Lmfit

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New features:

- add ``create_params`` function (PR 844)
- add ``chi2_out`` and ``nsigma`` options to ``conf_interval2d()``
- add ``ModelResult.summary()`` to return many resulting fit statistics and attributes into a JSON-able dict.
- add ``correl_table()`` function to ``lmfit.printfuncs`` and ``correl_mode`` option to ``fit_report()`` and
``ModelResult.fit_report()`` to optionally display a RST-formatted table of a correlation matrix.

Bug fixes/enhancements:

- fix bug in reported uncertainties for constrained parameters by better propating uncertainties (Issue 855; PR 856)
- Coercing of user input data and independent data for ``Model`` to float64 ndarrays is somewhat less aggressive and
will not increase the precision of numpy ndarrays (see :ref:`model_data_coercion_section` for details). The resulting
calculation from a model or objective function is more aggressively coerced to float64. (Issue 850; PR 853)
- the default value of ``epsfcn`` is increased to 1.e-10 to allow for handling of data with precision less than float64
(Issue 850; PR 853)
- fix ``conf_interval2d`` to use "increase chi-square by sigma**2*reduced chi-square" to give the ``sigma``-level
probabilities (Issue 848; PR 852)
- fix reading of older ``ModelResult`` (Issue 845; included in PR 844)
- fix deepcopy of ``Parameters`` and user data (mguhyo; PR 837)
- improve ``Model.make_params`` and ``create_params`` to take optional dict of Parameter attributes (PR 844)
- fix reporting of ``nfev`` from ``least_squares`` to better reflect actual number of function calls (Issue 842; PR 844)
- fix bug in ``Model.eval`` when mixing parameters and keyword arguments (PR 844, 839)
- re-adds ``residual`` to saved ``Model`` result (PR 844, 830)
- ``ConstantModel`` and ``ComplexConstantModel`` will return an ndarray of the same shape as the independent variable
``x`` (JeppeKlitgaard, Issue 840; PR 841)
- update tests for latest versions of NumPy and SciPy.
- many fixes of doc typos and updates of dependencies, pre-commit hooks, and CI.

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Supported Python Versions: 3.7, 3.8, 3.9, 3.10, 3.11
Minimal requirements: numpy>=1.19, scipy>=1.6, uncertainties>=3.1.4, asteval>=0.9.28

New features:

- add ``Pearson4Model`` (lellid; PR 800)
- add ``SplineModel`` (PR 804)
- add R^2 ``rsquared`` statistic to fit outputs and reports for Model fits (Issue 803; PR 810)
- add calculation of ``dely`` for model components of composite models (Issue 761; PR 826)

Bug fixes/enhancements:

- make sure variable ``spercent`` is always defined in ``params_html_table`` functions (reported by MySlientWind; Issue 768, PR 770)
- always initialize the variables ``success`` and ``covar`` the ``MinimizerResult`` (reported by Marc W. Pound; PR 771)
- build package following PEP517/PEP518; use ``pyproject.toml`` and ``setup.cfg``; leave ``setup.py`` for now (PR 777)
- components used to create a ``CompositeModel`` can now have different independent variables (Julian-Hochhaus; Discussion 787; PR 788)
- fixed function definition for ``StepModel(form='linear')``, was not consistent with the other ones (matpompili; PR 794)
- fixed height factor for ``Gaussian2dModel``, was not correct (matpompili; PR 795)
- for covariances with negative diagonal elements, we set the covariance to ``None`` (PR 813)
- fixed linear mode for ``RectangleModel`` (arunpersaud; Issue 815; PR 816)
- report correct initial values for parameters with bounds (Issue 820; PR 821)
- allow recalculation of confidence intervals (jagerber48; PR 798)
- include 'residual' in JSON output of ModelResult.dumps (mac01021; PR 830)
- supports and is tested against Python 3.11; updated minimum required version of SciPy, NumPy, and asteval (PR 832)

Deprecations:

- remove support for Python 3.6 which reached EOL on 2021-12-23 (PR 790)

========================================

New features:

- add calculation of ``dely`` for model components of composite models (Issue 761; PR 826)
- add R^2 ``rsquared`` statistic to fit outputs and reports for Model fits (Issue 803; PR 810)
- add ``SplineModel`` (PR 804)
- add ``Pearson4Model`` (lellid; PR 800)


Bug fixes/enhancements:

- make sure variable ``spercent`` is always defined in ``params_html_table`` functions (reported by MySlientWind; Issue 768, PR 770)
- always initialize the variables ``success`` and ``covar`` the ``MinimizerResult`` (reported by Marc W. Pound; PR 771)
- build package following PEP517/PEP518; use ``pyproject.toml`` and ``setup.cfg``; leave ``setup.py`` for now (PR 777)
- components used to create a ``CompositeModel`` can now have different independent variables (Julian-Hochhaus; Discussion 787; PR 788))
- fixed function definition for ``StepModel(form='linear')``, was not consistent with the other ones. (matpompili; PR 794)
- fixed height factor for ``Gaussian2dModel``, was not correct. (matpompili; PR 795)
- for covariances with negative diagonal elements, we set the covariance to ``None`` (PR 813)
- fixed linear mode for ``RectangleModel`` (arunpersaud; Issue 815; PR 816)
- report correct initial values for parameters with bounds (Issue 820; PR 821)
- allow recalculation of confidence intervals (jagerber48; PR 798)

Deprecations:

- remove support for Python 3.6 which reached EOL on 2021-12-23 (PR 790)

==============================================

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)

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)

============================

**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/*