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Changelog

All notable changes to this project will be documented in this file.

[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

[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

[3.0.3] - 2025-10-18

🚀 Features

  • Update Dockerfile to use Ubuntu 24.04 and set up Python virtual environment
  • Enhance HistGradientBoostingClassifier with improved parameter tuning and parallel processing
  • Add HistGBCLearner support for autotuning in semi-supervised learning
  • Add support for thread management in HistGradientBoosting to prevent oversubscription
  • Add documentation for thread management in HistGradientBoosting and HistGBCLearner
  • Add version checking utilities for PyProphet
  • Add update check and message display in CLI

🐛 Bug Fixes

  • Filter out invalid params for HistGradientBoostingClassifier to prevent TypeError
  • Remove stray return and fix indentation in HistGBCLearner.learn
  • Use permutation_importance fallback for HistGradientBoostingClassifier feature importances
  • Add check for importance attribute before logging feature importances
  • Store feature importance on classifier object to persist through set_parameters
  • Pi0 when passing single value as lambda
  • Update l2_regularization default value in HistGBCLearner to improve model performance
  • Initialize ll variable in pi0est function to prevent potential errors
  • Correct typo in comment regarding OMP_NUM_THREADS and numpy import order
  • Set OMP_NUM_THREADS before sklearn import for HistGBC
  • Ensure OMP_NUM_THREADS is set before any numpy imports for HistGradientBoosting
  • Set OMP_NUM_THREADS to 1 for pytest execution in CI workflow
  • Add 'packaging' to runtime dependencies in pyproject.toml

💼 Other

  • Dockerfile
  • Defaults for HistGBC
  • Impl. summary docs
  • Robust thread control\n- Safely derive total_jobs from TOTAL_CPUS or os.cpu_count() with fallback and clamping\n- Coordinate outer (RandomizedSearchCV n_jobs) vs inner (OpenMP) parallelism\n- Use threadpoolctl to enforce OpenMP limits during tune() and learn() fits\n- Avoid OMP_NUM_THREADS=0 and respect user-provided OMP_NUM_THREADS if set
  • Delete HISTGBC_TEST_ADDITIONS.md as part of documentation cleanup

🚜 Refactor

  • Move compare_classifiers.py to sandbox and update parameters for optimization
  • Clean up code formatting and improve readability in BaseWriter class
  • Remove unused pandas import from compare_classifiers.py
  • Move OMP_NUM_THREADS setup to main.py for HistGradientBoosting and update logging in runner

📚 Documentation

  • Clarify OMP_NUM_THREADS setup requirements in main.py

🧪 Testing

  • Add HistGradientBoosting classifier coverage across OSW/Parquet/Split/Multisplit; enable autotune and PFDR paths; extend strategies to support --classifier=HistGradientBoosting
  • Add regression test outputs for HistGradientBoosting classifier across various configurations
  • Add tests for version checking functionality

[3.0.2] - 2025-10-09

🚀 Features

  • Add log colorization option for improved logging visibility
  • Add exporting "score_peptide" and "score_protein" from OSW files
  • Start implementation of lib export with pyprophet
  • Option to keep significant decoys in lib refinement
  • Add option to export rt unit in non iRT
  • Sort by intensity if q value tie
  • Add calibration report export functionality
  • Support tuple input for lambda in pi0est function
  • More efficient sqMass to parquet export
  • Add transition ordinal and type to export
  • Implement export functionality for scored reports with parquet and osw support

🐛 Bug Fixes

  • Refactor SQL subquery for feature alignment in OSWReader
  • Alignment table fetching for ipf osw reader
  • QVALUE->Q_VALUE
  • Export protein info in lib
  • Lib export compute annotation col if empty
  • Error description
  • Bug in sql query
  • Bug resulting from code suggestions
  • Ensure score_ipf_qvalue is checked for NaN before filtering

💼 Other

  • _optimized cython bindings
  • Note that keep_decoys in lib gen is experimental feature
  • Chrom parquet schema documentation
  • Dependencies

