ID assignment and update score column references

⚙️ Miscellaneous Tasks

  • Update CHANGELOG.md
  • Replace xgboost with xgboost-cpu to reduce package size
  • Update Python version to 3.11 in GitHub Actions workflows
  • Remove local path for pyprophet in requirements.txt
  • Simplify command paths in GitHub Actions workflow for pyprophet
  • Remove tomli module exclusion from PyInstaller build scripts for Linux, macOS, and Windows
  • Remove pip install command from GitHub Actions workflow to resolve numpy source directory issue
  • Remove sklearn metadata copy from PyInstaller build script for Linux
  • Add error handling to cleanup commands in Windows build script
  • Remove pyarrow from main dependencies and add to parquet group
  • Update pyarrow dependency to optional for Parquet support
  • Exclude unnecessary modules from PyInstaller builds for Linux, macOS, and Windows
Assets 19
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