Accepting request 1186990 from devel:languages:python:numeric

Automatic submission by obs-autosubmit

OBS-URL: https://build.opensuse.org/request/show/1186990
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/python-lmfit?expand=0&rev=6

lmfit-1.2.2.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:044a052a11a61da0576274504c17eb7e2803b41128e25821e96632207f23c88c
-size 336346

lmfit-1.3.1.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bc386244adbd10ef1a2a2c4f9d17b3def905552c0a64aef854f0ad46cc309cc5
+size 629917

python-lmfit.changes

@@ -1,3 +1,42 @@
+-------------------------------------------------------------------
+Fri Jul  5 03:01:53 UTC 2024 - Steve Kowalik <steven.kowalik@suse.com>
+
+- Update to 1.3.1:
+  * 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:
+    + 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
+    + better allow (or re-allow) Model function independent variables / keyword
+      arguments to be given non-default values at model creation time
+    + add form as independent variable for builtin Step, Rectangle, Thermal
+      Distribution models.
+    + use Model._reprstring(long=True) for model Model.__repr__().
+    + restore best-fit parameter values for high accuracy values of constrained
+      values
+    + improvement to Model for the difference between Parameter, "independent
+      variable", and "option".
+    + better saving/loading saved states of Model now use dill, have several
+      cleanups, and are now versioned for future-proofing.
+    + fix bug calculating r-squared for fits with weights
+    + fix bug in modelresult.eval_uncertainty() after load_modelresult()
+    + add test for MinimizerResult.uvars after successful fit
+  * Maintenance/Deprecations:
+    + drop support for Python 3.7
+    + 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
+- Switch to autosetup macro.
+- Add patch support-numpy-2.patch:
+  * Support numpy 2.0 more thoroughly.
+
 -------------------------------------------------------------------
 Mon Aug 21 10:32:37 UTC 2023 - Markéta Machová <mmachova@suse.com>
 

python-lmfit.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package python-lmfit
 #
-# Copyright (c) 2023 SUSE LLC
+# Copyright (c) 2024 SUSE LLC
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -17,13 +17,15 @@
 
 
 Name:           python-lmfit
-Version:        1.2.2
+Version:        1.3.1
 Release:        0
 Summary:        Least-Squares Minimization with Bounds and Constraints
 License:        BSD-3-Clause AND MIT
 URL:            https://lmfit.github.io/lmfit-py/
 Source:         https://files.pythonhosted.org/packages/source/l/lmfit/lmfit-%{version}.tar.gz
-BuildRequires:  %{python_module base >= 3.7}
+# PATCH-FIX-UPSTREAM gh#lmfit/lmfit-py#959
+Patch0:         support-numpy-2.patch
+BuildRequires:  %{python_module base >= 3.8}
 BuildRequires:  %{python_module pip}
 BuildRequires:  %{python_module setuptools_scm}
 BuildRequires:  %{python_module setuptools}
@@ -31,19 +33,22 @@ BuildRequires:  %{python_module wheel}
 BuildRequires:  fdupes
 BuildRequires:  python-rpm-macros
 Requires:       python-asteval >= 0.9.28
-Requires:       python-numpy >= 1.19
+Requires:       python-dill >= 0.3.4
-Requires:       python-scipy >= 1.6
+Requires:       python-numpy >= 1.23
+Requires:       python-scipy >= 1.8
 Requires:       python-uncertainties >= 3.1.4
-Recommends:     python-dill
 Recommends:     python-emcee
 Recommends:     python-matplotlib
 Recommends:     python-pandas
 BuildArch:      noarch
 # SECTION test requirements
 BuildRequires:  %{python_module asteval >= 0.9.28}
-BuildRequires:  %{python_module numpy >= 1.19}
+BuildRequires:  %{python_module dill >= 0.3.4}
+BuildRequires:  %{python_module flaky}
+BuildRequires:  %{python_module numpy >= 1.23}
+BuildRequires:  %{python_module pytest-cov}
 BuildRequires:  %{python_module pytest}
-BuildRequires:  %{python_module scipy >= 1.6}
+BuildRequires:  %{python_module scipy >= 1.8}
 BuildRequires:  %{python_module uncertainties >= 3.1.4}
 # /SECTION
 %python_subpackages
@@ -68,10 +73,8 @@ estimating Parameter uncertainties from the covariance matrix is
 questionable.
 
