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next ; commitid rJaHzNzXdOdDIwmz; desc @@ 1.10 log @py-lmfit: updated to 1.3.4 1.3.4 Mostly maintenance and small bug fixes: capture and ignore std_dev=0 warnings from uncertainties package better ensure that parameter values and sterr are floats, not np.floats fix Doniach formula in docstring add bose and fermi lineshapes, and BoseModel and FermiModel (with tests) remove deprecated disp argument for ampgo fix typos in README.rst fix typos in doc update to latest SciPy/NumPy version update pre-commit and CI hooks update zenodo link several fixes for deprecations and test failures do not test for warnings from upstream code that might change or be suppressed or altered update license name for PyPI compatibiilty @ text @@@comment $NetBSD: PLIST,v 1.9 2025/04/15 16:31:38 adam Exp $ ${PYSITELIB}/${WHEEL_INFODIR}/METADATA ${PYSITELIB}/${WHEEL_INFODIR}/RECORD ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL ${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE ${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt ${PYSITELIB}/lmfit/__init__.py ${PYSITELIB}/lmfit/__init__.pyc ${PYSITELIB}/lmfit/__init__.pyo ${PYSITELIB}/lmfit/_ampgo.py ${PYSITELIB}/lmfit/_ampgo.pyc ${PYSITELIB}/lmfit/_ampgo.pyo ${PYSITELIB}/lmfit/confidence.py ${PYSITELIB}/lmfit/confidence.pyc ${PYSITELIB}/lmfit/confidence.pyo ${PYSITELIB}/lmfit/jsonutils.py ${PYSITELIB}/lmfit/jsonutils.pyc ${PYSITELIB}/lmfit/jsonutils.pyo ${PYSITELIB}/lmfit/lineshapes.py ${PYSITELIB}/lmfit/lineshapes.pyc ${PYSITELIB}/lmfit/lineshapes.pyo ${PYSITELIB}/lmfit/minimizer.py ${PYSITELIB}/lmfit/minimizer.pyc ${PYSITELIB}/lmfit/minimizer.pyo ${PYSITELIB}/lmfit/model.py ${PYSITELIB}/lmfit/model.pyc ${PYSITELIB}/lmfit/model.pyo ${PYSITELIB}/lmfit/models.py ${PYSITELIB}/lmfit/models.pyc ${PYSITELIB}/lmfit/models.pyo ${PYSITELIB}/lmfit/parameter.py ${PYSITELIB}/lmfit/parameter.pyc ${PYSITELIB}/lmfit/parameter.pyo ${PYSITELIB}/lmfit/printfuncs.py ${PYSITELIB}/lmfit/printfuncs.pyc ${PYSITELIB}/lmfit/printfuncs.pyo ${PYSITELIB}/lmfit/version.py ${PYSITELIB}/lmfit/version.pyc ${PYSITELIB}/lmfit/version.pyo @ 1.9 log @Fix PLIST after py-setuptools update; bump depends and revision @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.8 2024/08/02 07:39:27 adam Exp $ a4 1 ${PYSITELIB}/${WHEEL_INFODIR}/licenses/AUTHORS.txt @ 1.8 log @py-lmfit: updated to 1.3.2 Version 1.3.2 Release Notes (July 19, 2024) ==================================================== Fixes: - fix typo in restoring a ``_buildmodel`` dict - fixes for Numpy2 support - ensure that correct initial params are used when re-fitting a ModeRresult - make sure that CompositeModels cannot have a prefix Build, Maintenance: - update pre-commit hooks, adding codespell exceptions - update to latest SciPy/NumPy versions, including dependency versions for NumPy 2. - now require asteval>=1.0 and uncertainties>=3.2.2 Version 1.3.1 Release Notes (April 19, 2024) ==================================================== Mostly fixes for bugs introduced in 1.3.0 - 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, add test - better allow (or re-allow) Model function independent variables / keyword argumentss to be given non-default values at model creation time - add ``form`` as independent variable for builtin Step, Rectangle, Thermal Distribution models. - use a copy of ``sys.modules`` when iterating over it. - use ``Model._reprstring(long=True)`` for model ``Model.