CHANGELOG.md

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.

[1.1.4] - unpublished

Authors

• @orbeckst

Fixed

• Have cluster.ProcessProtein.reprocess() record "no result" if the gibbs.Gibbs.process_gibbs() step fails due to insufficient number of samples. Otherwise python -m cluster fails to process whole proteins.

[1.1.3] - 2025-09-11

Authors

• @orbeckst
• @rjoshi44

Fixed

• Fixed setting of gskip in ProcessProtein/cluster.py command line interface: set the default to 100 (as in the paper) and ensure that the correct value is used as Gibbs.gskip (which is relative to the save skip step of Gibbs.g) (Issue #48)

Changed

The following changes do not functionally change the code but users relying on default values need to be aware of the changes to gibbs.Gibbs.

• Default kwargs for the skipping in the Gibbs sampler are now gibbs.Gibbs(g=100, gskip=1) (used to be g=50, gskip=2) but for most users gskip for processing data is not important and it makes more sense to focus on g as the stride at which we sample AND process data (#48, PR #49)
• internal code refactor and clean-up: moved util.run_residue() to gibbs.run_residue() and use direct assignment instead of setattr() (PR #50)

[1.1.2] - 2025-07-22

Authors

• @rjoshi44
• @copilot
• @orbeckst

Fixed

• fixed contact script (issue #34)
• Fixed ProcessProtein command-line interface to accept gskip and burnin parameters, resolving TypeError in script execution. Added --gskip and --burnin arguments to cluster.py with default values from the research paper (gskip=1000, burnin=10000) (Issue #37)
• Fixed ProcessProtein.write_data() method to handle residues as numpy array instead of dictionary, resolving AttributeError when calling the method after reprocess() or get_taus(). Also fixed get_taus() method to return values as documented. Added comprehensive test coverage for write_data() functionality (Issue #37)

[1.1.1] - 2025-07-18

Authors

• @rsexton2
• @orbeckst

Changed

• The default name for the contacts file changed from "contacts.pkl" to "contacts_max10.0.pkl" as it now embeds the max_cutoff (Issue #27, PR #31)

Fixed

• distinguished max_cutoff from cutoff in contact file metadata (Issues #27 and #32)

[1.1.0] - 2025-07-04

Authors

• @rsexton2
• @copilot
• @orbeckst

Added

• Support for combining contact timeseries from multiple repeat runs through new CombineContacts class and python -m basicrta.combine CLI interface. Enables pooled analysis of binding kinetics data with metadata preservation and trajectory source tracking (Issue #16)

Changed

• package has final paper citation

[1.0.0] - 2025-05-24

Authors

• @rsexton2
• @ianmkenney
• @rjoshi44
• @orbeckst

Added

• added option processing for label-cutoff to cluster.py (PR #13)

Fixed

• Fix package detection and installation (PR #12)
• fix citation in reST docs (PR #7)
• update codcov action in workflow (PR #9)

Removed

• no testing on Windows, temporarily exclude windows-latest from CI (PR #11)

[0.2.0] - 2024-11-14

Authors

• @rsexton2

Summary

Feature-complete release.

Added

• Workflow executable through command-line
• updated docs/tutorial