PyProphet v3.0.14

What's Changed

• fix: matrix exports with 0 data by @singjc in #207

Full Changelog: v3.0.13...v3.0.14

PyProphet v3.0.13

What's Changed

• fix: osw to parquet export with global peptide/protein scores by @singjc in #206

Full Changelog: v3.0.12...v3.0.13

PyProphet v3.0.12

What's Changed

• feat: direct subsampling and applying of OSW during scoring by @singjc in #205

Full Changelog: v3.0.11...v3.0.12

PyProphet v3.0.11

What's Changed

• add version number by @jcharkow in #203

Full Changelog: v3.0.10...v3.0.11

PyProphet v3.0.10

What's Changed

• fix: pin pandas version in docker image by @singjc in #202

Full Changelog: v3.0.9...v3.0.10

PyProphet v3.0.9

What's Changed

• fix: osw export bug and memory view bug by @singjc in #200
• Update cython version to 3.2.4 by @singjc in #201

Full Changelog: v3.0.8...v3.0.9

PyProphet v3.0.8

What's Changed

• Fix pandas IndexError in export matrix summarization (pandas ≥2.1) by @Copilot in #194
• Remove PyInstaller standalone binary packaging infrastructure by @Copilot in #195

Full Changelog: v3.0.7...v3.0.8

PyProphet v3.0.7

What's Changed

• Refactor GitHub Actions for Python publishing by @singjc in #190
• Bump version from 3.0.6 to 3.0.7 by @singjc in #191

Full Changelog: v3.0.6...v3.0.7

PyProphet v3.0.6

What's Changed

• Add/im boundaries to tsv export by @singjc in #175
• chore(deps): bump fonttools from 4.58.1 to 4.60.2 by @dependabot[bot] in #180
• chore(deps): bump urllib3 from 2.5.0 to 2.6.0 by @dependabot[bot] in #176
• Update Python version requirement to <3.14 by @singjc in #188
• Bump version from 3.0.5 to 3.0.6 by @singjc in #189

Full Changelog: v3.0.5...v3.0.6

PyProphet v3.0.5

[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