📚 Documentation

  • Update schema with new columns

🧪 Testing

  • Add test for lib generation
  • Update tests with new snapshots

[3.0.1] - 2025-07-24

🐛 Bug Fixes

  • Ipf osw alignment data fetching

💼 Other

  • Test nb

[3.0.0] - 2025-06-13

🚀 Features

  • Add option to split transition data in convert_osw_to_parquet function
  • Add memory usage information to parquet export
  • Improve memory usage reporting in parquet export
  • Enhance feature transition data extraction in convert_osw_to_parquet
  • Add functionality to extract and export memory usage information in convert_osw_to_parquet
  • Move format_bytes function to data handling
  • Improve coalesce handling and data processing in convert_osw_to_parquet
  • Remove batch_size option and optimize memory usage in parquet export
  • Include FEATURE_ID in feature transition columns for improved data extraction in convert_osw_to_parquet
  • Include RUN_ID in feature transition data extraction for improved data processing in convert_osw_to_parquet
  • Introduce normalized peptides and IPF peptide mapping in convert_osw_to_parquet function
  • Implement RunnerConfig and RunnerIOConfig dataclasses for handling scoring and configuration in IO operations
  • Add ErrorEstimationConfig dataclass for error estimation configuration in IO operations
  • Add properties for Base reader and writer for common used fields from config
  • Implement different io reader and writer classes
  • Add method to write PDF report with scoring results
  • Add subsample_ratio parameter for data subsampling in PyProphet scoring
  • Add function to retrieve feature mapping across runs in glycoform.py
  • Add LevelContextIOConfig for context-based configuration in peptide inference
  • Add trained model path for alignment in RunnerIOConfig
  • Introduce LevelContextIOConfig for context-based configuration in ReaderDispatcher and WriterDispatcher
  • Implement feature to scale features
  • Add support for autotuning hyperparameters in SVM classifier and XGBoost in RunnerConfig
  • Add new commands for glycopeptide, gene, and protein in levels context
  • Add export_scored_report function to export PyProphet scored reports
  • Add method to merge precursor and transition features files into single parquet files
  • Install seaborn and psutil dependencies in Dockerfile
  • Add HistGradientBoostingClassifier for improved learning performance
  • Add new test data files for PyProphet score split parquet outputs
  • Collapse IPF peptide IDs to avoid duplicating feature data in DataFrame
  • Add function to convert a sequence with unimod modifications to a codename
  • Enhance export functionality with logging for legacy formats
  • Enhance peptide and protein data merging with improved logging and handling for run-specific and global scores
  • Improve logger formatting based on log level for easier debbugging and tracing
  • Enhance logging for legacy export format with data size and shape information
  • Add score column selection and joins for osw to parquet export

🐛 Bug Fixes

  • How weights are saved for xgboost and how they're loaded
  • Parquet ms1 data fetching
  • Parquet transition data fetching
  • Score parquet reader, ensure scores get added to proper block
  • Peptide and protein data merging with improved handling of run-specific and global scores for tsv export
  • Change debug logs to info level for legacy export formats
  • Update test output for peptide and protein data export
  • Correct SQL queries to use appropriate scoring values for peptide and protein data

💼 Other

  • Click logs
  • Scoring with parquet directory
  • Ipf to accept split parquet files
  • Fix xgboost feat importance printing
  • Logging to loguru, and handle multi directory of split parquet runs
  • Option to split by run
  • Test io scoring module
  • Test pyp score
  • Pyp test score regtest output
  • Pyp score tests
  • Io reading tests
  • Subsampling in parquet scoring reader
  • Report for post scored OSW-PYP results
  • Optimized c
  • Init to glyco module
  • Apply ruff formatting
  • Format with ruff
  • Apply ruff formatting
  • Cli
  • Test io for levels context
  • Io export module
  • Assets logo
  • Parquet test data
  • Pyp call in glyco scoring

