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        "author": "Paul Kienzle",
        "author_email": "paul.kienzle@nist.gov",
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            "Development Status :: 4 - Beta",
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            "Intended Audience :: Science/Research",
            "License :: Public Domain",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Scientific/Engineering :: Physics"
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        "description": "==============================================\nBumps: data fitting and uncertainty estimation\n==============================================\n\nBumps provides data fitting and Bayesian uncertainty modeling for inverse\nproblems.  It has a variety of optimization algorithms available for locating\nthe most like value for function parameters given data, and for exploring\nthe uncertainty around the minimum.\n\nInstallation is with the usual python installation command::\n\n    pip install bumps\n\nOnce the system is installed, you can verify that it is working with::\n\n    bumps doc/examples/peaks/model.py --chisq\n\nDocumentation is available at `readthedocs <http://bumps.readthedocs.org>`_\n\nIf a compiler is available, then significant speedup is possible for DREAM using::\n\n    (cd bumps/dream && cc compiled.c -I ../../Random123/include/ -O2 -fopenmp -shared -lm -o _compiled.so -fPIC)\n\nFor now this requires an install from source rather than pip.\n\n|TravisStatus|_ |DOI|_\n\n.. |TravisStatus| image:: https://travis-ci.org/bumps/bumps.svg?branch=master\n.. _TravisStatus: https://travis-ci.org/bumps/bumps\n\n.. |DOI| image:: https://zenodo.org/badge/18489/bumps/bumps.svg\n.. _DOI: https://zenodo.org/badge/latestdoi/18489/bumps/bumps\n\nRelease notes\n=============\n\nv0.7.13 2019-10-15\n------------------\n\n* fix pickle problem for parameterized functions\n* support multi-valued functions in Curve, shown with a coupled ODE example\n* update support for newer numpy and matplotlib\n\nv0.7.12 2019-07-30\n------------------\n\n* --parallel defaults to using one process per CPU.\n* --pop=-k sets population size to k rather than k times num parameters\n* --resume=- resumes from --store=/path/to/store\n* use expanded canvas for parameter histograms to make plots more readable\n* use regular spaced tics for parameter histograms rather than 1- and 2-sigma\n* improve consistency between values of cov, stderr and chisq\n* fix handling of degenerate ranges on parameter output\n* add entropy calculator using gaussian mixture models (default is still Kramer)\n* vfs module allows loading of model and data from zip file (not yet enabled)\n* warn when model has no fitted parameters\n* update mpfit to support python 3\n* support various versions of scipy and numpy\n\nv0.7.11 2018-09-24\n------------------\n\n* add support for parameter serialization\n\nv0.7.10 2018-06-15\n------------------\n\n* restructure parameter table in gui\n\nv0.7.9 2018-06-14\n-----------------\n\n* full support for python 3 in wx GUI\n* allow added or missing parameters in reloaded .par file\n* add dream state to return from fit() call\n\nv0.7.8 2018-05-18\n-----------------\n\n* fix source distribution (bin directory was missing)\n\nv0.7.7 2018-05-17\n-----------------\n\n* merge in amdahl branch for improved performance\n* update plot so that the displayed \"chisq\" is consistent with nllf\n* slight modification to the DREAM DE crossover ratio so that no crossover\n  weight ever goes to zero.\n* par.dev(std) now uses the initial value of the parameter as the center of the\n  distribution for a gaussian prior on par, as stated in the documentation. In\n  older releases it was incorrectly defaulting to mean=0 if the mean was\n  not specified.\n* save parameters and uncertainties as JSON as well as text\n* convert discrete variables to integer prior to computing DREAM statistics\n* allow relative imports from model files\n* support latest numpy/matplotlib stack\n* initial support for wxPhoenix/python 4 GUI (fit ranges can't yet be set)\n\nv0.7.6 2016-08-05\n-----------------\n\n* add --view option to command line which gets propagated to the model plotter\n* add support for probability p(x) for vector x using VectorPDF(f,x0)\n* rename DirectPDF to DirectProblem, and allow it to run in GUI\n* data reader supports multi-part files, with parts separated by blank lines\n* add gaussian mixture and laplace examples\n* bug fix: plots were failing if model name contains a '.'\n* miscellaneous code cleanup\n\nv0.7.5.10 2016-05-04\n--------------------\n\n* gui: undo code cleaning operation which broke the user interface\n\nv0.7.5.9 2016-04-22\n-------------------\n\n* population initializers allow indefinite bounds\n* use single precision criterion for levenberg-marquardt and bfgs\n* implement simple, faster, less accurate Hessian & Jacobian\n* compute uncertainty estimate from Jacobian if problem is sum of squares\n* gui: fit selection window acts like a dialog\n\nv0.7.5.8 2016-04-18\n-------------------\n\n* accept model.par output from a different model\n* show residuals with curve fit output\n* only show correlations for selected variables\n* show tics on correlations if small number\n* improve handling of uncertainty estimate from curvature\n* tweak dream algorithm -- maybe improve the acceptance ratio?\n* allow model to set visible variables in output\n* improve handling of arbitrary probability density functions\n* simplify loading of pymc models\n* update to numdifftools 0.9.14\n* bug fix: improved handling of ill-conditioned fits\n* bug fix: avoid copying mcmc chain during run\n* bug fix: more robust handling of --time limit\n* bug fix: support newer versions of matplotlib and numpy\n* miscellaneous tweaks and fixes\n\nv0.7.5.7 2015-09-21\n-------------------\n\n* add entropy calculator (still unreliable for high dimensional problems)\n* adjust scaling of likelihood (the green line) to match histogram area\n* use --samples to specify the number of samples from the distribution\n* mark this and future releases with a DOI at zenodo.org\n\nv0.7.5.6 2015-06-03\n-------------------\n\n* tweak uncertainty calculations so they don't fail on bad models\n\nv0.7.5.5 2015-05-07\n-------------------\n\n* documentation updates\n\nv0.7.5.4 2014-12-05\n-------------------\n\n* use relative rather than absolute noise in dream, which lets us fit target\n  values in the order of 1e-6 or less.\n* fix covariance population initializer\n\nv0.7.5.3 2014-11-21\n-------------------\n\n* use --time to stop after a given number of hours\n* Levenberg-Marquardt: fix \"must be 1-d or 2-d\" bug\n* improve curvefit interface\n\nv0.7.5.2 2014-09-26\n-------------------\n\n* pull numdifftools dependency into the repository\n\nv0.7.5.1 2014-09-25\n-------------------\n\n* improve the load_model interface\n\nv0.7.5 2014-09-10\n-----------------\n\n* Pure python release",
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