 %prep
-%setup -q -n lmfit-%{version}
+%autosetup -p1 -n lmfit-%{version}
 sed -i -e '/^#!\//, 1d' lmfit/jsonutils.py
-# only coverage related pytest flags here. remove
-sed -i '/addopts/d' setup.cfg
 
 %build
 %pyproject_wheel
@@ -97,6 +100,6 @@ fi
 %doc README.rst AUTHORS.txt
 %license LICENSE
 %{python_sitelib}/lmfit
-%{python_sitelib}/lmfit-%{version}*-info
+%{python_sitelib}/lmfit-%{version}.dist-info
 
 %changelog

support-numpy-2.patch

@@ -0,0 +1,343 @@
+From eee021f650833f0a2667315b2ab5d8351f0b1a1f Mon Sep 17 00:00:00 2001
+From: Matthew Newville <newville@cars.uchicago.edu>
+Date: Sat, 29 Jun 2024 10:27:59 -0500
+Subject: [PATCH 1/6] clean un-serializable symbols with NumPy2 that should be
+ removed from asteval
+
+---
+ lmfit/parameter.py | 31 ++++++++++++++++++++++++-------
+ pyproject.toml     |  3 ++-
+ 2 files changed, 26 insertions(+), 8 deletions(-)
+
+diff --git a/lmfit/parameter.py b/lmfit/parameter.py
+index ca9ccc72..b68584c4 100644
+--- a/lmfit/parameter.py
++++ b/lmfit/parameter.py
+@@ -5,6 +5,8 @@
+ 
+ from asteval import Interpreter, get_ast_names, valid_symbol_name
+ from numpy import arcsin, array, cos, inf, isclose, sin, sqrt
++from numpy import version as npvers
++from packaging.version import Version
+ from scipy.linalg import LinAlgError
+ import scipy.special
+ from uncertainties import correlated_values, ufloat
+@@ -21,6 +23,18 @@
+     SCIPY_FUNCTIONS[fnc_name] = getattr(scipy.special, fnc_name)
+ 
+ 
++def clean_np2_symbols(user_syms):
++    """clean symbols from self._asteval.user_defined_symbols()
++    that have been deprecated in numpy 2.0
++    This should be a short term fix, as these are removed from asteval.
++    """
++    if Version(npvers.version) > Version('1.9'):
++        for sym in ('ogrid', 'mgrid', 'c_', 'r_', 's_', 'index_exp'):
++            if sym in user_syms:
++                user_syms.remove(sym)
++    return user_syms
++
++
+ def check_ast_errors(expr_eval):
+     """Check for errors derived from asteval."""
+     if len(expr_eval.error) > 0:
+@@ -95,7 +109,8 @@ def update(self, other):
+         if not isinstance(other, Parameters):
+             raise ValueError(f"'{other}' is not a Parameters object")
+         self.add_many(*other.values())
+-        for sym in other._asteval.user_defined_symbols():
++        usersyms = clean_np2_symbols(other._asteval.user_defined_symbols())
++        for sym in usersyms:
+             self._asteval.symtable[sym] = other._asteval.symtable[sym]
+         return self
+ 
+@@ -114,7 +129,8 @@ def __deepcopy__(self, memo):
+ 
+         # find the symbols that were added by users, not during construction
+         unique_symbols = {}
+-        for key in self._asteval.user_defined_symbols():
++        usersyms = clean_np2_symbols(self._asteval.user_defined_symbols())
++        for key in usersyms:
+             try:
+                 val = deepcopy(self._asteval.symtable[key])
+                 unique_symbols[key] = val
+@@ -161,7 +177,8 @@ def __add__(self, other):
+             raise ValueError(f"'{other}' is not a Parameters object")
+         out = deepcopy(self)
+         out.add_many(*other.values())
+-        for sym in other._asteval.user_defined_symbols():
++        usersyms = clean_np2_symbols(other._asteval.user_defined_symbols())
++        for sym in usersyms:
+             if sym not in out._asteval.symtable:
+                 out._asteval.symtable[sym] = other._asteval.symtable[sym]
+         return out
+@@ -181,9 +198,9 @@ def __reduce__(self):
+         params = [self[k] for k in self]
+ 
