Markéta Machová
5cfc2ad4f7
- Update to 1.2.2
* add create_params function
* add ModelResult.summary() to return many resulting fit statistics
and attributes into a JSON-able dict.
* update tests for latest versions of NumPy and SciPy.
* 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
* improve Model.make_params and create_params to take optional dict
of Parameter attributes
* Outputs of residual functions, including Model._residual, are more
explicitly coerced to 1d-arrays of datatype Float64. This decreases the
expectation for the user-supplied code to return ndarrays, and increases
the tolerance for more “array-like” objects or ndarrays that are not
Float64 or 1-dimensional.
OBS-URL: https://build.opensuse.org/request/show/1105049
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-lmfit?expand=0&rev=9
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-------------------------------------------------------------------
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Mon Aug 21 10:32:37 UTC 2023 - Markéta Machová <mmachova@suse.com>
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- Update to 1.2.2
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* add create_params function
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* add ModelResult.summary() to return many resulting fit statistics
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and attributes into a JSON-able dict.
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* update tests for latest versions of NumPy and SciPy.
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* Coercing of user input data and independent data for Model to
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float64 ndarrays is somewhat less aggressive and will not increase
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the precision of numpy ndarrays
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* improve Model.make_params and create_params to take optional dict
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of Parameter attributes
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* Outputs of residual functions, including Model._residual, are more
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explicitly coerced to 1d-arrays of datatype Float64. This decreases the
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expectation for the user-supplied code to return ndarrays, and increases
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the tolerance for more “array-like” objects or ndarrays that are not
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Float64 or 1-dimensional.
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-------------------------------------------------------------------
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Fri Jan 13 15:42:09 UTC 2023 - Ben Greiner <code@bnavigator.de>
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- Update to v1.1.0
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## New features:
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* add Pearson4Model (@lellid; PR #800)
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* add SplineModel (PR #804)
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* add R^2 rsquared statistic to fit outputs and reports for Model
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fits (Issue #803; PR #810)
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* add calculation of dely for model components of composite
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models (Issue #761; PR #826)
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## Bug fixes/enhancements:
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* make sure variable spercent is always defined in
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params_html_table functions (reported by @MySlientWind; Issue
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#768, PR #770)
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* always initialize the variables success and covar the
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MinimizerResult (reported by Marc W. Pound; PR #771)
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* build package following PEP517/PEP518; use pyproject.toml and
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setup.cfg; leave setup.py for now (PR #777)
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* components used to create a CompositeModel can now have
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different independent variables (@Julian-Hochhaus; Discussion
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#787; PR #788)
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* fixed function definition for StepModel(form='linear'), was not
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consistent with the other ones (@matpompili; PR #794)
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* fixed height factor for Gaussian2dModel, was not correct
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(@matpompili; PR #795)
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* for covariances with negative diagonal elements, we set the
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covariance to None (PR #813)
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* fixed linear mode for RectangleModel (@arunpersaud; Issue #815;
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PR #816)
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* report correct initial values for parameters with bounds (Issue
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#820; PR #821)
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* allow recalculation of confidence intervals (@jagerber48; PR
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#798)
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* include 'residual' in JSON output of ModelResult.dumps
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(@mac01021; PR #830)
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* supports and is tested against Python 3.11; updated minimum
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required version of SciPy, NumPy, and asteval (PR #832)
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## Deprecations:
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* remove support for Python 3.6 which reached EOL on 2021-12-23
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(PR #790)
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- Clean check section from extra example
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-------------------------------------------------------------------
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Tue Dec 28 19:11:00 UTC 2021 - Ben Greiner <code@bnavigator.de>
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- Update to v1.0.3
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**Potentially breaking change:**
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* argument ``x`` is now required for the ``guess`` method of
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Models (Issue #747; PR #748)
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To get reasonable estimates for starting values one should
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always supply both ``x`` and ``y`` values; in some cases it
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would work when only providing ``data`` (i.e., y-values). With
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the change above, ``x`` is now required in the ``guess`` method
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call, so scripts might need to be updated to explicitly supply
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``x``.
