CVS commit: pkgsrc/math/py-lmfit

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

Module Name:    pkgsrc
Committed By:   adam
Date:           Fri Aug  2 07:39:27 UTC 2024

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

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r1.19 -r1.20 pkgsrc/math/py-lmfit/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/py-lmfit/PLIST
cvs rdiff -u -r1.12 -r1.13 pkgsrc/math/py-lmfit/distinfo

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:1.19 pkgsrc/math/py-lmfit/Makefile:1.20
--- pkgsrc/math/py-lmfit/Makefile:1.19  Tue Aug  1 23:20:47 2023
+++ pkgsrc/math/py-lmfit/Makefile       Fri Aug  2 07:39:27 2024
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.19 2023/08/01 23:20:47 wiz Exp $
+# $NetBSD: Makefile,v 1.20 2024/08/02 07:39:27 adam Exp $
 
-DISTNAME=      lmfit-1.0.3
+DISTNAME=      lmfit-1.3.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   1
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=l/lmfit/}
 
@@ -11,16 +10,18 @@ HOMEPAGE=   https://lmfit.github.io/lmfit-
 COMMENT=       Least-squares minimization with bounds and constraints
 LICENSE=       modified-bsd
 
-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
-TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools_scm-[0-9]*:../../devel/py-setuptools_scm
-TEST_DEPENDS+= ${PYPKGPREFIX}-test-[0-9]*:../../devel/py-test
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=45:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools_scm>=6.2:../../devel/py-setuptools_scm
+TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
+DEPENDS+=      ${PYPKGPREFIX}-asteval>=1.0:../../math/py-asteval
+DEPENDS+=      ${PYPKGPREFIX}-dill>=0.3.4:../../textproc/py-dill
+DEPENDS+=      ${PYPKGPREFIX}-numpy>=1.19:../../math/py-numpy
+DEPENDS+=      ${PYPKGPREFIX}-scipy>=1.6:../../math/py-scipy
+DEPENDS+=      ${PYPKGPREFIX}-uncertainties>=3.2.2:../../math/py-uncertainties
 
 USE_LANGUAGES= # none
 
-PYTHON_VERSIONS_INCOMPATIBLE=  27 38
+PYTHON_VERSIONS_INCOMPATIBLE=  27 38 39
 
-.include "../../lang/python/egg.mk"
+.include "../../lang/python/wheel.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/math/py-lmfit/PLIST
diff -u pkgsrc/math/py-lmfit/PLIST:1.7 pkgsrc/math/py-lmfit/PLIST:1.8
--- pkgsrc/math/py-lmfit/PLIST:1.7      Sun Nov  7 11:58:47 2021
+++ pkgsrc/math/py-lmfit/PLIST  Fri Aug  2 07:39:27 2024
@@ -1,9 +1,10 @@
-@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
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+@comment $NetBSD: PLIST,v 1.8 2024/08/02 07:39:27 adam Exp $
+${PYSITELIB}/${WHEEL_INFODIR}/AUTHORS.txt
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/lmfit/__init__.py
 ${PYSITELIB}/lmfit/__init__.pyc
 ${PYSITELIB}/lmfit/__init__.pyo

Index: pkgsrc/math/py-lmfit/distinfo
diff -u pkgsrc/math/py-lmfit/distinfo:1.12 pkgsrc/math/py-lmfit/distinfo:1.13
--- pkgsrc/math/py-lmfit/distinfo:1.12  Sun Nov  7 11:58:47 2021
+++ pkgsrc/math/py-lmfit/distinfo       Fri Aug  2 07:39:27 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.12 2021/11/07 11:58:47 adam Exp $
+$NetBSD: distinfo,v 1.13 2024/08/02 07:39:27 adam Exp $
 
-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
+BLAKE2s (lmfit-1.3.2.tar.gz) = 4b693c220ecfa9f8a1d3f963684d6e4bc826d7acc699ca483c8409b97aeaa390
+SHA512 (lmfit-1.3.2.tar.gz) = 2dbba258aa14bd9bdb032cfe93086e207da5398137a06031aa1f09a0f9c35636e89488ed1bd348cdc2a5ea140df839f5cb414d9d208ac7ddda5f7f11d0c058d4
+Size (lmfit-1.3.2.tar.gz) = 623945 bytes