+         # find the symbols from _asteval.symtable, that need to be remembered.
+-        sym_unique = self._asteval.user_defined_symbols()
++        usersyms = clean_np2_symbols(self._asteval.user_defined_symbols())
+         unique_symbols = {key: deepcopy(self._asteval.symtable[key])
+-                          for key in sym_unique}
++                          for key in usersyms}
+ 
+         return self.__class__, (), {'unique_symbols': unique_symbols,
+                                     'params': params}
+@@ -567,9 +584,9 @@ def dumps(self, **kws):
+ 
+         """
+         params = [p.__getstate__() for p in self.values()]
+-        sym_unique = self._asteval.user_defined_symbols()
++        usersyms = clean_np2_symbols(self._asteval.user_defined_symbols())
+         unique_symbols = {key: encode4js(deepcopy(self._asteval.symtable[key]))
+-                          for key in sym_unique}
++                          for key in usersyms}
+         return json.dumps({'unique_symbols': unique_symbols,
+                            'params': params}, **kws)
+ 
+diff --git a/pyproject.toml b/pyproject.toml
+index 623c6a2d..511e9a97 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -10,7 +10,8 @@ dependencies = [
+     "numpy>=1.19",
+     "scipy>=1.6",
+     "uncertainties>=3.1.4",
+-    "dill>=0.3.4"
++    "dill>=0.3.4",
++    "packaging",
+ ]
+ requires-python = ">= 3.8"
+ authors = [
+
+From 2a195ac6a375b34245f330f8e60824f564e086bd Mon Sep 17 00:00:00 2001
+From: Matthew Newville <newville@cars.uchicago.edu>
+Date: Sat, 29 Jun 2024 10:36:34 -0500
+Subject: [PATCH 2/6] fix numpy2 deprecation
+
+---
+ tests/test_model.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tests/test_model.py b/tests/test_model.py
+index 396ea0b1..24dfbfcd 100644
+--- a/tests/test_model.py
++++ b/tests/test_model.py
+@@ -900,7 +900,7 @@ def test_independent_var_parsing(self):
+         yatan = stepmod2.eval(pars, x=x)
+ 
+         assert (yatan-yline).std() > 0.1
+-        assert (yatan-yline).ptp() > 1.0
++        assert np.ptp(yatan-yline) > 1.0
+ 
+         voigtmod = Model(voigt)
+         assert 'x' in voigtmod.independent_vars
+
+From 48d3b5f9338312078186543044fb5d0109cec429 Mon Sep 17 00:00:00 2001
+From: Matthew Newville <newville@cars.uchicago.edu>
+Date: Sat, 29 Jun 2024 10:38:23 -0500
+Subject: [PATCH 3/6] specify numpy>=2  for latest tests
+
+---
+ azure-pipelines.yml | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/azure-pipelines.yml b/azure-pipelines.yml
+index 53c7c7f1..54f70890 100644
+--- a/azure-pipelines.yml
++++ b/azure-pipelines.yml
+@@ -139,7 +139,7 @@ stages:
+             swig libmpc-dev
+           displayName: 'Install dependencies'
+         - script: |
+-            python -m pip install --upgrade build pip setuptools wheel
++            python -m pip install --upgrade build pip setuptools wheel "numpy>=2.0"
+           displayName: 'Install latest available version of Python dependencies'
+         - script: |
+             python -m build
+@@ -183,7 +183,7 @@ stages:
+             versionSpec: '$(python.version)'
+           displayName: 'Use Python $(python.version)'
+         - script: |
+-            python -m pip install --upgrade build pip setuptools wheel
++            python -m pip install --upgrade build pip setuptools wheel "numpy>=2.0"
+           displayName: 'Install latest available version of Python dependencies'
+         - script: |
+             python -m build
+@@ -218,7 +218,7 @@ stages:
+             versionSpec: '$(python.version)'
+           displayName: 'Use Python $(python.version)'
+         - script: |