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**Bug fixes/enhancements:**
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* do not overwrite user-specified figure titles in Model.plot()
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functions and allow setting with ``title`` keyword argument (PR
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#711)
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* preserve Parameters subclass in deepcopy (@jenshnielsen; PR
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#719)
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* coerce ``data`` and ``indepdent_vars`` to NumPy array with
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``dtype=float64`` or ``dtype=complex128`` where applicable
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(Issues #723 and #728)
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* fix collision between parameter names in built-in models and
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user-specified parameters (Issue #710 and PR #732)
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* correct error message in PolynomialModel (@kremeyer; PR #737)
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* improved handling of altered JSON data (Issue #739; PR #740,
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reported by Matthew Giammar)
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* map ``max_nfev`` to ``maxiter`` when using
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``differential_evolution`` (PR #749, reported by Olivier B.)
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* correct use of noise versus experimental uncertainty in the
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documentation (PR #751, reported by Andrés Zelcer)
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* specify return type of ``eval`` method more precisely and allow
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for plotting of (Complex)ConstantModel by coercing their
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``float``, ``int``, or ``complex`` return value to a
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``numpy.ndarray`` (Issue #684 and PR #754)
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* fix ``dho`` (Damped Harmonic Oscillator) lineshape (PR #755;
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@rayosborn)
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* reset ``Minimizer._abort`` to ``False`` before starting a new
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fit (Issue #756 and PR #757; @azelcer)
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* fix typo in ``guess_from_peak2d`` (@ivan-usovl; PR #758)
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**Various:**
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* update asteval dependency to >= 0.9.22 to avoid
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DeprecationWarnings from NumPy v1.20.0 (PR #707)
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* remove incorrectly spelled ``DonaichModel`` and ``donaich``
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lineshape, deprecated in version 1.0.1 (PR #707)
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* remove occurrences of OrderedDict throughout the code; dict is
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order-preserving since Python 3.6 (PR #713)
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* update the contributing instructions (PR #718; @martin-majlis)
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* (again) defer import of matplotlib to when it is needed
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(@zobristnicholas; PR #721)
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* fix description of ``name`` argument in ``Parameters.add``
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(@kristianmeyerr; PR #725)
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* update dependencies, make sure a functional development
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environment is installed on Windows (Issue #712)
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* use ``setuptools_scm`` for version info instead of
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``versioneer`` (PR #729)
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* transition to using ``f-strings`` (PR #730)
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* mark ``test_manypeaks_speed.py`` as flaky to avoid intermittent
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test failures (repeat up to 5 times; PR #745)
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* update scipy dependency to >= 1.14.0 (PR #751)
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* improvement to output of examples in sphinx-gallery and use
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higher resolution figures (PR #753)
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* remove deprecated functions ``lmfit.printfuncs.report_errors``
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and ``asteval`` argument in ``Parameters`` class (PR #759)
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-------------------------------------------------------------------
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Wed Feb 17 11:46:57 UTC 2021 - Ben Greiner <code@bnavigator.de>
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- Update to version 1.0.2
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* officially supports Python 3.9 and has dropped support for
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Python 3.5. The minimum version of the following dependencies
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were updated: asteval>=0.9.21, numpy>=1.18, and scipy>=1.3.
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New features:
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* added two-dimensional Gaussian lineshape and model (PR #642;
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@mpmdean)
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* all built-in models are now registered in lmfit.models.
