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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 - preserve Parameters subclass in deepcopy - coerce ``data`` and ``indepdent_vars`` to NumPy array with ``dtype=float64`` or ``dtype=complex128`` where applicable - fix collision between parameter names in built-in models and user-specified parameters - correct error message in PolynomialModel - improved handling of altered JSON data - map ``max_nfev`` to ``maxiter`` when using ``differential_evolution`` - correct use of noise versus experimental uncertainty in the documentation - 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`` - fix ``dho`` (Damped Harmonic Oscillator) lineshape - reset ``Minimizer._abort`` to ``False`` before starting a new fit - fix typo in ``guess_from_peak2d`` Various: - update asteval dependency to >= 0.9.22 to avoid DeprecationWarnings from NumPy v1.20.0 - remove incorrectly spelled ``DonaichModel`` and ``donaich`` lineshape, deprecated in version 1.0.1 - remove occurrences of OrderedDict throughout the code; dict is order-preserving since Python 3.6 - update the contributing instructions - (again) defer import of matplotlib to when it is needed - fix description of ``name`` argument in ``Parameters.add`` - update dependencies, make sure a functional development environment is installed on Windows - use ``setuptools_scm`` for version info instead of ``versioneer`` - transition to using ``f-strings`` - mark ``test_manypeaks_speed.py`` as flaky to avoid intermittent test failures - update scipy dependency to >= 1.14.0 - improvement to output of examples in sphinx-gallery and use higher resolution figures - remove deprecated functions ``lmfit.printfuncs.report_errors`` and ``asteval`` argument in ``Parameters`` class .. _whatsnew_102_label: Version 1.0.2 Release Notes (February 7, 2021) ============================================== 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 - all built-in models are now registered in ``lmfit.models.lmfit_models``; new Model class attribute ``valid_forms`` - added a SineModel - add the ``run_mcmc_kwargs argument`` to ``Minimizer.emcee`` to pass to the ``emcee.EnsembleSampler.run_mcmc`` function Bug fixes: - ``ModelResult.eval_uncertainty`` should use provided Parameters - center in lognormal model can be negative - restore best-fit values after calculation of covariance matrix - add helper-function ``not_zero`` to prevent ZeroDivisionError in lineshapes and use in exponential lineshape - save ``last_internal_values`` and use to restore internal values if fit is aborted - dumping a fit using the ``lbfgsb`` method now works, convert bytes to string if needed - fix use of callable Jacobian for scalar methods - preserve float/int types when encoding for JSON - better support for saving/loading of ExpressionModels and assure that ``init_params`` and ``init_fit`` are set when loading a ``ModelResult`` Various: - update minimum dependencies - improvements in coding style, docstrings, CI, and test coverage - fix typo in Oscillator - add example using SymPy - allow better custom pool for emcee() - update NIST Strd reference functions and tests - make building of documentation cross-platform - relax module name check in ``test_check_ast_errors`` for Python 3.9 - fix/update layout of documentation, now uses the sphinx13 theme - fixed DeprecationWarnings reported by NumPy v1.2.0 - increase value of ``tiny`` and check for it in bounded parameters to avoid "parameter not moving from initial value" - add ``max_nfev`` to ``basinhopping`` and ``brute`` (now supported everywhere in lmfit) and set to more uniform default values - use Azure Pipelines for CI, drop Travis @ text @$NetBSD: distinfo,v 1.11 2021/10/26 10:56:02 nia Exp $ BLAKE2s (lmfit-1.0.3.tar.gz) = af27a0fd80fb6f26ca92b13ec72f3eca1482e5591e14f4a39f3198696c112e1d SHA512 (lmfit-1.0.3.tar.gz) = 33febdd68104bb41ca379a8acd03a8bb985ba8785d607ab110b63bc7b3b39b9d95161a683fe015613bee6d99100ede82d1f3574515a6bfb9160300a5791fcc55 Size (lmfit-1.0.3.tar.gz) = 292475 bytes @ 1.11 log @math: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.10 2021/10/07 14:28:24 