Changelog

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

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • collect_files script to gather localization files from nested acquisition folders

  • trace_split_labels script to split traces by assigned mask labels

  • localization_analyzer script for localization quality-control analysis

  • Support for assigning barcode genomic coordinates from BED files in trace_genomic_coordinates

  • Pipe/stdin input support across trace-processing scripts, including trace_stats

  • New tutorials for trace merging, quality control, filtering, label splitting, matrix visualization, multi-way colocalization, dataset comparison, and pipe usage

  • Test coverage for localization tables, trace filtering, trace merging, matrix plotting, matrix conversion, and file collection

Fixed

  • NumPy 2 compatibility for NaN handling in matrix and plotting workflows

  • Localization table formatting and comment-field handling when reading, merging, and updating localization tables

  • Missing comments in chromatin trace tables

  • trace_filter --clean_spots test discovery and behavior coverage

  • FOF-CT import/export compatibility and standardized input option naming

  • Multi-worker output collisions by including the trace file name in generated output paths

Changed

  • Refactored localization table handling and homogenized command-line arguments across scripts

  • Renamed trace_impute_genomic_coordinates to trace_genomic_coordinates

  • Default spot-table output format is now ecsv

  • plot_3way_coloc can write plots in user-selected output formats

  • Updated documentation structure, script pages, pipe examples, release guidance, and project logo

Removed

  • trace_correct_coordinates: superseded by trace_genomic_coordinates

  • localization_cp_files: superseded by collect_files

  • analyze_localizations: replaced by localization_analyzer

  • plot_single_cell: unused & deprecated script

  • plot_n_him_matrices: unused & deprecated script

[0.5.0] - 2025-04-17

Added

  • This CHANGELOG.md file

Fixed

  • figure_him_matrix: Apply delta margin to avoid massive tick generation for narrow color ranges (Matplotlib <3.7)

Changed

  • rename figure_him_matrix to plot_him_matrix

  • rename compare_pwd_matrices to plot_matrix_comparison

  • rename plot_3way to trace_3way_coloc

  • rename replot_3way to plot_3way_coloc

Removed

  • process_him_matrix: unused & deprecated script

  • trace_combinator: unused & deprecated script

  • pwd_matrix_2_pdb: unused & deprecated script

[0.4.0] - 2025-04-09

Added

  • Doc: Reliability status for each script (development < beta-test < stable)

  • trace_filter: localization intensity filtering

  • Import from pyHiM post-processing scripts:

    • trace_to_matrix

    • trace_stats

    • trace_splitter

    • trace_plot

    • trace_pearsons

    • trace_genomic_coordinates

    • trace_import_from_fofct

    • trace_export_to_fofct

    • trace_filter_advanced

    • trace_correct_coordinates

    • trace_combinator

    • trace_assign_mask

    • trace_analyzer

    • pwd_matrix_2_pdb

    • process_him_matrix

    • localization_merge

    • localization_cp_files

    • compare_pwd_matrices

    • analyze_localizations

  • Import from pyHiM plot scripts:

    • replot_3way.py

    • plot_bootstrapping.py

    • plot_4m.py

    • plot_3way.py

    • plot_single_cell.py

    • plot_n_him_matrices.py

    • plot_compare2matrices.py

[0.3.0] - 2025-03-25

Added

  • trace_merge script (import from pyHiM)

    • prevent ROI number merge conflict

Fixed

  • figure_him_matrix: change default proximity normalization (By default, NaN values per bin are removed before compute statistics for proximity).

Changed

  • figure_him_matrix: --remove_nan become --keep_nan

[0.2.0] - 2025-03-20

Added

  • Installation guide

  • trace_filter script (import from pyHiM)

  • Documentation available online

  • figure_him_matrix script (import from pyHiM)

    • nan_matrix: plot with him_matrix the nan percentage

    • add a threshold based on NaN percentage #26

Fixed

  • Fix the --clean_spots option of trace_filter to ensure that a spot_ID is unique to a single trace_ID

  • Windows compatibility

  • figure_him_matrix: fix --shuffle option

Changed

  • figure_him_matrix: --norm option become --remove_nan

[0.1.0] - 2025-03-07

Added

  • Documentation can be build locally

  • Project can be installed locally with pip install . or pip install .[dev]

[Template] - YYYY-MM-DD

Added

Fixed

Changed

Removed