Release Notes

This section discusses changes between versions, especially changes significant to the use and behavior of the library. This is not meant to be a comprehensive list of changes. For such a complete record, consult the lmfit github repository.

Version 0.9.6 Release Notes

Support for SciPy 0.14 has been dropped: SciPy 0.15 is now required. This is especially important for lmfit maintenance, as it means we can now rely on SciPy having code for differential evolution and do not need to keep a local copy.

A brute force method was added, which can be used either with Minimizer.brute() or using the method=’brute’ option to Minimizer.minimize(). This method requires finite bounds on all varying parameters, or that parameters have a finite brute_step attribute set to specify the step size.

Custom cost functions can now be used for the scalar minimizers using the reduce_fcn option.

Many improvements to documentation and docstrings in the code were made. As part of that effort, all API documentation in this main Sphinx documentation now derives from the docstrings.

Uncertainties in the resulting best-fit for a model can now be calculated from the uncertainties in the model parameters.

Parameters have two new attributes: brute_step, to specify the step size when using the brute method, and user_data, which is unused but can be used to hold additional information the user may desire. This will be preserved on copy and pickling.

Several bug fixes and cleanups.

Versioneer was updated to 0.18.

Tests can now be run either with nose or pytest.

Version 0.9.5 Release Notes

Support for Python 2.6 and SciPy 0.13 has been dropped.

Version 0.9.4 Release Notes

Some support for the new least_squares routine from SciPy 0.17 has been added.

Parameters can now be used directly in floating point or array expressions, so that the Parameter value does not need sigma = params[‘sigma’].value. The older, explicit usage still works, but the docs, samples, and tests have been updated to use the simpler usage.

Support for Python 2.6 and SciPy 0.13 is now explicitly deprecated and wil be dropped in version 0.9.5.

Version 0.9.3 Release Notes

Models involving complex numbers have been improved.

The emcee module can now be used for uncertainty estimation.

Many bug fixes, and an important fix for performance slowdown on getting parameter values.

ASV benchmarking code added.

Version 0.9.0 Release Notes

This upgrade makes an important, non-backward-compatible change to the way many fitting scripts and programs will work. Scripts that work with version 0.8.3 will not work with version 0.9.0 and vice versa. The change was not made lightly or without ample discussion, and is really an improvement. Modifying scripts that did work with 0.8.3 to work with 0.9.0 is easy, but needs to be done.

Summary

The upgrade from 0.8.3 to 0.9.0 introduced the MinimizerResult class (see MinimizerResult – the optimization result) which is now used to hold the return value from minimize() and Minimizer.minimize(). This returned object contains many goodness of fit statistics, and holds the optimized parameters from the fit. Importantly, the parameters passed into minimize() and Minimizer.minimize() are no longer modified by the fit. Instead, a copy of the passed-in parameters is made which is changed and returns as the params attribute of the returned MinimizerResult.

Impact

This upgrade means that a script that does:

my_pars = Parameters()
my_pars.add('amp',    value=300.0, min=0)
my_pars.add('center', value=  5.0, min=0, max=10)
my_pars.add('decay',  value=  1.0, vary=False)

result = minimize(objfunc, my_pars)

will still work, but that my_pars will NOT be changed by the fit. Instead, my_pars is copied to an internal set of parameters that is changed in the fit, and this copy is then put in result.params. To look at fit results, use result.params, not my_pars.

This has the effect that my_pars will still hold the starting parameter values, while all of the results from the fit are held in the result object returned by minimize().

If you want to do an initial fit, then refine that fit to, for example, do a pre-fit, then refine that result different fitting method, such as:

result1 = minimize(objfunc, my_pars, method='nelder')
result1.params['decay'].vary = True
result2 = minimize(objfunc, result1.params, method='leastsq')

and have access to all of the starting parameters my_pars, the result of the first fit result1, and the result of the final fit result2.

Discussion

The main goal for making this change were to

  1. give a better return value to minimize() and Minimizer.minimize() that can hold all of the information about a fit. By having the return value be an instance of the MinimizerResult class, it can hold an arbitrary amount of information that is easily accessed by attribute name, and even be given methods. Using objects is good!
  2. To limit or even eliminate the amount of “state information” a Minimizer holds. By state information, we mean how much of the previous fit is remembered after a fit is done. Keeping (and especially using) such information about a previous fit means that a Minimizer might give different results even for the same problem if run a second time. While it’s desirable to be able to adjust a set of Parameters re-run a fit to get an improved result, doing this by changing an internal attribute (Minimizer.params) has the undesirable side-effect of not being able to “go back”, and makes it somewhat cumbersome to keep track of changes made while adjusting parameters and re-running fits.