+-            python -m pip install --upgrade build pip setuptools wheel
++            python -m pip install --upgrade build pip setuptools wheel "numpy>=2.0"
+           displayName: 'Install latest available version of Python dependencies'
+         - script: |
+             python -m build
+
+From 2a40772b20e2c1c48807c6b50d36217d72472d28 Mon Sep 17 00:00:00 2001
+From: Matthew Newville <newville@cars.uchicago.edu>
+Date: Sat, 29 Jun 2024 10:55:24 -0500
+Subject: [PATCH 4/6] numpy2 not available for Python3.8
+
+---
+ azure-pipelines.yml | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/azure-pipelines.yml b/azure-pipelines.yml
+index 54f70890..98f8674b 100644
+--- a/azure-pipelines.yml
++++ b/azure-pipelines.yml
+@@ -107,13 +107,13 @@ stages:
+         - script: |
+             ./codecov -v -f "coverage.xml"
+           displayName: 'Upload to codecov.io'
+-
+ - stage: tests_latest_dependencies
+   dependsOn: check_codestyle
+   condition: succeededOrFailed()
+   jobs:
+     - job:
+       pool:
++
+         vmImage: 'ubuntu-latest'
+       strategy:
+         matrix:
+@@ -139,7 +139,7 @@ stages:
+             swig libmpc-dev
+           displayName: 'Install dependencies'
+         - script: |
+-            python -m pip install --upgrade build pip setuptools wheel "numpy>=2.0"
++            python -m pip install --upgrade build pip setuptools wheel numpy
+           displayName: 'Install latest available version of Python dependencies'
+         - script: |
+             python -m build
+
+From 4a986540dec49cc714faa726a060c5d9dda66feb Mon Sep 17 00:00:00 2001
+From: Matthew Newville <newville@cars.uchicago.edu>
+Date: Sun, 30 Jun 2024 13:46:26 -0500
+Subject: [PATCH 5/6] remove packaging, clarify when clean_np2_symbols() can be
+ removed
+
+---
+ lmfit/parameter.py | 10 +++++++---
+ pyproject.toml     |  1 -
+ 2 files changed, 7 insertions(+), 4 deletions(-)
+
+diff --git a/lmfit/parameter.py b/lmfit/parameter.py
+index b68584c4..56e37f94 100644
+--- a/lmfit/parameter.py
++++ b/lmfit/parameter.py
+@@ -6,7 +6,6 @@
+ from asteval import Interpreter, get_ast_names, valid_symbol_name
+ from numpy import arcsin, array, cos, inf, isclose, sin, sqrt
+ from numpy import version as npvers
+-from packaging.version import Version
+ from scipy.linalg import LinAlgError
+ import scipy.special
+ from uncertainties import correlated_values, ufloat
+@@ -26,9 +25,9 @@
+ def clean_np2_symbols(user_syms):
+     """clean symbols from self._asteval.user_defined_symbols()
+     that have been deprecated in numpy 2.0
+-    This should be a short term fix, as these are removed from asteval.
++    This function can be removed when asteval 0.9.33 is no longer supported
+     """
+-    if Version(npvers.version) > Version('1.9'):
++    if npvers.version.startswith('2'):
+         for sym in ('ogrid', 'mgrid', 'c_', 'r_', 's_', 'index_exp'):
+             if sym in user_syms:
+                 user_syms.remove(sym)
+@@ -109,6 +108,7 @@ def update(self, other):
+         if not isinstance(other, Parameters):
+             raise ValueError(f"'{other}' is not a Parameters object")
+         self.add_many(*other.values())
++        # FIXME: clear_np2_symbols() can be removed when asteval 0.9.33 is not supported
+         usersyms = clean_np2_symbols(other._asteval.user_defined_symbols())
+         for sym in usersyms:
+             self._asteval.symtable[sym] = other._asteval.symtable[sym]
+@@ -129,6 +129,7 @@ def __deepcopy__(self, memo):
+ 
+         # find the symbols that were added by users, not during construction
+         unique_symbols = {}