🚜 Refactor

  • Optimize join and column selection in convert_osw_to_parquet function
  • Remove unused code related to writing parquet batches
  • Repalce monolith passed params with runner config
  • Runner, abstract data reading and writer to separate classes
  • Update data_handling module with new check_sqlite_table function and refactor PyProphetRunner class to use runner_config properties
  • Update import paths for configuration modules in various IO-related files
  • Update error estimation configuration access in StandardSemiSupervisedLearner
  • Update runner config to use specific properties for dynamic main score setting
  • Update data handling module with new check_sqlite_table function and refactor PyProphetRunner class to use runner config properties
  • Replace Exception with ValueError for zero standard deviation in decoy scores
  • Update base class methods for file type detection and handling in IO-related files
  • Update import paths for IO-related files to use new utility functions
  • Update import paths for IO-related files to use new utility functions
  • Update import paths for IO-related files to use new utility functions and io.util module
  • Refactor read_parquet_dir function for improved data handling and code organization
  • Improve data handling and code organization in read_parquet_dir function
  • Update DuckDB table checking to be case-insensitive
  • Update alignment_table view query to include new columns and ordering
  • Update BaseReader class with additional module specific config for reading and deprecate swath_pretrained main score option
  • Split io into context modules for reading/writing and use a single dispatcher for delegating
  • Add config io dispatcher to IPF
  • Filter persisted weights by current level in PyProphetWeightApplier
  • Comment out unnecessary exception for missing transition-level feature table
  • Remove unnecessary code for creating views in SplitParquetReader
  • Update SplitParquetReader and SplitParquetWriter to handle alignemnt when multi run
  • Update IPF CLI to use IPFIOConfig
  • Update ErrorEstimationConfig with default values and numpy import
  • Update feature selection query in convert_osw_to_parquet function
  • Update logging messages for semi-supervised learning levels in main.py
  • Remove redundant SQL queries for gene and protein inference
  • Update IO configurations to use specific config classes for runners and IPF
  • Update context_fdr usage in ParquetReader and SplitParquetReader
  • Update context_fdr assignment in ParquetReader and SplitParquetReader
  • Update logging and setup_logger usage in various modules
  • Group level context subcommands and add global stats decoratory for shared stat params
  • Scoring to single parquet file with blocked nulls
  • Introduce export command group for different formats and update TSV export functionality
  • Update column renaming logic in BaseWriter for different file types
  • Update column data types to BIGINT in convert_osw_to_parquet function
  • Update xgb param space
  • Update product charge field name in OSWReader class
  • Merge ms1 data into feature table for ms1ms2 level in OSWReader class
  • Finalize feature table column names for semi-supervised scoring
  • Update convert_osw_to_parquet to include necessary fields for mapping to TRANSITION data
  • Validate row count consistency after joining scores in ParquetWriter classes
  • Update table references from 'transitions' to 'transition' in SplitParquetReader class
  • Include FEATURE_ID field in convert_osw_to_parquet for mapping to TRANSITION data
  • Validate row count consistency after joining scores in ParquetWriter and SplitParquetWriter classes
  • Replace click.echo with logger for informative messages in scoring classes
  • Add subsampling option in test functions for Parquet scoring
  • Add SVM classifier support and autotuning in PyProphetRunner and SemiSupervisedLearner classes
  • Improve logging format in setup_logger function
  • Report
  • Level context stats, move report writing to base writer
  • Update logging level to 'trace' for creating views in SplitParquetReader
  • Remove optional model retraining in SVMLearner class
  • Update logging level to 'debug' for generating main panel plot
  • Remove redundant comments and unnecessary code in BaseWriter class
  • Update logging message to remove f-string usage in export_parquet.py
  • Update BaseIOConfig class to include str and repr methods
  • Implement str and repr methods for ErrorEstimationConfig, RunnerConfig, and RunnerIOConfig classes
  • Improve logging for scaling columns in Experiment class
  • Add setup_logger function for initializing logging with specified log level
  • Update CombinedGroup class and shared statistics options for PyProphet CLI
  • Improve error handling and logging for classifier weights validation
  • Update PyProphetWeightApplier to handle SVM classifier and improve code readability
  • Update classifier handling in LinearLearner and SVMLearner classes
  • Update data source references in ParquetReader and ParquetWriter classes
