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

PyProphet v3.0.4

[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

PyProphet 3.0.3

What's Changed

• Add/hist gbc by @singjc in #144
• Add version checker update notification by @singjc in #164

Full Changelog: 3.0.2...3.0.3

PyProphet 3.0.2

What's Changed

• Fix/ipf osw alignment table by @singjc in #152
• change explode to using polars by @jcharkow in #153
• chore(deps): bump pillow from 11.2.1 to 11.3.0 by @dependabot[bot] in #149
• chore(deps): bump urllib3 from 2.4.0 to 2.5.0 by @dependabot[bot] in #148
• chore(deps): bump requests from 2.32.3 to 2.32.4 by @dependabot[bot] in #147
• Add: log colorizer option to global pyprophet settings by @singjc in #154
• chore(deps): bump pypdf from 5.6.0 to 6.0.0 by @dependabot[bot] in #157
• Feature: add exporting "score_peptide" and "score_protein" from .osw by @jcharkow in #159
• Feature: Export Library by @jcharkow in #156
• feat: support tuple input for lambda in pi0est function by @singjc in #160
• feature: more efficient sqMass to parquet export by @jcharkow in #158
• feat: add calibration report export functionality by @singjc in #161
• Update/export scored report by @singjc in #162

New Contributors

• @dependabot[bot] made their first contribution in #149

Full Changelog: 3.0.1...3.0.2

PyProphet 3.0.1

What's Changed

• fix pypdf out of date by @jcharkow in #150

Full Changelog: 3.0.0...3.0.1

PyProphet 3.0.0

Release Highlights (Major Version Update)

This release introduces significant structural changes to improve modularity:

• Introduced I/O Module: I/O logic is now modularized by file type (e.g., SQLite .osw, Parquet), to support new parquet format support.

• Configurable Data Classes: Core algorithms (scoring, IPF, levels contexts) now use configuration dataclasses for cleaner parameter management and easier extension.

• Click CLI Restructure: Command chaining has been removed to enable grouped subcommands (e.g., peptide, protein, peptidoform) for better CLI organization.

• Deprecation Notice: Original flat subcommands remain for backwards compatibility but will be removed in a future release.

• Added readthedocs for API and CLI documentation

• Added linear SVM classifier model for scoring module.

All existing functionality should continue to work as is. Please report any issues if any.

What's Changed

• Patch/pq memory opt by @singjc in #141
• Refactor/codebase by @singjc in #142

Full Changelog: 2.3.4...3.0.0

PyProphet 2.3.4

Full Changelog: 2.3.3...2.3.4

PyProphet 2.3.3

What's Changed

• add: export sqMass to parquet by @singjc in #138

Full Changelog: 2.3.2...2.3.3

PyProphet 2.3.2

Fix Dockerfile pyprophet installation. Previously used setup.py, but changed over to pyproject.toml, so installation needed to be changed to use pip install
Full Changelog: 2.3.1...2.3.2

PyProphet 2.3.1

What's Changed

• Add: Full parquet support for scoring and inference by @singjc in #137

Full Changelog: 2.3.0...2.3.1