File lmfit-pr965-asteval.patch of Package python-lmfit

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File lmfit-pr965-asteval.patch of Package python-lmfit (Revision 37a1078cf69d592a519c9382024799dc)

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From e62b1784e7516f543402c013cfd532d6003aa859 Mon Sep 17 00:00:00 2001
From: Matthew Newville <newville@cars.uchicago.edu>
Date: Sun, 4 Aug 2024 20:34:44 -0500
Subject: [PATCH 1/9] BUG: fix typo in 'create_uvars' method

Closes: #962
---
 lmfit/parameter.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lmfit/parameter.py b/lmfit/parameter.py
index a7ec9a65..243d4227 100644
--- a/lmfit/parameter.py
+++ b/lmfit/parameter.py
@@ -515,9 +515,9 @@ def create_uvars(self, covar=None):
                 vindex += 1
                 vnames.append(par.name)
                 vbest.append(par.value)
-                if getattr(par, 'sdterr', None) is None and covar is not None:
+                if getattr(par, 'stderr', None) is None and covar is not None:
                     par.stderr = sqrt(covar[vindex, vindex])
-            uvars[par.name] = ufloat(par.value, getattr(par, 'sdterr', 0.0))
+            uvars[par.name] = ufloat(par.value, getattr(par, 'stderr', 0.0))
 
         corr_uvars = None
         if covar is not None:

From 7fd4e42e84b3ab8f0bdc05274aa270d4ded765bf Mon Sep 17 00:00:00 2001
From: Matthew Newville <newville@cars.uchicago.edu>
Date: Sun, 11 Aug 2024 12:40:21 -0500
Subject: [PATCH 2/9] MAINT: 'uncertainties' fails if 'stderr' is None, so set
 to zero

---
 lmfit/parameter.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lmfit/parameter.py b/lmfit/parameter.py
index 243d4227..cd6d9626 100644
--- a/lmfit/parameter.py
+++ b/lmfit/parameter.py
@@ -517,7 +517,10 @@ def create_uvars(self, covar=None):
                 vbest.append(par.value)
                 if getattr(par, 'stderr', None) is None and covar is not None:
                     par.stderr = sqrt(covar[vindex, vindex])
-            uvars[par.name] = ufloat(par.value, getattr(par, 'stderr', 0.0))
+            stderr = getattr(par, 'stderr', 0.0)
+            if stderr is None:
+                stderr = 0.0
+            uvars[par.name] = ufloat(par.value, stderr)
 
         corr_uvars = None
         if covar is not None:

From b812b4731805f9d85d717aff0ad34031c747d1d4 Mon Sep 17 00:00:00 2001
From: Matthew Newville <newville@cars.uchicago.edu>
Date: Sun, 11 Aug 2024 12:44:30 -0500
Subject: [PATCH 3/9] MAINT: asteval no longer raises NameError to Python

- so we suppress 'asteval' expections to stderr and look for them when creating parameters
---
 lmfit/parameter.py       | 25 +++++++++++++++++++++++--
 tests/test_parameters.py |  3 +--
 2 files changed, 24 insertions(+), 4 deletions(-)

diff --git a/lmfit/parameter.py b/lmfit/parameter.py
index cd6d9626..77ba882c 100644
--- a/lmfit/parameter.py
+++ b/lmfit/parameter.py
@@ -27,6 +27,20 @@ def check_ast_errors(expr_eval):
         expr_eval.raise_exception(None)
 
 
+class Writer:
+    """Replace 'stdout' and 'stderr' for asteval."""
+    def __init__(self, **kws):
+        self.messages = []
+        for k, v in kws.items():
+            setattr(self, k, v)
+
+    def write(self, msg):
+        """Internal writer."""
+        o = msg.strip()
+        if len(o) > 0:
+            self.messages.append(msg)
+
+
 def asteval_with_uncertainties(*vals, obj=None, pars=None, names=None, **kwargs):
     """Calculate object value, given values for variables.
 