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lmfit_models; new Model class attribute valid_forms (PR #663;
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@rayosborn)
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* added a SineModel (PR #676; @lneuhaus)
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* add the run_mcmc_kwargs argument to Minimizer.emcee to pass to
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the emcee.EnsembleSampler.run_mcmc function (PR #694; @rbnvrw)
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- Skip python36 build: Numpy 1.20 dropped support for Python 3.6
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(NEP 29)
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-------------------------------------------------------------------
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Tue Jun 16 08:44:01 UTC 2020 - Tomáš Chvátal <tchvatal@suse.com>
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- Skip two failing tests that are borked on non 64bit intel
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-------------------------------------------------------------------
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Mon Jun 8 07:06:22 UTC 2020 - John Paul Adrian Glaubitz <adrian.glaubitz@suse.com>
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- Update to version 1.0.1
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+ New features:
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- added thermal distribution model and lineshape (PR #620; @mpmdean)
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- introduced a new argument ``max_nfev`` to uniformly specify the maximum
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number of function evalutions (PR #610)
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**Please note: all other arguments (e.g., ``maxfev``, ``maxiter``, ...)
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will no longer be passed to the underlying solver. A warning will be emitted
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stating that one should use ``max_nfev``.**
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- the attribute ``call_kws`` was added to the ``MinimizerResult`` class and
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contains the keyword arguments that are supplied to the solver in SciPy.
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+ Bug fixes:
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- fixes to the ``load`` and ``__setstate__`` methods of the Parameter class
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- fixed failure of ModelResult.dump() due to missing attributes
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(Issue #611, PR #623; @mpmdean)
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- ``guess_from_peak`` function now also works correctly with decreasing
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x-values or when using pandas (PRs #627 and #629; @mpmdean)
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- the ``Parameter.set()`` method now correctly first updates the boundaries
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and then the value (Issue #636, PR #637; @arunpersaud)
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+ Various:
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- fixed typo for the use of expressions in the documentation
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(Issue #610; @jkrogager)
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- removal of PY2-compatibility and unused code and improved test
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coverage (PRs #619, #631, and #633)
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- removed deprecated ``isParameter`` function and automatic conversion of
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an ``uncertainties`` object (PR #626)
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- inaccurate FWHM calculations were removed from built-in models, others
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labeled as estimates (Issue #616 and PR #630)
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- corrected spelling mistake for the Doniach lineshape and model
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(Issue #634; @rayosborn)
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- removed unsupported/untested code for IPython notebooks in lmfit/ui/*
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- from version 1.0.0
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+ New features:
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- no new features are introduced in 1.0.0.
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+ Improvements:
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- support for Python 2 and use of the ``six`` package are removed. (PR #612)
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+ Various:
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- documentation updates to clarify the use of ``emcee``. (PR #614)
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- from version 0.9.15
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+ New features, improvements, and bug fixes:
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- move application of parameter bounds to setter instead of getter (PR #587)
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- add support for non-array Jacobian types in least_squares
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(Issue #588, @ezwelty in PR #589)
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- add more information (i.e., acor and acceptance_fraction) about
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emcee fit (@j-zimmermann in PR #593)
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- "name" is now a required positional argument for Parameter class,
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update the magic methods (PR #595)
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- fix nvars count and bound handling in confidence interval
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calculations (Issue #597, PR #598)
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- support Python 3.8; requires asteval >= 0.9.16 (PR #599)
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- only support emcee version 3 (i.e., no PTSampler anymore) (PR #600)
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- fix and refactor prob_bunc in confidence interval calculations (PR #604)
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- fix adding Parameters with custom user-defined symbols
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(Issue #607, PR #608; thanks to @gbouvignies for the report)
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+ Various:
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- bump requirements to LTS version of SciPy/ NumPy and code clean-up (PR #591)
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- documentation updates (PR #596, and others)
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- improve test coverage and Travis CI updates (PR #595, and others)
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- update pre-commit hooks and configuration in setup.cfg
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+ To-be deprecated:
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- function Parameter.isParameter and conversion from
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uncertainties.core.Variable to value in _getval (PR #595)
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- from version 0.9.14
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+ New features:
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- the global optimizers ``shgo`` and ``dual_annealing`` (new in SciPy v1.2)
