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| Name: python310-lmfit | Distribution: openSUSE Tumbleweed |
| Version: 1.3.2 | Vendor: openSUSE |
| Release: 1.1 | Build date: Thu Sep 5 11:41:05 2024 |
| Group: Unspecified | Build host: reproducible |
| Size: 728585 | Source RPM: python-lmfit-1.3.2-1.1.src.rpm |
| Packager: https://bugs.opensuse.org | |
| Url: https://lmfit.github.io/lmfit-py/ | |
| Summary: Least-Squares Minimization with Bounds and Constraints | |
A library for least-squares minimization and data fitting in Python. Built on top of scipy.optimize, lmfit provides a Parameter object which can be set as fixed or free, can have upper and/or lower bounds, or can be written in terms of algebraic constraints of other Parameters. The user writes a function to be minimized as a function of these Parameters, and the scipy.optimize methods are used to find the optimal values for the Parameters. The Levenberg-Marquardt (leastsq) is the default minimization algorithm, and provides estimated standard errors and correlations between varied Parameters. Other minimization methods, including Nelder-Mead's downhill simplex, Powell's method, BFGS, Sequential Least Squares, and others are also supported. Bounds and constraints can be placed on Parameters for all of these methods. In addition, methods for explicitly calculating confidence intervals are provided for exploring minmization problems where the approximation of estimating Parameter uncertainties from the covariance matrix is questionable.
BSD-3-Clause AND MIT
* Thu Sep 05 2024 Ben Greiner <code@bnavigator.de>
- Update to 1.3.2
* fix typo in restoring a _buildmodel dict (PR #957, Issue #956)
* fixes for Numpy2 support (PR #959, Issue #958)
* ensure that correct initial params are used when re-fitting a
ModeRresult (PR #961, Issue #960)
* make sure that CompositeModels cannot have a prefix (PR #961,
Issue #954)
* now require asteval>=1.0 and uncertainties>=3.2.2
- Fix requirements
- Drop support-numpy-2.patch
- Add lmfit-pr965-asteval.patch gh#lmfit/lmfit-py#965
* Fri Jul 05 2024 Steve Kowalik <steven.kowalik@suse.com>
- Update to 1.3.1:
* New features:
+ add 'min_rel_change' as optional variable in calculation of confidence
intervals with Model.conf_interval().
+ Model.eval_uncertainty now takes an optional dscale parameter (default
value of 0.01) to set the step size for calculating derivatives
+ add calculation of predicted_interval to Model.eval_uncertainty
* Bug fixes/enhancements:
+ allow Model.eval_uncertainty to be performed with single points for x
independent variables
+ allow Model._parse_param to handle older-style passed-in 'argnames' and
'kwargs' as for variadic function
+ better allow (or re-allow) Model function independent variables / keyword
arguments to be given non-default values at model creation time
+ add form as independent variable for builtin Step, Rectangle, Thermal
Distribution models.
+ use Model._reprstring(long=True) for model Model.__repr__().
+ restore best-fit parameter values for high accuracy values of constrained
values
+ improvement to Model for the difference between Parameter, "independent
variable", and "option".
+ better saving/loading saved states of Model now use dill, have several
cleanups, and are now versioned for future-proofing.
+ fix bug calculating r-squared for fits with weights
+ fix bug in modelresult.eval_uncertainty() after load_modelresult()
+ add test for MinimizerResult.uvars after successful fit
* Maintenance/Deprecations:
+ drop support for Python 3.7
+ fix tests for Python 3.12 and Python 3.13-dev
+ increase minimum numpy verstio to 1.23 and scipy to 1.8.
+ updates for compatibility with numpy 2.0
+ the dill package is now required
- Switch to autosetup macro.
- Add patch support-numpy-2.patch:
* Support numpy 2.0 more thoroughly.
* Mon Aug 21 2023 Markéta Machová <mmachova@suse.com>
- 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.
* Fri Jan 13 2023 Ben Greiner <code@bnavigator.de>
- Update to v1.1.0
[#]# 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)
- Clean check section from extra example
* Tue Dec 28 2021 Ben Greiner <code@bnavigator.de>
- Update to v1.0.3
* *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)
* Wed Feb 17 2021 Ben Greiner <code@bnavigator.de>
- Update to 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)
- Skip python36 build: Numpy 1.20 dropped support for Python 3.6
(NEP 29)
* Tue Jun 16 2020 Tomáš Chvátal <tchvatal@suse.com>
- Skip two failing tests that are borked on non 64bit intel
* Mon Jun 08 2020 John Paul Adrian Glaubitz <adrian.glaubitz@suse.com>
- Update to version 1.0.1
+ 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/*
- from version 1.0.0
+ 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)
- from version 0.9.15
+ 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)
- from version 0.9.14
+ 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
- Update BuildRequires and Requires from setup.py
* Wed Apr 24 2019 pgajdos@suse.com
- version update to 0.9.13
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 managements:
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.
- deleted patches
- lmfit-scipy.patch (upstreamed)
* Tue Mar 05 2019 Todd R <toddrme2178@gmail.com>
- Fix spurious unit test errors.
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