  • Update SVMLearner class to include class_weight parameter for hyperparameter tuning
  • Update logging functionality to include header information for PyProphet CLI commands
  • Update dependencies in pyproject.toml, optimize imports, and restructure code in various modules
  • Update Base classes to use BaseOSWReader and BaseOSWWriter for consistency across modules
  • Separate out subcommands into separate files in cli module to clean up main
  • Add export_scored_report command and measure memory usage and time for various export functions
  • Add measure_memory_usage_and_time decorator to score function
  • Remove unused format_bytes function for better code cleanliness
  • Update module paths for optimized C files
  • Improve readability and documentation in scoring classes
  • Update CLI module paths for improved organization
  • Improve CLI option descriptions for better clarity and understanding
  • Imports
  • Update file paths in read_parquet method for consistency
  • Update CLI option descriptions and variable names for consistency and clarity
  • Enhance logging and diagnostics for row mismatch in score DataFrame
  • Add 'PROTEIN_ID' column handling for 'ms1', 'ms2', and 'ms1ms2' levels in parquet scoring
  • Collapse protein IDs to avoid duplicating feature data in DataFrames
  • Set alignment_file to None if it doesn't exist to handle missing file gracefully
  • Remove unnecessary print statement in SplitParquetWriter class
  • Update print_alignment_file handling in BaseSplitParquetReader class
  • Update handling of SCORE_MS2_SCORE column in ParquetReader and SplitParquetReader classes
  • Improve handling of multiple runs in report generation
  • Update handling of run_id for different levels in report generation
  • Improve handling of file paths and deep copy in BaseIOConfig and score functions
  • Update handling of score and key columns based on file type in BaseWriter class
  • Update handling of group_id formatting in OSWReader class
  • Improve test fixtures and validation functions for peptide and protein level analysis
  • Enhance utility functions for SQLite and Parquet file handling
  • Update data handling imports to pyprophet.scoring module
  • Update test utilities for reading and comparing data across different levels and contexts
  • Update level data extraction for IPF in ParquetReader class
  • Add ExportIOConfig class for exporting results to various formats
  • Update column names for P-value and Q-value in OSWWriter class
  • Update import paths for SQLite table checking in export modules
  • Update export module to include ExportIOConfig for flexible result exporting
  • Update ParquetReader to include 'export' context for printing parquet tree
  • Update ordering of columns in SQL queries for consistency in SplitParquetReader class
  • Pyp export test
  • Improve clarity of help messages in export_tsv function
  • Generalize ipf unimod - codename peptide id mapping
  • Update SQL queries to include additional conditions for transition scoring data
  • Update logging format for summary display in PlotGenerator class
  • Collapse IPF peptide IDs to avoid duplicating feature data in DataFrame
  • Update BaseSplitParquetReader to inherit from BaseParquetReader to share similar methods
  • Drop duplicates in ParquetReader and SplitParquetReader
  • Update compare_dataframes function to accept sort_cols parameter for flexible sorting
  • Align column naming for consistency in OSW file handling across modules
  • Update levels_contexts.py to pass a copy of data to _write_levels_context_pdf_report
  • Improve SQLite table column checking functions for better code organization and clarity
  • Enhance file type inference with detailed logging for unsupported formats
  • Standardize Q_VALUE to QVALUE in SQL queries for consistency
  • Add function to check if a file is likely a TSV file based on its content
  • Standardize Q_VALUE to QVALUE in SQL queries for consistency
  • Add debug logging for reader class and file type in PyProphetRunner
  • Replace xgboost autotune flag with standardized flag for consistency
  • Add support for sqmass file type in WriterDispatcher and update export logic
  • Move export_parquet.py to sandbox
  • Add parquet export configuration options for compression and file splitting
  • Add pyopenms to project dependencies
  • Remove unused import for parquet conversion in export module
  • Update memory usage and execution time measurement decorator
  • Update XGBoost configuration by removing hyperparameters and standardizing parameters, change hyperopt to use sklearn randomized grid search
  • Improve basename extraction logic in OSWWriter for consistency
  • Remove scoring_format option and update help text for input file formats
  • Remove unused XGBoost hyperparameters and standardize parameter configuration
  • Update test output files for consistency and add new parquet output
  • Add new test output file for unscored OSW data in parquet format
  • Update import statement for merge function in CLI module