++        # FIXME: clear_np2_symbols() can be removed when asteval 0.9.33 is not supported
+         usersyms = clean_np2_symbols(self._asteval.user_defined_symbols())
+         for key in usersyms:
+             try:
+@@ -177,6 +178,7 @@ def __add__(self, other):
+             raise ValueError(f"'{other}' is not a Parameters object")
+         out = deepcopy(self)
+         out.add_many(*other.values())
++        # FIXME: clear_np2_symbols() can be removed when asteval 0.9.33 is not supported
+         usersyms = clean_np2_symbols(other._asteval.user_defined_symbols())
+         for sym in usersyms:
+             if sym not in out._asteval.symtable:
+@@ -198,6 +200,7 @@ def __reduce__(self):
+         params = [self[k] for k in self]
+ 
+         # find the symbols from _asteval.symtable, that need to be remembered.
++        # FIXME: clear_np2_symbols() can be removed when asteval 0.9.33 is not supported
+         usersyms = clean_np2_symbols(self._asteval.user_defined_symbols())
+         unique_symbols = {key: deepcopy(self._asteval.symtable[key])
+                           for key in usersyms}
+@@ -584,6 +587,7 @@ def dumps(self, **kws):
+ 
+         """
+         params = [p.__getstate__() for p in self.values()]
++        # FIXME: clear_np2_symbols() can be removed when asteval 0.9.33 is not supported
+         usersyms = clean_np2_symbols(self._asteval.user_defined_symbols())
+         unique_symbols = {key: encode4js(deepcopy(self._asteval.symtable[key]))
+                           for key in usersyms}
+diff --git a/pyproject.toml b/pyproject.toml
+index 511e9a97..a40dad96 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -11,7 +11,6 @@ dependencies = [
+     "scipy>=1.6",
+     "uncertainties>=3.1.4",
+     "dill>=0.3.4",
+-    "packaging",
+ ]
+ requires-python = ">= 3.8"
+ authors = [
+
+From 8c49b0cebef3bc1e05f6c8ccf3278f1049d8cae2 Mon Sep 17 00:00:00 2001
+From: Matthew Newville <newville@cars.uchicago.edu>
+Date: Sun, 30 Jun 2024 13:47:14 -0500
+Subject: [PATCH 6/6] revert azure pipeline to not specify numpy version for
+ most tests
+
+---
+ azure-pipelines.yml | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/azure-pipelines.yml b/azure-pipelines.yml
+index 98f8674b..03a3b132 100644
+--- a/azure-pipelines.yml
++++ b/azure-pipelines.yml
+@@ -139,7 +139,7 @@ stages:
+             swig libmpc-dev
+           displayName: 'Install dependencies'
+         - script: |
+-            python -m pip install --upgrade build pip setuptools wheel numpy
++            python -m pip install --upgrade build pip setuptools wheel
+           displayName: 'Install latest available version of Python dependencies'
+         - script: |
+             python -m build
+@@ -183,7 +183,7 @@ stages:
+             versionSpec: '$(python.version)'
+           displayName: 'Use Python $(python.version)'
+         - script: |
+-            python -m pip install --upgrade build pip setuptools wheel "numpy>=2.0"
++            python -m pip install --upgrade build pip setuptools wheel
+           displayName: 'Install latest available version of Python dependencies'
+         - script: |
+             python -m build
+@@ -218,7 +218,7 @@ stages:
+             versionSpec: '$(python.version)'
+           displayName: 'Use Python $(python.version)'
+         - script: |
+-            python -m pip install --upgrade build pip setuptools wheel "numpy>=2.0"
++            python -m pip install --upgrade build pip setuptools wheel
+           displayName: 'Install latest available version of Python dependencies'
+         - script: |
+             python -m build