{ "info": { "author": "Kamil Erguler", "author_email": "k.erguler@cyi.ac.cy", "bugtrack_url": null, "classifiers": [ "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "An adaptive basin-hopping Markov-chain Monte Carlo algorithm for Bayesian optimisation\n======================================================================================\n\nThis is the python (v3.7) implementation of the hoppMCMC algorithm aiming to identify and sample from the high-probability regions of a posterior distribution. The algorithm combines three strategies: (i) parallel MCMC, (ii) adaptive Gibbs sampling and (iii) simulated annealing. Overall, hoppMCMC resembles the basin-hopping algorithm implemented in the optimize module of scipy, but it is developed for a wide range of modelling approaches including stochastic models with or without time-delay.\n\nContents\n--------\n\n1) Prerequisites\n2) Linux installation\n\n1) Prerequisites\n----------------\n\nThe hoppMCMC algorithm requires the following packages, which are not included in this package:\n\n\tnumpy\n\tscipy\n\tmpi4py (MPI parallelisation)\n\nThe mpi4py package is required for parallelisation; however, it can be omitted.\n\n2) Linux installation\n---------------------\n\n1) Easy way:\n\nIf you have pip installed, you can use the following command to download and install the package.\n\tpip install hoppMCMC\n\nAlternatively, you can download the source code from PyPI and run pip on the latest version xxx.\n\tpip install hoppMCMC-xxx.tar.gz\n\n2) Hard way:\n\nIf pip is not available, you can unpack the package contents and perform a manual install.\n\ttar -xvzf hoppMCMC-xxx.tar.gz\n\tcd hoppMCMC-xxx\n\tpython setup.py install\n\nThis will install the package in the site-packages directory of your python distribution. If you do not have root privileges or you wish to install to a different directory, you can use the --prefix argument.\n\n\tpython setup.py install --prefix=\n\nIn this case, please make sure that is in your PYTHONPATH, or you can add it with the following command.\n\nIn bash shell:\n\texport PYTHONPATH=:$PYTHONPATH\nIn c shell:\n\tsetenv PYTHONPATH :$PYTHONPATH\n\nCredits\n-------\n\n'modern-package-template' - http://pypi.python.org/pypi/modern-package-template\n\n\n\nNews\n====\n\n1.1\n-----\n\n*Release date: 13-Sep-2018*\n\n* Fixed a bug in reading output (Python 3)\n\n1.0\n-----\n\n*Release date: 30-Jul-2018*\n\n* Compatible with Python 3\n\n0.6\n-----\n\n*UNRELEASED*\n\n* Print out the covariates in addition to the parameters\n\n0.5\n-----\n\n*Release date: 14-Feb-2017*\n\n* Minor improvement on pulsevarUpdate\n\n0.4\n-----\n\n*Release date: 14-Oct-2015*\n\n* Fixed an issue with default parameters\n\n0.3\n-----\n\n*Release date: 09-Oct-2015*\n\n* This version includes an 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