Hopsy

- [115](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/115): Improve initialization of custom PyProposals in MarkovChain
- [114](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/114): Disable inheriting from PyProposal and PyModel

- [138](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/138): Ignore fixed dimensions when computing ESS & rhat
- [157](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/157): Pin numpy<2.0
- [141](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/141): Add minimal example for genome-scale sampling
- [152](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/152): Add test-case for selecting start point with equality constraints
- [69](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/69): Add CLA
- [155](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/155): Increase numerical accuracy for parallel tempering when using python multiprocessing
- [153](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/153): Add tuning target selection to setup function

- [145](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/145): Improve docs
- [127](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/127): Add method to heuristically setup good sampling configurations depending on the problem
- [139](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/139): Add transformation of start points during add\_equality\_constraints
- [88](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/88): Fix parallelization for sampling with mcbackend as sample storage
- [123](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/123): Add parallel tempering support for non-MPI users
- [137](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/137): Fix rare bug for users implementing their own PyProposals for non-uniform sampling
- [136](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/136): Improve numerical stability of mixture models
- [133](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/133): Add default starting point to proposals and markov chains when none is given
- [128](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/128): Add stepsize tuning with Python TuningTargets
- [122](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/122): Fix rounding for Reversible Jump MCMC
- [125](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/125): Update Readme.md & Fix automatic docs generation
- [106](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/106): Add official support for python 3.12
- [130](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/130): Update requirements-dev.txt
- [108](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/108): For development: Fix setup.py warning on missing commit ID
- [119](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/119): Fix numpy deprecation warnings in unit tests
- [121](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/121): Update docs for problem

v.1.4.1
- [120](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/120): Fix parallel sampling with additional equality constraints
- [117](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/117): Update Optlang, sympy and numpy dependencies
- [118](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/118): Fix back\_transform when manually adding equality constraints and rounding

- [113](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/113): Fix small bug in back\_transform
- [111](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/111): Update documentation
- [92](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/92): Add convenience functions for generating hybercubes, simplices and Birkhoff polytopes
- [110](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/110): Add convenience method to problem for computing slacks
- [82](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/82): Add option to compute\_chebyshev to return point in transformed or original space
- [102](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/102): Add RJMCMC
- [104](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/104): Add multiphase sampling
- [83](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/83): Readd vectorization for hopsy
- [103](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/103): Fix callback example
- [105](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/105): Drop support for unsupported python 3.7
- [101](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/101): Add helper functions for testing if polytope is empty
- [99](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/99): Fix benchmark example typo
- [98](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/98): Consistent names for model functions
- [97](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/97): Disable jekyll in automatic doc building
- [96](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/96): Fix pickling for problem
- [95](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/95): Fix parallel sampling for PyProposals
- [91](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/91): Add benchmark example
- [90](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/90): Reduce ci build times
- [87](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/87): Reduce boilerplate for custom pyproposals
- [71](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/71): Rename functions and deprecate old variants

- [85](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/85): Fix release for Python 3.10 and Python 3.11 windows

- [78](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/78): Make (mac+linux+win compatible) sdist
- [79](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/79): Add installation example for arch linux
- [33](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/33): Add direct support for equality constraints
- [77](https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy/-/issues/77): Add feasibility check to compute\_chebyshev\_center