nia Exp $ d3 3 a5 3 BLAKE2s (lmfit-1.0.1.tar.gz) = 5b2b858893b10255c1c5966cb029e8958eeacd0cc123647c7fdfbccba9e24570 SHA512 (lmfit-1.0.1.tar.gz) = 1ae3e2cb25625a9b24c261d81c8f1ba0389266724581762f6e0a96140c84e43acd527ab1b83b862bf7b3b4c0b1b9755ee38d0c52e63fe89ea41f2d010b1e5c0d Size (lmfit-1.0.1.tar.gz) = 258368 bytes @ 1.10 log @math: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.9 2020/05/13 15:36:27 adam Exp $ d3 1 a3 1 RMD160 (lmfit-1.0.1.tar.gz) = e641f717229828c32375e6d4f22c66bc998e3a55 @ 1.9 log @py-lmfit: updated to 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 - introduced a new argument ``max_nfev`` to uniformly specify the maximum number of function evalutions **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 - ``guess_from_peak`` function now also works correctly with decreasing x-values or when using pandas - the ``Parameter.set()`` method now correctly first updates the boundaries and then the value Various: - fixed typo for the use of expressions in the documentation - removal of PY2-compatibility and unused code and improved test coverage - removed deprecated ``isParameter`` function and automatic conversion of an ``uncertainties`` object - inaccurate FWHM calculations were removed from built-in models, others labeled as estimates - corrected spelling mistake for the Doniach lineshape and model - removed unsupported/untested code for IPython notebooks in lmfit/ui/* @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.8 2020/04/28 13:27:03 adam Exp $ a2 1 SHA1 (lmfit-1.0.1.tar.gz) = ef4337a6c647058dfad609a0ee4ca024bf1ec7c8 @ 1.8 log @py-lmfit: updated to 1.0.0 Version 1.0.0 Release Notes New features: - no new features are introduced in 1.0.0. Improvements: - support for Python 2 and use of the ``six`` package are removed. Various: - documentation updates to clarify the use of ``emcee``. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.7 2019/06/15 07:21:21 adam Exp $ d3 4 a6 4 SHA1 (lmfit-1.0.0.tar.gz) = 263c0939fa8fb6b499e9f09aeac2ed65f0bc0f9f RMD160 (lmfit-1.0.0.tar.gz) = 82123f8030de979e44f451a2e3a80e2bf879ab28 SHA512 (lmfit-1.0.0.tar.gz) = 9195fcb528fd9c7d6a3c74ce071724ec1cd556df51785ba54baaeb694821299d30cf49941fd6fbd7fe4ff5651be94c9ee303a5cadbe9be63467b8b29c71829b2 Size (lmfit-1.0.0.tar.gz) = 258821 bytes @ 1.7 log @py-lmfit: updated to 0.9.13 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 SplitLorenztianModel and split_lorentzian function HTML representations for Parameter, MinimizerResult, and Model so that they can be printed better with Jupyter support parallelization for differential evolution Bug fixes: delay import of matplotlib (and so, the selection of its backend) as late as possible fix for saving, loading, and reloading ModelResults fix to leastsq to report the best-fit values, not the values tried last fix synchronization of all parameter values on Model.guess() improve deprecation warnings for outdated nan_policy keywords fix for edge case in gformat() Project managements: using pre-commit framework to improve and enforce coding style added code coverage report to github main page updated docs, github templates, added several tests. dropped support and testing for Python 3.4. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.6 2018/12/03 20:41:44 adam Exp $ d3 4 a6 4 SHA1 (lmfit-0.9.13.tar.gz) = a2693d63ef4be4719c52ff6d2463c53244a7fe53 RMD160 (lmfit-0.9.13.tar.gz) = e9c725baacf92b9255960e76fd0ed32ba52dd92f SHA512 (lmfit-0.9.13.tar.gz) = cd82f190d798e854afaf0087659271b7f1b53ec9a346e7974e81d07d6270493062546d71baeb077c87026185b33d3648a7d901b0805b4a165e52c721782a9234 Size (lmfit-0.9.13.tar.gz) = 1457657 bytes @ 1.6 log @py-lmfit: updated to 0.9.12 Version 0.9.12 Release Notes New features: - SkewedVoigtModel was added as built-in model - Parameter uncertainties and correlations are reported for least_squares - Plotting of complex-valued models is now handled in ModelResult class - A model's independent variable is allowed to be an object - Added usersyms to Parameters() initialization to make it easier to add custom functions and symbols - the numdifftools package can be used to calculate parameter