1.0.3

Version 1.0.3 Release Notes (October 14, 2021)

Potentially breaking change:

• argument x is now required for the guess method of Models (Issue #747; PR #748)

To get reasonable estimates for starting values one should always supply both x and y values; in some cases it would work
when only providing data (i.e., y-values). With the change above, x is now required in the guess method call, so scripts might
need to be updated to explicitly supply x.

Bug fixes/enhancements:

• do not overwrite user-specified figure titles in Model.plot() functions and allow setting with title keyword argument (PR #711)
• preserve Parameters subclass in deepcopy (@jenshnielsen; PR #719)
• coerce data and indepdent_vars to NumPy array with dtype=float64 or dtype=complex128 where applicable (Issues #723 and #728)
• fix collision between parameter names in built-in models and user-specified parameters (Issue #710 and PR #732)
• correct error message in PolynomialModel (@kremeyer; PR #737)
• improved handling of altered JSON data (Issue #739; PR #740, reported by Matthew Giammar)
• map max_nfev to maxiter when using differential_evolution (PR #749, reported by Olivier B.)
• correct use of noise versus experimental uncertainty in the documentation (PR #751, reported by Andrés Zelcer)
• specify return type of eval method more precisely and allow for plotting of (Complex)ConstantModel by coercing their
  float, int, or complex return value to a numpy.ndarray (Issue #684 and PR #754)
• fix dho (Damped Harmonic Oscillator) lineshape (PR #755; @rayosborn)
• reset Minimizer._abort to False before starting a new fit (Issue #756 and PR #757; @azelcer)
• fix typo in guess_from_peak2d (@ivan-usovl; PR #758)

Various:

• update asteval dependency to >= 0.9.22 to avoid DeprecationWarnings from NumPy v1.20.0 (PR #707)
• remove incorrectly spelled DonaichModel and donaich lineshape, deprecated in version 1.0.1 (PR #707)
• remove occurrences of OrderedDict throughout the code; dict is order-preserving since Python 3.6 (PR #713)
• update the contributing instructions (PR #718; @martin-majlis)
• (again) defer import of matplotlib to when it is needed (@zobristnicholas; PR #721)
• fix description of name argument in Parameters.add (@kristianmeyerr; PR #725)
• update dependencies, make sure a functional development environment is installed on Windows (Issue #712)
• use setuptools_scm for version info instead of versioneer (PR #729)
• transition to using f-strings (PR #730)
• mark test_manypeaks_speed.py as flaky to avoid intermittent test failures (repeat up to 5 times; PR #745)
• update scipy dependency to >= 1.14.0 (PR #751)
• improvement to output of examples in sphinx-gallery and use higher resolution figures (PR #753)
• remove deprecated functions lmfit.printfuncs.report_errors and asteval argument in Parameters class (PR #759)

1.0.2

Version 1.0.2 officially supports Python 3.9 and has dropped support for Python 3.5. The minimum version
of the following dependencies were updated: asteval>=0.9.21, numpy>=1.18, and scipy>=1.3.

New features:

• added two-dimensional Gaussian lineshape and model (PR #642; @mpmdean)
• all built-in models are now registered in lmfit.models.lmfit_models; new Model class attribute valid_forms (PR #663; @rayosborn)
• added a SineModel (PR #676; @lneuhaus)
• add the run_mcmc_kwargs argument to Minimizer.emcee to pass to the emcee.EnsembleSampler.run_mcmc function (PR #694; @rbnvrw)

Bug fixes:

