Changelog

All notable changes to ProteoPy will be documented in this file. The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Fixed

  • Datasets (pr.datasets) and Download (pr.download): williams_2018() no longer conflates measured zeros with missing values. Three defects, each masked by another:

    • zeros in .X were coerced to np.nan, discarding 13,547 genuine measurements

    • charge-state summation used pandas’ default min_count=0, so a group with no measurements at all summed to 0.0, inventing 3,324

    • the same summation skipped NaN inside a partially measured group, reporting a partial total as complete for 260 cells

    • this changes .X, and therefore the output of pr.download.williams_2018(). Verified against the PRIDE deposit used by the original publication: the two are now bit-identical with an identical missingness pattern.

Changed

  • Datasets (pr.datasets) and Download (pr.download): williams_2018() gained a zero_to_na parameter (default False), for consistency with sibling functions. It is mutually exclusive with fill_na. Note it governs zero semantics only and does not restore the summation defects above.

  • Preprocessing (pr.pp): normalize_median()

    • now defaults to log_space=True

    • renamed the batch_id parameter to group_by

    • renamed the zeros_to_na parameter to zero_to_na, for consistency with sibling functions

    • no longer accepts sparse .X input

[0.1.1] - 2025-03-24

Added

  • Preprocessing (pr.pp): summarize_modifications() for modification summarization

  • Analysis (pr.tl): ANOVA support in differential_abundance()

  • Visualization (pr.pl): binary_heatmap(), box(), volcano(), peptides_on_sequence(), peptides_on_prot_sequence(); print_stats parameter across multiple plot functions

  • Datasets (pr.datasets): williams_2018() and karayel_2020() download functions

  • Utilities (pr.utils): Public API with is_proteodata(), check_proteodata(), is_log_transformed()

  • Documentation: Sphinx documentation site; proteoform inference and protein-level analysis tutorials

Changed

  • Reader (pr.read): diann() now supports version >=1.9.1 with automatic version dispatch

  • Preprocessing (pr.pp): impute_downshift() now supports group_by; normalize_median() gains method parameter; remove_contaminants() defaults to inplace=True

  • Validation: is_proteodata() now checks for NaN in ID columns, infinite values in .X/layers, and obs/var index sync

Fixed

  • volcano_plot type incompatibility and label display

  • n_cat1_per_cat2_hist minimum bin width

[0.1.0] - 2025-01-29

Initial release of ProteoPy.

Added

  • Data import (pr.read): Support for DIA-NN and generic long-format tables

  • Annotation (pr.ann): Functions to annotate samples (.obs) and variables (.var)

  • Quality control (pr.pp): Completeness filtering, CV calculation, contaminant removal

  • Preprocessing (pr.pp): Median normalization, downshift imputation

  • Differential abundance (pr.tl): t-test, Welch’s test, ANOVA with multiple testing correction

  • Proteoform inference (pr.tl): COPF algorithm reimplementation for detecting functional proteoform groups

  • Visualization (pr.pl): Volcano plots, abundance rank plots, intensity distributions, CV plots, correlation matrices, hierarchical clustering profiles

  • Datasets (pr.datasets): Built-in example datasets (Karayel 2020)