uncertainties and correlations for all solvers that do not natively support this - emcee can now be used as method keyword-argument to Minimizer.minimize and minimize function, which allows for using emcee in the Model class (Bug)fixes: - asteval errors are now flushed after raising - max_time and evaluation time for ExpressionModel increased to 1 hour - loading a saved ModelResult now restores all attributes - development versions of scipy and emcee are now supported - ModelResult.eval() do no longer overwrite the userkws dictionary - running the test suite requires pytest only - improved FWHM calculation for VoigtModel @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2018/07/13 06:22:35 adam Exp $ d3 4 a6 4 SHA1 (lmfit-0.9.12.tar.gz) = 7c4a15975d9920c9cf12fd98aca7e7706daf18c9 RMD160 (lmfit-0.9.12.tar.gz) = dc4bb6835e34fadd8786c1dd760f09df694dba6b SHA512 (lmfit-0.9.12.tar.gz) = 09b840955867d64ecf6cb64fcc06b6426a1644b510b34ef27d8cee55a8c65d9002f0e76276f9e05feabed0b49656c5a78cf286e423203769f1de292f01f6ccb0 Size (lmfit-0.9.12.tar.gz) = 1569497 bytes @ 1.5 log @py-lmfit: updated to 0.9.11 0.9.11: make exception explicit 0.9.10: add AMPGO and basin-hopping global optimization methods. aborting a fit from the objective function now raises AbortFitException fit statistics are more uniformly calculated. the uncertainties package is now an external dependency, and an out-dated copy is no longer kept in lmfit. more exceptions when import matplotlib are now tolerated. many documentation fixes. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2018/04/14 05:32:22 adam Exp $ d3 4 a6 4 SHA1 (lmfit-0.9.11.tar.gz) = 4ddfa62357990ad2dcaa49077442f5789d8efa61 RMD160 (lmfit-0.9.11.tar.gz) = fe1c29354627524f769cde7f03517dad45d7cacb SHA512 (lmfit-0.9.11.tar.gz) = fb09fe90e99e0468a04195a3ee1d95d84f5cd2933133fced00fc4118559f0fa38f243a893cbda9b3e9b23fd24e0def562a1658da12b5485ff6645ea5aaf5296b Size (lmfit-0.9.11.tar.gz) = 1600601 bytes @ 1.4 log @py-lmfit: updated to 0.9.9 Version 0.9.9: 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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2018/02/27 06:40:07 adam Exp $ d3 4 a6 4 SHA1 (lmfit-0.9.9.tar.gz) = a9f10957b05333f9af4f5a5fa1513e7232d376d2 RMD160 (lmfit-0.9.9.tar.gz) = b2891fa6b125ea11e88769dc31704e681cde91a8 SHA512 (lmfit-0.9.9.tar.gz) = 084dd74743a2f88932520c4ff564d56ef3a421adbd91b2e3b30685f5a30df04cdf9eacfa4dbfa38d4ad410f63581ac41e93b05590acdce713278bc251da2b6ad Size (lmfit-0.9.9.tar.gz) = 1574912 bytes @ 1.3 log @py-lmfit: updated to 0.9.8 0.9.8: update doc for 5 digit-precision fit statistics increase default precision for chi-square, etc from 3 to 5 @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2017/08/31 08:27:42 prlw1 Exp $ d3 4 a6 4 SHA1 (lmfit-0.9.8.tar.gz) = 69f4e3a2f769c534376db36e876d4d4cecd6273a RMD160 (lmfit-0.9.8.tar.gz) = ce509062cff8e0110c2ff93296455c42458057b8 SHA512 (lmfit-0.9.8.tar.gz) = 2b2fe869f196c809baa5e73cecae80b7b9652349834ec7bc0ed9bde4325b0f3645c870951ddc556b6cc275515381cba43e4ecab5f08e0e442da53e3b77adbba4 Size (lmfit-0.9.8.tar.gz) = 1602986 bytes @ 1.2 log @Update py-lmfit to 0.9.7 Changes to 0.9.7 not immediately obvious 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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1 2016/09/16 15:20:31 prlw1 Exp $ d3 4 a6 4 SHA1 (lmfit-0.9.7.tar.gz) = 28c7ace0159f1197495235b124ef8c6e78aad2f9 RMD160 (lmfit-0.9.7.tar.gz) = 010acd89cd1039bfc8180d3fa32ce23755e42929 SHA512 (lmfit-0.9.7.tar.gz) = 424c0d19baaf48597c14cc75b8048c6f2e9cb91e4cd68843b62ffabbaed720f3ac7a8c306db8df5d4fe1cb22f299519555805546e32d9ce0054d972ef7720d72 Size (lmfit-0.9.7.tar.gz) = 1175660 bytes @ 1.1 log @Add py-lmfit 0.9.5 A library for least-squares minimization and data fitting in Python, based on scipy.optimize. @ text @d1 1 a1 1 $NetBSD$ d3 4 a6 4 SHA1 (lmfit-0.9.5.tar.gz) = e18d8f5c2fc21c327780a13e50051fcd13401ac4 RMD160 (lmfit-0.9.5.tar.gz) = 3e9c32c8fe88987e35211e4d7ed694eff292dc7d SHA512 (lmfit-0.9.5.tar.gz) = 9bbc38f7837d139877d344f293c070a16b53876a982e578558690fb833724bb3373075c0c8e8829610c76aeb5d5500c629f51090e8deb5fee42762a5294ed25d Size (lmfit-0.9.5.tar.gz) = 1128987 bytes @