• ModelResult.eval_uncertainty should use provided Parameters (PR #646)
• center in lognormal model can be negative (Issue #644, PR #645; @YoshieraHuang)
• restore best-fit values after calculation of covariance matrix (Issue #655, PR #657)
• add helper-function not_zero to prevent ZeroDivisionError in lineshapes and use in exponential lineshape (Issue #631, PR #664; @s-weigand)
• save last_internal_values and use to restore internal values if fit is aborted (PR #667)
• dumping a fit using the lbfgsb method now works, convert bytes to string if needed (Issue #677, PR #678; @leonfoks)
• fix use of callable Jacobian for scalar methods (PR #681; @mstimberg)
• preserve float/int types when encoding for JSON (PR #696; @jedzill4)
• better support for saving/loading of ExpressionModels and assure that init_params and init_fit are set when loading a ModelResult (PR #706)

Various:

• update minimum dependencies (PRs #688, #693)
• improvements in coding style, docstrings, CI, and test coverage (PRs #647, #649, #650, #653, #654; #685, #668, #689)
• fix typo in Oscillator (PR #658; @flothesof)
• add example using SymPy (PR #662)
• allow better custom pool for emcee() (Issue #666, PR #667)
• update NIST Strd reference functions and tests (PR #670)
• make building of documentation cross-platform (PR #673; @s-weigand)
• relax module name check in test_check_ast_errors for Python 3.9 (Issue #674, PR #675; @mwhudson)
• fix/update layout of documentation, now uses the sphinx13 theme (PR #687)
• fixed DeprecationWarnings reported by NumPy v1.2.0 (PR #699)
• increase value of tiny and check for it in bounded parameters to avoid "parameter not moving from initial value" (Issue #700, PR #701)
• add max_nfev to basinhopping and brute (now supported everywhere in lmfit) and set to more uniform default values (PR #701)
• use Azure Pipelines for CI, drop Travis (PRs #696 and #702)

1.0.1

Version 1.0.1 Release Notes

Version 1.0.1 is the last release that supports Python 3.5. All newer version will
require 3.6+ so that we can use formatting-strings and rely on dictionaries being ordered.

New features:

• added thermal distribution model and lineshape (PR #620; @mpmdean)
• introduced a new argument max_nfev to uniformly specify the maximum number of function evalutions (PR #610)
  Please note: all other arguments (e.g., maxfev, maxiter, ...) will no longer be passed to the underlying
  solver. A warning will be emitted stating that one should use max_nfev.
• the attribute call_kws was added to the MinimizerResult class and contains the keyword arguments that are
  supplied to the solver in SciPy.

Bug fixes:

• fixes to the load and __setstate__ methods of the Parameter class
• fixed failure of ModelResult.dump() due to missing attributes (Issue #611, PR #623; @mpmdean)
• guess_from_peak function now also works correctly with decreasing x-values or when using
  pandas (PRs #627 and #629; @mpmdean)
• the Parameter.set() method now correctly first updates the boundaries and then the value (Issue #636, PR #637; @arunpersaud)

Various:

• fixed typo for the use of expressions in the documentation (Issue #610; @jkrogager)
• removal of PY2-compatibility and unused code and improved test coverage (PRs #619, #631, and #633)
• removed deprecated isParameter function and automatic conversion of an uncertainties object (PR #626)
• inaccurate FWHM calculations were removed from built-in models, others labeled as estimates (Issue #616 and PR #630)
• corrected spelling mistake for the Doniach lineshape and model (Issue #634; @rayosborn)
• removed unsupported/untested code for IPython notebooks in lmfit/ui/*

1.0.0

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)

Merge pull request #611 from lmfit/v0.9.15

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_func 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)

0.9.15rc1: Merge pull request #611 from lmfit/v0.9.15

version 0.9.15rc1

Version 0.9.15 is the last release that supports Python 2.7; it now also fully supports 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)

0.9.14: Merge pull request #586 from reneeotten/nan_policy_message

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

0.9.14rc1: Merge pull request #582 from lmfit/asteval_maxtime

remove deprecated max_time from asteval.Interpreter() creation

0.9.13: Merge pull request #548 from lmfit/html_repr

alternative html_repr

0.9.12: Merge pull request #520 from reneeotten/pytest

test-suite: use pytest features, improve coverage, fix mistakes