CVS commit: pkgsrc/math/py-lmfit

["Adam Ciarcinski" <adam%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   adam
Date:           Sun Nov  7 11:58:47 UTC 2021

Modified Files:
        pkgsrc/math/py-lmfit: Makefile PLIST distinfo

Log Message:
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


To generate a diff of this commit:
cvs rdiff -u -r1.11 -r1.12 pkgsrc/math/py-lmfit/Makefile \
    pkgsrc/math/py-lmfit/distinfo
cvs rdiff -u -r1.6 -r1.7 pkgsrc/math/py-lmfit/PLIST

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/py-lmfit/Makefile
diff -u pkgsrc/math/py-lmfit/Makefile:1.11 pkgsrc/math/py-lmfit/Makefile:1.12
--- pkgsrc/math/py-lmfit/Makefile:1.11  Fri Apr  9 14:41:35 2021
+++ pkgsrc/math/py-lmfit/Makefile       Sun Nov  7 11:58:47 2021
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.11 2021/04/09 14:41:35 tnn Exp $
+# $NetBSD: Makefile,v 1.12 2021/11/07 11:58:47 adam Exp $
 
-DISTNAME=      lmfit-1.0.1
+DISTNAME=      lmfit-1.0.3
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=l/lmfit/}
@@ -10,14 +10,15 @@ HOMEPAGE=   https://lmfit.github.io/lmfit-
 COMMENT=       Least-squares minimization with bounds and constraints
 LICENSE=       modified-bsd
 
-DEPENDS+=      ${PYPKGPREFIX}-asteval>=0.9.16:../../math/py-asteval
-DEPENDS+=      ${PYPKGPREFIX}-numpy>=1.16:../../math/py-numpy
-DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.2:../../math/py-scipy
+DEPENDS+=      ${PYPKGPREFIX}-asteval>=0.9.22:../../math/py-asteval
+DEPENDS+=      ${PYPKGPREFIX}-numpy>=1.18:../../math/py-numpy
+DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.4:../../math/py-scipy
 DEPENDS+=      ${PYPKGPREFIX}-uncertainties>=3.0.1:../../math/py-uncertainties
+TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test
 
 USE_LANGUAGES= # none
 
-PYTHON_VERSIONS_INCOMPATIBLE=  36 27   # py-scipy
+PYTHON_VERSIONS_INCOMPATIBLE=  27 36   # py-scipy
 
 .include "../../lang/python/egg.mk"
 .include "../../mk/bsd.pkg.mk"
Index: pkgsrc/math/py-lmfit/distinfo
diff -u pkgsrc/math/py-lmfit/distinfo:1.11 pkgsrc/math/py-lmfit/distinfo:1.12
--- pkgsrc/math/py-lmfit/distinfo:1.11  Tue Oct 26 10:56:02 2021
+++ pkgsrc/math/py-lmfit/distinfo       Sun Nov  7 11:58:47 2021
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.11 2021/10/26 10:56:02 nia Exp $
+$NetBSD: distinfo,v 1.12 2021/11/07 11:58:47 adam Exp $
 
-BLAKE2s (lmfit-1.0.1.tar.gz) = 5b2b858893b10255c1c5966cb029e8958eeacd0cc123647c7fdfbccba9e24570
-SHA512 (lmfit-1.0.1.tar.gz) = 1ae3e2cb25625a9b24c261d81c8f1ba0389266724581762f6e0a96140c84e43acd527ab1b83b862bf7b3b4c0b1b9755ee38d0c52e63fe89ea41f2d010b1e5c0d
-Size (lmfit-1.0.1.tar.gz) = 258368 bytes
+BLAKE2s (lmfit-1.0.3.tar.gz) = af27a0fd80fb6f26ca92b13ec72f3eca1482e5591e14f4a39f3198696c112e1d
+SHA512 (lmfit-1.0.3.tar.gz) = 33febdd68104bb41ca379a8acd03a8bb985ba8785d607ab110b63bc7b3b39b9d95161a683fe015613bee6d99100ede82d1f3574515a6bfb9160300a5791fcc55
+Size (lmfit-1.0.3.tar.gz) = 292475 bytes

Index: pkgsrc/math/py-lmfit/PLIST
diff -u pkgsrc/math/py-lmfit/PLIST:1.6 pkgsrc/math/py-lmfit/PLIST:1.7
--- pkgsrc/math/py-lmfit/PLIST:1.6      Wed May 13 15:36:27 2020
+++ pkgsrc/math/py-lmfit/PLIST  Sun Nov  7 11:58:47 2021
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.6 2020/05/13 15:36:27 adam Exp $
+@comment $NetBSD: PLIST,v 1.7 2021/11/07 11:58:47 adam Exp $
 ${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
 ${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
 ${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
@@ -10,9 +10,6 @@ ${PYSITELIB}/lmfit/__init__.pyo
 ${PYSITELIB}/lmfit/_ampgo.py
 ${PYSITELIB}/lmfit/_ampgo.pyc
 ${PYSITELIB}/lmfit/_ampgo.pyo
-${PYSITELIB}/lmfit/_version.py
-${PYSITELIB}/lmfit/_version.pyc
-${PYSITELIB}/lmfit/_version.pyo
 ${PYSITELIB}/lmfit/confidence.py
 ${PYSITELIB}/lmfit/confidence.pyc
 ${PYSITELIB}/lmfit/confidence.pyo
@@ -37,3 +34,6 @@ ${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