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CHANGELOG.md

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Changelog

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

The format is inspired by Keep a Changelog, and Element and this project adheres to Semantic Versioning.

Unreleased

Added Features and Improvements 🙌:

  • Supporting latest Python 3.12 🎉

Other changes:

  • Support latest version of pplt
  • Fix docs

1.1.1 - 2023-11-10

Bugfix 🐛:

  • Fix mutable properties of mh.StateTraj and mh.LumpedStateTraj, #43

Other changes:

  • Improved performance of mh.LumpedStateTraj.microtrajs

1.1.0 - 2023-11-03

API changes warning ⚠️:

  • Python 3.7 support was dropped!

Added Features and Improvements 🙌:

  • Supporting latest Python 3.11 🎉

Bugfix 🐛:

  • Fixed wrong connectivity in mh.datasets.utils.propagate_MCMC for different datatypes, #39

1.0.4 - 2023-05-22

Other changes:

  • Improvements of the README and the documentation, suggested by the JOSS reviewers @yuxuanzhuang and @lorenzo-rovigatti
  • Added zenodo setup
  • Added issue templates

1.0.3 - 2023-04-17

Bugfix 🐛:

  • Fix that mh.LumpedStateTraj.index_trajs and mh.LumpedStateTraj.index_trajs_flatten return now index trajectories corresponding to the macrostate trajectories

Other changes:

  • Improve the x-axis limits, use more distinguishable colors, and lower the number of bins for the MD for the cli msmhelper waiting-times
  • Updated contribution and added maintenance guidelines
  • Minor improvements of docs suggested by JOSS reviewer

1.0.2 - 2023-03-13

Added Features and Improvements 🙌:

  • Added cli for compare-discretization

Bugfix 🐛:

  • Fix missing import of msm.utils.linalg when importing msm.utils
  • Fix bug of similarity measure (mh.md.compare_discretization) being infinite

1.0.1 - 2023-03-08

Other changes:

  • Added basic test for msmhelper waiting-times command-line interface
  • Using scientific y-labels for msmhelper waiting-times and msmhelper waiting-time-dist command-line interfaces to improve figures for real data

Bugfix 🐛:

  • Fix bug where --frames-per-unit and unit where neglected in the cli msmhelper waiting-time-dist
  • Fix undesired behavior where msmhelper implied-timescales used gray spines instead of true black

1.0.0 - 2023-03-03

API changes warning ⚠️:

  • Completely refactoring of the API, this release has many breaking changes to v0.6.2
    • Renamed module iotext to io
    • Moved all functions related to msm to msm module
    • Moved all functions related to raw state trajectories to md module
    • Moved all remaining functions into utils module
  • Removed StateTraj.trajs property to reduce confusion between index and state trajectories.
  • Removed Python 3.6 support.

Added Features and Improvements 🙌:

  • Add an all new mkdocs documentation with material design 🎉
  • Add a command line interface for standalone tasks 🎉
  • Add follow-along tutorials, FAQ, and better code references 🎉
  • Add the submodule plot to create commonly-used figures
  • Improved MSM generation by a factor of 2-3 for continuously named states.

Other changes:

  • Add gaussian_filter functionality
  • Add implementation of dynamical_coring
  • Add estimation of transition times
  • Add contact representation of states
  • And many more improvements

Bugfix 🐛:

  • Fixed bug where propagate_MCMC returns index trajectory instead of a state trajectory

0.6.2 - 2022-09-20

Other changes:

  • Moved to package to src directory
  • Add nvals parameter to all eigenvalues/-vectors functions
  • Add ntimescales parameter to implied_timescales
  • Improved tests for implied_timescales

Bugfix 🐛:

  • Fix complex matrices for LumpedStateTraj due to complex eigenvalues

0.6.1 - 2022-08-01

Bugfix 🐛:

  • Include extra-requirements via MANIFEST.in

0.6.0 - 2022-08-01

API changes warning ⚠️:

  • Remove pyemma to ensure better pip support
  • Remove build_MSM use instead estimate_markov_model

Added Features and Improvements 🙌:

  • Upload test coverage to Codecov
  • Add extra-requirements to pip installation
  • Added Changelog file 🎉
  • Add new parameter allow_non_ergodic to mh.equilibrium_population
  • Upload docs to gh-pages 🚀
  • Add module md with functions for estimating timescales and pathways

Other changes:

  • Added beartype dependency for adding dynamic type checking
  • Parallelize and refactor compare_discretization
  • replaced decorators with decorit package

Bugfix 🐛:

  • Fix source code rendering in documentation
  • Fix deprecated warnings of numpy and pytest
  • Fix most LGTM warnings
  • Many more minor fixes
  • Add parameter atol to tests functions to make them more robust

0.5.0 - 2021-07-22

Added Features and Improvements 🙌:

  • Add LumpedStateTraj class which allows optimal projection of microstate dynamics to macrostates, method taken from Szabo and Hummer
  • Add estimation of MD waiting times
  • Add tests for is_transition_matrix, is_ergodic

Bugfix 🐛:

  • Minor improvements and tweaks.

Other changes:

0.4.0 - 2020-09-14

API changes warning ⚠️:

  • Removed n_iterations parameter from Clustering

Added Features and Improvements 🙌:

  • Added clustering mode mode='kmedoids' for k-medoids clustering
  • Added tools module to reopen clusters

Other changes:

  • Improved some test functions

0.3.0 - 2020-08-25

Added Features and Improvements 🙌:

  • Add StateTraj class to speed up calcualations by a factor of 50.
  • Refactor code to use/be compatible with StateTraj class
  • Add benchmark module with an numba optimized version of the Chapman-Kolmogorov test
  • Add function for estimating implied timescales

Bugfix 🐛:

  • Minor bug fixes and im

Other changes:

  • Improving documentation/docstrings
  • Adding tests including benchmarks

0.2.0 - 2020-08-14

Added Features and Improvements 🙌:

  • Major speed improvement by rewriting parts of msm module with numba

0.1.0 - 2020-02-20

  • Initial release