__repr__()``. Version 1.3.0 Release Notes (April 4, 2024) =========================================== 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: - restore best-fit parameter values for high accuracy values of constrained values - improvement to Model for the difference between Parameter, "independent variable", and "option". With this change, keyword arguments to model functions with non-numerice default values such as ``do_thing=True``, or ``form='linear'`` has those arguments become clearly identified as independent variables,and use the provided values as default values. - better saving/loading saved states of Model now use dill, have several cleanups, and are now versioned for future-proofing. Also, propagate funcdets for Parameters when loading a Model. - in the TNC method, ``maxfun`` is used instead of ``maxiter``. - fix bug calculating r-squared for fits with weights - fix bug in ``modelresult.eval_uncertainty()`` after ``load_modelresult()`` - use StringIO for ``pandas.read_json``. - add test for MinimizerResult.uvars after successful fit - adding an example using basinhopping, can take other methods as command-line argument Maintenance/Deprecations: - drop support for Python 3.7 that reached EOL on 2023-06-27 - 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. - build switchded to use pyproject.toml - fix broken links in Examples gallery - fix intersphinx mapping to scipy docs. @ text @d1 1 a1 3 @@comment $NetBSD: PLIST,v 1.7 2021/11/07 11:58:47 adam Exp $ ${PYSITELIB}/${WHEEL_INFODIR}/AUTHORS.txt ${PYSITELIB}/${WHEEL_INFODIR}/LICENSE d5 2 @ 1.7 log @py-lmfit: updated to 1.0.3 Version 1.0.3 Release Notes (October 14, 2021) ============================================== Potentially breaking change: - argument ``x`` is now required for the ``guess`` method of Models 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 - 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 @d1 7 a7 6 @@comment $NetBSD: PLIST,v 1.6 2020/05/13 15:36:27 adam Exp $ ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt ${PYSITELIB}/${EGG_INFODIR}/requires.txt ${PYSITELIB}/${EGG_INFODIR}/top_level.txt @ 1.6 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 @@comment $NetBSD: PLIST,v 1.5 2018/07/13 06:22:35 adam Exp $ a12 3 ${PYSITELIB}/lmfit/_version.py ${PYSITELIB}/lmfit/_version.pyc ${PYSITELIB}/lmfit/_version.pyo d37 3 @ 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 @@comment $NetBSD: PLIST,v 1.4 2018/04/14 05:32:22 adam Exp $ a39 9 ${PYSITELIB}/lmfit/ui/__init__.py ${PYSITELIB}/lmfit/ui/__init__.pyc ${PYSITELIB}/lmfit/ui/__init__.pyo ${PYSITELIB}/lmfit/ui/basefitter.py ${PYSITELIB}/lmfit/ui/basefitter.pyc ${PYSITELIB}/lmfit/ui/basefitter.pyo ${PYSITELIB}/lmfit/ui/ipy_fitter.py ${PYSITELIB}/lmfit/ui/ipy_fitter.pyc ${PYSITELIB}/lmfit/ui/ipy_fitter.pyo @ 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 @@comment $NetBSD: PLIST,v 1.3 2018/02/27 06:40:07 adam Exp $ d10 3 a48 6 ${PYSITELIB}/lmfit/uncertainties/__init__.py ${PYSITELIB}/lmfit/uncertainties/__init__.pyc ${PYSITELIB}/lmfit/uncertainties/__init__.pyo ${PYSITELIB}/lmfit/uncertainties/umath.py ${PYSITELIB}/lmfit/uncertainties/umath.pyc ${PYSITELIB}/lmfit/uncertainties/umath.pyo @ 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 @@comment $NetBSD: PLIST,v 1.2 2017/08/31 08:27:42 prlw1 Exp $ a12 6 ${PYSITELIB}/lmfit/asteval.py ${PYSITELIB}/lmfit/asteval.pyc ${PYSITELIB}/lmfit/asteval.pyo ${PYSITELIB}/lmfit/astutils.py ${PYSITELIB}/lmfit/astutils.pyc ${PYSITELIB}/lmfit/astutils.pyo @ 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 @@comment $NetBSD: PLIST,v 1.1 2016/09/16 15:20:31 prlw1 Exp $ d22 3 @ 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 @@comment $NetBSD$ d10 1 a10 2 ${PYSITELIB}/lmfit/_differentialevolution.pyc ${PYSITELIB}/lmfit/_differentialevolution.pyo d13 1 d16 1 d19 1 d22 1 d25 1 d28 1 d31 1 d34 1 a34 2 ${PYSITELIB}/lmfit/ordereddict.pyc ${PYSITELIB}/lmfit/ordereddict.pyo d37 1 a39 12 ${PYSITELIB}/lmfit/_differentialevolution.py ${PYSITELIB}/lmfit/_version.py ${PYSITELIB}/lmfit/asteval.py ${PYSITELIB}/lmfit/astutils.py ${PYSITELIB}/lmfit/confidence.py ${PYSITELIB}/lmfit/lineshapes.py ${PYSITELIB}/lmfit/minimizer.py ${PYSITELIB}/lmfit/model.py ${PYSITELIB}/lmfit/models.py ${PYSITELIB}/lmfit/ordereddict.py ${PYSITELIB}/lmfit/parameter.py ${PYSITELIB}/lmfit/printfuncs.py d43 1 d46 1 a48 2 ${PYSITELIB}/lmfit/ui/basefitter.py ${PYSITELIB}/lmfit/ui/ipy_fitter.py d52 1 a54 1 ${PYSITELIB}/lmfit/uncertainties/umath.py @