📚 Documentation

  • Add doc-string to runner configs
  • Update README with examples of running specific tests using pytest -k option
  • Add API reference documentation for core module and configuration data classes
  • Add Makefile for Sphinx documentation
  • Add instructions for running tests in parallel with pytest-xdist

⚙️ Miscellaneous Tasks

  • Comment out unnecessary print statement in SplitParquetReader
  • Update SplitParquetReader to log column extraction and retrieved columns
  • Add loguru and seaborn dependencies
  • Check for and log duplicate entries in score DataFrame on join column
  • Add Sphinx documentation configuration and update dependencies for documentation tools
  • Mv some test data to sandbox
  • Add pytest-xdist to testing dependencies for parallel test execution
  • Update dependencies in requirements.txt to latest versions
  • Update test output files for consistency and add new parquet output
  • Enable parallel test execution with pytest-xdist
  • Doc string documentation
  • Update .gitignore to exclude generated documentation files
  • Remove unused import statements from configuration and test files
  • Update documentation to reflect change from --split_by_run to --split_runs option
  • Add user guide and update documentation structure
  • Refactor test file to use dynamic data folder paths
  • Add scoring documentation and update API reference
  • Update test output files to reflect new data structure
  • Update documentation to include new scoring parameters
  • Sort DataFrame columns in test cases for consistency
  • Update test output files to reflect new scoring results
  • Update test output files to reflect new scoring results
  • Update subsample_ratio in pyprophet scoring test for consistency
  • Add new API documentation for IPF and levels context, and update CLI documentation for merging files
  • Update API documentation for levels context and scoring modules
  • Update subsample_ratio in scoring tests for consistency
  • Update Python version to 3.10 and adjust requirements in ReadTheDocs configuration
  • Update README to include logo and CI badge
  • Fix formatting in ReadTheDocs configuration for requirements
  • Update subsample_ratio in scoring tests for consistency
  • Update Sphinx documentation dependencies for consistency
  • Reorganize Sphinx extensions for improved documentation structure
  • Update documentation for consistency and clarity
  • Specify Python version requirements in pyproject.toml
  • Bump version to 3.0.0 in pyproject.toml
  • Update README with additional PyPI and Docker badges
  • Bump version to 3.0.0 in documentation configuration
  • Update version retrieval in documentation configuration
  • Add custom CSS and badges to documentation homepage
  • Update README to improve structure and add references section
  • Remove unnecessary split_runs option from pyprophet export command
  • Add hidden div to have a hidden title in home page to avoid in rendered docs when not having the title
  • Rename levels context command to infer
  • Update help text for memory profiling option in score command
  • Mark deprecated commands for future removal and update command structure
  • Update CLI documentation to reflect command renaming to 'infer'
  • Update tests to use 'infer' command instead of 'levels-context' for consistency
  • Add Parquet schema and compression types documentation for XIC Parquet format
  • Add Precursors and Transition Features Parquet schema documentation
  • Add concurrency to CI workflow to cancel previous runs
  • Update Python version requirement to support 3.9 and above

[2.3.3] - 2025-04-30

🚀 Features

  • Add support for converting sqMass files to Parquet format
  • Refactor code to load and use the sqlite_scanner extension
  • Update Dockerfile to include sqlite_scanner extension
  • Add detecting transition column to Parquet export

