Accepting request 812430 from home:glaubitz:branches:devel:languages:python:numeric
- 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/*
OBS-URL: https://build.opensuse.org/request/show/812430
OBS-URL: https://build.opensuse.org/package/show/devel:languages:python:numeric/python-lmfit?expand=0&rev=1
This commit is contained in:
Tomáš Chvátal
Git OBS Bridge
commit
25ca3857f9
23
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## Default LFS
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*.7z filter=lfs diff=lfs merge=lfs -text
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*.bsp filter=lfs diff=lfs merge=lfs -text
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.osc
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lmfit-1.0.1.tar.gz
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version https://git-lfs.github.com/spec/v1
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size 258368
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python-lmfit.changes
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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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123
python-lmfit.spec
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python-lmfit.spec
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#
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# spec file for package python-lmfit
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#
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# Copyright (c) 2020 SUSE LLC.
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# upon. The license for this file, and modifications and additions to the
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# file, is the same license as for the pristine package itself (unless the
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# license for the pristine package is not an Open Source License, in which
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# case the license is the MIT License). An "Open Source License" is a
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# license that conforms to the Open Source Definition (Version 1.9)
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# published by the Open Source Initiative.
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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#
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%{?!python_module:%define python_module() python-%{**} python3-%{**}}
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%define skip_python2 1
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Name: python-lmfit
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Version: 1.0.1
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Release: 0
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Summary: Least-Squares Minimization with Bounds and Constraints
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License: MIT AND BSD-3-Clause
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URL: https://lmfit.github.io/lmfit-py/
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Source: https://files.pythonhosted.org/packages/source/l/lmfit/lmfit-%{version}.tar.gz
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BuildRequires: %{python_module setuptools}
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BuildRequires: fdupes
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BuildRequires: python-rpm-macros
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Requires: python-asteval >= 0.9.16
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Requires: python-numpy >= 1.16
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Requires: python-scipy >= 1.2
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Recommends: python-dill
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Recommends: python-emcee
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Recommends: python-matplotlib
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Recommends: python-pandas
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Recommends: python-uncertainties >= 3.0.1
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BuildArch: noarch
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# SECTION test requirements
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BuildRequires: %{python_module asteval >= 0.9.16}
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BuildRequires: %{python_module numpy >= 1.16}
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BuildRequires: %{python_module pytest}
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BuildRequires: %{python_module scipy >= 1.2}
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BuildRequires: %{python_module uncertainties >= 3.0.1}
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# /SECTION
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%python_subpackages
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%description
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A library for least-squares minimization and data fitting in
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Python. Built on top of scipy.optimize, lmfit provides a Parameter object
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which can be set as fixed or free, can have upper and/or lower bounds, or
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can be written in terms of algebraic constraints of other Parameters. The
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user writes a function to be minimized as a function of these Parameters,
|
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and the scipy.optimize methods are used to find the optimal values for the
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Parameters. The Levenberg-Marquardt (leastsq) is the default minimization
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algorithm, and provides estimated standard errors and correlations between
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varied Parameters. Other minimization methods, including Nelder-Mead's
|
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downhill simplex, Powell's method, BFGS, Sequential Least Squares, and
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others are also supported. Bounds and constraints can be placed on
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Parameters for all of these methods.
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In addition, methods for explicitly calculating confidence intervals are
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provided for exploring minmization problems where the approximation of
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estimating Parameter uncertainties from the covariance matrix is
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questionable.
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%prep
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%setup -q -n lmfit-%{version}
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sed -i -e '/^#!\//, 1d' lmfit/jsonutils.py
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%build
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%python_build
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%install
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%python_install
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%python_expand %fdupes %{buildroot}%{$python_sitelib}
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%check
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python3 -c "import sys, lmfit, numpy, scipy, asteval, uncertainties, six;print('Python: {}\n\nlmfit: {}, scipy: {}, numpy: {}, asteval: {}, uncertainties: {}, six: {}'.format(sys.version, lmfit.__version__, scipy.__version__, numpy.__version__, asteval.__version__, uncertainties.__version__, six.__version__))"
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cat << 'EOF' >> testexample.py
|
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import numpy as np
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import lmfit
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from lmfit.lineshapes import gaussian
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from lmfit.models import PseudoVoigtModel
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x = np.linspace(0, 10, 201)
|
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np.random.seed(0)
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y = gaussian(x, 10.0, 6.15, 0.8)
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y += gaussian(x, 8.0, 6.35, 1.1)
|
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y += gaussian(x, 0.25, 6.00, 7.5)
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y += np.random.normal(size=len(x), scale=0.5)
|
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# with NaN values in the input data
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y[55] = y[91] = np.nan
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mod = PseudoVoigtModel()
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params = mod.make_params(amplitude=20, center=5.5,
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sigma=1, fraction=0.25)
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params['fraction'].vary = False
|
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|
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# with propagate, should get no error, but bad results
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result = mod.fit(y, params, x=x, nan_policy='propagate')
|
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lmfit.report_fit(result)
|
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print(result.__dict__)
|
||||
EOF
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cat testexample.py
|
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python3 testexample.py
|
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||||
# We don't care about speed, and test_itercb is architecture-specific
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%pytest -k 'not speed'
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%files %{python_files}
|
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%doc README.rst THANKS.txt
|
||||
%license LICENSE
|
||||
%{python_sitelib}/*
|
||||
|
||||
%changelog
|
||||
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