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 1.0.0 Release Notes

Version 1.0.0 supports Python 3.5, 3.6, 3.7, and 3.8

New features:

  • no new features are introduced in 1.0.0.

Improvements:

  • support for Python 2 and use of the six package are removed. (PR #612)

Various:

  • documentation updates to clarify the use of emcee. (PR #614)

Version 0.9.15 Release Notes

Version 0.9.15 is the last release that supports Python 2.7; it now also fully suports Python 3.8.

New features, improvements, and bug fixes:

  • move application of parameter bounds to setter instead of getter (PR #587)

  • add support for non-array Jacobian types in least_squares (Issue #588, @ezwelty in PR #589)

  • add more information (i.e., acor and acceptance_fraction) about emcee fit (@j-zimmermann in PR #593)

  • “name” is now a required positional argument for Parameter class, update the magic methods (PR #595)

  • fix nvars count and bound handling in confidence interval calculations (Issue #597, PR #598)

  • support Python 3.8; requires asteval >= 0.9.16 (PR #599)

  • only support emcee version 3 (i.e., no PTSampler anymore) (PR #600)

  • fix and refactor prob_bunc in confidence interval calculations (PR #604)

  • fix adding Parameters with custom user-defined symbols (Issue #607, PR #608; thanks to @gbouvignies for the report)

Various:

  • bump requirements to LTS version of SciPy/ NumPy and code clean-up (PR #591)

  • documentation updates (PR #596, and others)

  • improve test coverage and Travis CI updates (PR #595, and others)

  • update pre-commit hooks and configuration in setup.cfg

To-be deprecated: - function Parameter.isParameter and conversion from uncertainties.core.Variable to value in _getval (PR #595)

Version 0.9.14 Release Notes

New features:

  • the global optimizers shgo and dual_annealing (new in SciPy v1.2) are now supported (Issue #527; PRs #545 and #556)

  • eval method added to the Parameter class (PR #550 by @zobristnicholas)

  • avoid ZeroDivisionError in printfuncs.params_html_table (PR #552 by @aaristov and PR #559)

  • add parallelization to brute method (PR #564, requires SciPy v1.3)

Bug fixes:

  • consider only varying parameters when reporting potential issues with calculating errorbars (PR #549) and compare value to both min and max (PR #571)

  • guard against division by zero in lineshape functions and FWHM and height expression calculations (PR #545)

  • fix issues with restoring a saved Model (Issue #553; PR #554)

  • always set result.method for emcee algorithm (PR #558)

  • more careful adding of parameters to handle out-of-order constraint expressions (Issue #560; PR #561)

  • make sure all parameters in Model.guess() use prefixes (PRs #567 and #569)

  • use inspect.signature for PY3 to support wrapped functions (Issue #570; PR #576)

  • fix result.nfev` for brute method when using parallelization (Issue #578; PR #579)

Various:

  • remove “missing” in the Model class (replaced by nan_policy) and “drop” as option to nan_policy (replaced by omit) deprecated since 0.9 (PR #565).

  • deprecate ‘report_errors’ in printfuncs.py (PR #571)

  • updates to the documentation to use jupyter-sphinx to include examples/output (PRs #573 and #575)

  • include a Gallery with examples in the documentation using sphinx-gallery (PR #574 and #583)

  • improve test-coverage (PRs #571, #572 and #585)

  • add/clarify warning messages when NaN values are detected (PR #586)

  • several updates to docstrings (Issue #584; PR #583, and others)

  • update pre-commit hooks and several docstrings

Version 0.9.13 Release Notes

New features:

  • Clearer warning message in fit reports when uncertainties should but cannot be estimated, including guesses of which Parameters to examine (#521, #543)

  • SplitLorenztianModel and split_lorentzian function (#523)

  • HTML representations for Parameter, MinimizerResult, and Model so that they can be printed better with Jupyter (#524, #548)

  • support parallelization for differential evolution (#526)

Bug fixes:

  • delay import of matplotlib (and so, the selection of its backend) as late as possible (#528, #529)

  • fix for saving, loading, and reloading ModelResults (#534)

  • fix to leastsq to report the best-fit values, not the values tried last (#535, #536)

  • fix synchronization of all parameter values on Model.guess() (#539, #542)

  • improve deprecation warnings for outdated nan_policy keywords (#540)

  • fix for edge case in gformat() (#547)

Project management:

  • using pre-commit framework to improve and enforce coding style (#533)

  • added code coverage report to github main page

  • updated docs, github templates, added several tests.

  • dropped support and testing for Python 3.4.

Version 0.9.12 Release Notes

Lmfit package is now licensed under BSD-3.

New features:

  • SkewedVoigtModel was added as built-in model (Issue #493)

  • Parameter uncertainties and correlations are reported for least_squares

  • Plotting of complex-valued models is now handled in ModelResult class (PR #503)

  • A model’s independent variable is allowed to be an object (Issue #492)

  • Added usersyms to Parameters() initialization to make it easier to add custom functions and symbols (Issue #507)

  • the numdifftools package can be used to calculate parameter uncertainties and correlations for all solvers that do not natively support this (PR #506)

  • emcee can now be used as method keyword-argument to Minimizer.minimize and minimize function, which allows for using emcee in the Model class (PR #512; see examples/example_emcee_with_Model.py)

(Bug)fixes:

  • asteval errors are now flushed after raising (Issue #486)

  • max_time and evaluation time for ExpressionModel increased to 1 hour (Issue #489)

  • loading a saved ModelResult now restores all attributes (Issue #491)

  • development versions of scipy and emcee are now supported (Issue #497 and PR #496)

  • ModelResult.eval() do no longer overwrite the userkws dictionary (Issue #499)

  • running the test suite requires pytest only (Issue #504)

  • improved FWHM calculation for VoigtModel (PR #514)

Version 0.9.10 Release Notes

Two new global algorithms were added: basinhopping and AMPGO. Basinhopping wraps the method present in scipy, and more information can be found in the documentation (basinhopping() and scipy.optimize.basinhopping). The Adaptive Memory Programming for Global Optimization (AMPGO) algorithm was adapted from Python code written by Andrea Gavana. A more detailed explanation of the algorithm is available in the AMPGO paper and specifics for lmfit can be found in the ampgo() function.

Lmfit uses the external uncertainties (https://github.com/lebigot/uncertainties) package (available on PyPI), instead of distributing its own fork.

An AbortFitException is now raised when the fit is aborted by the user (i.e., by using iter_cb).

Bugfixes:

  • all exceptions are allowed when trying to import matplotlib

  • simplify and fix corner-case errors when testing closeness of large integers

Version 0.9.9 Release Notes

Lmfit now uses the asteval (https://github.com/newville/asteval) package instead of distributing its own copy. The minimum required asteval version is 0.9.12, which is available on PyPI. If you see import errors related to asteval, please make sure that you actually have the latest version installed.

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.