🐛 Bug Fixes

  • Bug in convert_osw_to_parquet

⚙️ Miscellaneous Tasks

  • Update PyProphet CLI options for Parquet export

[2.3.2] - 2025-04-29

🚀 Features

  • Add duckdb and its extensions to Dockerfile

🐛 Bug Fixes

  • Dockerfile

💼 Other

  • Function to create indices if they do no exist when using duckdb connections

[2.3.1] - 2025-04-28

💼 Other

  • Dependencies

[2.3.0] - 2025-04-07

🚀 Features

  • Transition lvl string in prec level data
  • Option to exlcude decoys
  • Add level parameter to prepare_data_table function
  • Add peptide mass calculators for glyco peptides
  • Add glycopeptide scoring deom GproDIA
  • Add glycopeptide export from GproDIA
  • Update PyProphet score CLI help doc for input and output files
  • Merge transition_df and transition_peptide_df on TRANSITION_ID
  • Add parquet input support for levels context inferences
  • Update PyProphet CLI options for input and output files
  • Update numpy and polars dependencies in pyproject.toml
  • Update PyProphet WeightApplier with Glyco args

🐛 Bug Fixes

  • Stats tests
  • Fix level context tests
  • ValueError: Buffer dtype mismatch, expected 'DATA_TYPE' but got 'double'
  • Export parquet peptide global level
  • Export parqeut add FEATURE_MS1.AREA_INTENSITY column
  • Failing tests
  • Control for if propagation across runs is no desired
  • Transfer_confident_evidence_across_runs function. ffil converts the feature_id to a float, which causes downtream areas when downcasting back to int64
  • Optimize save_parquet_results for transition level
  • Add try-catch exception handling for loading sqlite_scanner

💼 Other

  • Mergeps method to merge feature alignment tables if present
  • Alignment scoring
  • Propagate signal for ipf if using aligned mapping
  • Across run ipf
  • Tests
  • Glyco scoring from GproDIA
  • LDAGlycoPeptideScorer class for glyco scoring from GproDIA
  • Glycoform inference and add across run signal propagation
  • Glyco report
  • Osw to parquet exporting for scoring
  • Function to check if file is a parquet file
  • Scorer parquet input reader and parquet score results writer
  • Parquet input for IPF scoring
  • Convert_osw_to_parquet for backward compatability with older OSW files that have missing Gene tables and IM related columns
  • Tests for scoring with parquet input
  • Tests for osw to parquet scoring format
  • Optimized cython code

🚜 Refactor

  • New function for normlaizing score to decoys
  • Combine queries into one
  • Merge across_run_feature_map into peptidoform_table
  • Update IPF code to use DuckDB for database connection

📚 Documentation

  • Decrease size of merged_osw_zstd_level_11_33s.parquet by 62%

🧪 Testing

  • Set tree method as exact for tests
  • Add tests for no-decoys flag
  • Fix parquet tests
  • Feature_id is long integer

⚙️ Miscellaneous Tasks

  • Add removed comments back

[2.2.9] - 2024-10-30

🐛 Bug Fixes

  • Export parquet bugs

[2.2.8] - 2024-10-12

💼 Other

  • D_score cuttoff line at 1% qvalue and add PP plot

[2.2.6] - 2024-10-09

🚀 Features

  • Option to only export precursors with features
  • Auto populate var columns

🐛 Bug Fixes

  • Minor bug fixes
  • Featureless transition not appearing properly

💼 Other

  • Bug with experiment wide context

📚 Documentation

  • Fix doc strings

🧪 Testing

  • Add test files for .osw

[2.2.2] - 2022-12-15

💼 Other

  • Export before scoring with MS1MS2 scores

[2.1.5] - 2020-04-07

💼 Other

  • Merge UPDATE]: Added merging scored osw output files option
  • Merge UPDATE]: Correct else if statement for def merge_osw
  • Merge UPDATE]: Correcting indentation for def merge_osw
  • Merge UPDATE]: Correcting indentation for def merge_osw
  • Merge UPDATE]: Make merged_post_scored_runs boolean flag for def merge
  • Merge UPDATE]: Debugging def merge_osw
  • Merge UPDATE]: Debugging def merge_osw
  • Merge UPDATE]: Debugging def merge_osw
  • Merge UPDATE]: Debugging def merge_osw
  • Merge UPDATE]: Debugging def merge_osw
  • Subsample Merged File]: Subsampling a merged file, and appending PRECURSOR table for scoring

[2.1.0] - 2019-04-02

💼 Other

  • Support for MAYU export
  • Compute d_score & q-value based on all peak groups
  • Remove fdr_all_pg option