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are now supported (Issue #527; PRs #545 and #556)
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- ``eval`` method added to the Parameter class (PR #550 by @zobristnicholas)
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- avoid ZeroDivisionError in ``printfuncs.params_html_table``
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(PR #552 by @aaristov and PR #559)
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- add parallelization to ``brute`` method (PR #564, requires SciPy v1.3)
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+ Bug fixes:
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- consider only varying parameters when reporting potential issues with calculating
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errorbars (PR #549) and compare ``value`` to both ``min`` and ``max`` (PR #571)
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- guard against division by zero in lineshape functions and ``FWHM``
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and ``height`` expression calculations (PR #545)
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- fix issues with restoring a saved Model (Issue #553; PR #554)
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- always set ``result.method`` for ``emcee`` algorithm (PR #558)
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- more careful adding of parameters to handle out-of-order
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constraint expressions (Issue #560; PR #561)
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- make sure all parameters in Model.guess() use prefixes (PRs #567 and #569)
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- use ``inspect.signature`` for PY3 to support wrapped functions
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(Issue #570; PR #576)
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- fix ``result.nfev``` for ``brute`` method when using parallelization
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(Issue #578; PR #579)
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+ Various:
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- remove "missing" in the Model class (replaced by nan_policy) and "drop"
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as option to nan_policy (replaced by omit) deprecated since 0.9 (PR #565).
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- deprecate 'report_errors' in printfuncs.py (PR #571)
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- updates to the documentation to use ``jupyter-sphinx`` to include
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examples/output (PRs #573 and #575)
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- include a Gallery with examples in the documentation
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using ``sphinx-gallery`` (PR #574 and #583)
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- improve test-coverage (PRs #571, #572 and #585)
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- add/clarify warning messages when NaN values are detected (PR #586)
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- several updates to docstrings (Issue #584; PR #583, and others)
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- update pre-commit hooks and several docstrings
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- Update BuildRequires and Requires from setup.py
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-------------------------------------------------------------------
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Wed Apr 24 08:42:15 UTC 2019 - pgajdos@suse.com
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- version update to 0.9.13
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New features:
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Clearer warning message in fit reports when uncertainties should
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but cannot be estimated, including guesses of which Parameters
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to examine (#521, #543)
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SplitLorenztianModel and split_lorentzian function (#523)
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HTML representations for Parameter, MinimizerResult, and Model
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so that they can be printed better with Jupyter (#524, #548)
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support parallelization for differential evolution (#526)
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Bug fixes:
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delay import of matplotlib (and so, the selection of its backend)
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as late as possible (#528, #529)
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fix for saving, loading, and reloading ModelResults (#534)
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fix to leastsq to report the best-fit values, not the values tried
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last (#535, #536)
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fix synchronization of all parameter values on Model.guess() (#539, #542)
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improve deprecation warnings for outdated nan_policy keywords (#540)
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fix for edge case in gformat() (#547)
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Project managements:
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using pre-commit framework to improve and enforce coding style (#533)
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added code coverage report to github main page
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updated docs, github templates, added several tests.
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dropped support and testing for Python 3.4.
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- deleted patches
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- lmfit-scipy.patch (upstreamed)
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-------------------------------------------------------------------
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Tue Mar 5 14:57:02 UTC 2019 - Todd R <toddrme2178@gmail.com>
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- Fix spurious unit test errors.
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-------------------------------------------------------------------
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Fri Jan 18 10:24:44 UTC 2019 - Tomáš Chvátal <tchvatal@suse.com>
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- Apply patch to fix build with new scipy:
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* lmfit-scipy.patch
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-------------------------------------------------------------------
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Fri Jan 18 10:19:27 UTC 2019 - Tomáš Chvátal <tchvatal@suse.com>
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- Update to 0.9.12:
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* make exceptions explicit
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* use inspect.getfullargspec for Python3
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* test-suite: use pytest features, improve coverage, fix mistakes
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-------------------------------------------------------------------
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Thu Mar 22 04:46:08 UTC 2018 - toddrme2178@gmail.com
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- Initial version
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