File python-lmfit.changes of Package python-lmfit

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File python-lmfit.changes of Package python-lmfit

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Mon Aug 21 10:32:37 UTC 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.

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Fri Jan 13 15:42:09 UTC 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

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Tue Dec 28 19:11:00 UTC 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)

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Wed Feb 17 11:46:57 UTC 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)

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Tue Jun 16 08:44:01 UTC 2020 - Tomáš Chvátal <tchvatal@suse.com>

- Skip two failing tests that are borked on non 64bit intel

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Mon Jun  8 07:06:22 UTC 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

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Wed Apr 24 08:42:15 UTC 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)

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Tue Mar  5 14:57:02 UTC 2019 - Todd R <toddrme2178@gmail.com>

- Fix spurious unit test errors.

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Fri Jan 18 10:24:44 UTC 2019 - Tomáš Chvátal <tchvatal@suse.com>

- Apply patch to fix build with new scipy:
  * lmfit-scipy.patch

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Fri Jan 18 10:19:27 UTC 2019 - Tomáš Chvátal <tchvatal@suse.com>

- Update to 0.9.12:
  * make exceptions explicit
  * use inspect.getfullargspec for Python3
  * test-suite: use pytest features, improve coverage, fix mistakes

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Thu Mar 22 04:46:08 UTC 2018 - toddrme2178@gmail.com

- Initial version

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