File support-numpy-2.patch of Package python-lmfit

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File support-numpy-2.patch of Package python-lmfit (Revision fb785471af99e99a321b9ce12e64eedd)

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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

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File support-numpy-2.patch of Package python-lmfit (Revision fb785471af99e99a321b9ce12e64eedd)

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