@@ -76,8 +90,9 @@ def __init__(self, usersyms=None):
 
         """
         super().__init__(self)
-
-        self._asteval = Interpreter()
+        self._ast_msgs = Writer()
+        self._asteval = Interpreter(writer=self._ast_msgs,
+                                    err_writer=self._ast_msgs)
 
         _syms = {}
         _syms.update(SCIPY_FUNCTIONS)
@@ -86,6 +101,9 @@ def __init__(self, usersyms=None):
         for key, val in _syms.items():
             self._asteval.symtable[key] = val
 
+    def _writer(self, msg):
+        self._asteval_msgs.append(msg)
+
     def copy(self):
         """Parameters.copy() should always be a deepcopy."""
         return self.__deepcopy__(None)
@@ -433,6 +451,9 @@ def add(self, name, value=None, vary=True, min=-inf, max=inf, expr=None,
             self.__setitem__(name, Parameter(value=value, name=name, vary=vary,
                                              min=min, max=max, expr=expr,
                                              brute_step=brute_step))
+        if len(self._asteval.error) > 0:
+            err = self._asteval.error[0]
+            raise err.exc(err.msg)
 
     def add_many(self, *parlist):
         """Add many parameters, using a sequence of tuples.
diff --git a/tests/test_parameters.py b/tests/test_parameters.py
index 7e12b1f0..998341e3 100644
--- a/tests/test_parameters.py
+++ b/tests/test_parameters.py
@@ -39,8 +39,7 @@ def assert_parameter_attributes(par, expected):
 def test_check_ast_errors():
     """Assert that an exception is raised upon AST errors."""
     pars = lmfit.Parameters()
-
-    msg = r"at expr='<_?ast.Module object at"
+    msg = "name 'par2' is not defined"
     with pytest.raises(NameError, match=msg):
         pars.add('par1', expr='2.0*par2')

From 05fb78e8ebab8d3cc3360f3eb1ee852c8f4a7528 Mon Sep 17 00:00:00 2001
From: reneeotten <reneeotten@users.noreply.github.com>
Date: Fri, 16 Aug 2024 10:50:54 -0400
Subject: [PATCH 4/9] DOC: tweak 'sphinx-gallery' settings

---
 doc/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/conf.py b/doc/conf.py
index 1a36156b..972b552b 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -167,7 +167,7 @@
     'examples_dirs': '../examples',
     'gallery_dirs': 'examples',
     'filename_pattern': r'(\\|/)documentation|(\\|/)example_',
-    'ignore_pattern': r'(\\|/)doc_',
+    'ignore_pattern': 'doc_',
     'ignore_repr_types': r'matplotlib',
     'image_srcset': ["3x"],
 }

From 07d65bf8ebcf013e7b47ce0c4930aa39d7cd2cc3 Mon Sep 17 00:00:00 2001
From: reneeotten <reneeotten@users.noreply.github.com>
Date: Fri, 16 Aug 2024 10:51:28 -0400
Subject: [PATCH 5/9] MAINT: update pre-commit hooks

---
 .pre-commit-config.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ee53e906..bad4bf3f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ exclude: 'doc/conf.py'
 
 repos:
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.16.0
+    rev: v3.17.0
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
@@ -12,18 +12,18 @@ repos:
     hooks:
     -   id: check-ast
     -   id: check-builtin-literals
+    -   id: check-docstring-first
     -   id: check-case-conflict
     -   id: check-merge-conflict
     -   id: check-toml
+    -   id: check-yaml
     -   id: debug-statements
     -   id: end-of-file-fixer
     -   id: mixed-line-ending
     -   id: trailing-whitespace
-    -   id: fix-encoding-pragma
-        args: [--remove]
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: 7.1.0
+    rev: 7.1.1
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-deprecated, flake8-mutable, Flake8-pyproject]

From 805263ddfac4f877dfd2c4e834155bd274020e3d Mon Sep 17 00:00:00 2001
From: reneeotten <reneeotten@users.noreply.github.com>
Date: Fri, 16 Aug 2024 10:53:22 -0400
Subject: [PATCH 6/9] CI: update to latest NumPy version

---
 azure-pipelines.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 314d8704..01bc9d6e 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -256,7 +256,7 @@ stages:
           displayName: 'Install build, pip, setuptools, wheel, pybind11, and cython'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            export numpy_version=2.0.0
+            export numpy_version=2.0.1
             wget https://github.com/numpy/numpy/releases/download/v${numpy_version}/numpy-${numpy_version}.tar.gz
             tar xzvf numpy-${numpy_version}.tar.gz
             cd numpy-${numpy_version}

From 16f8cbd176ed5b9f5e1ac6a369c7bd75dbd5046a Mon Sep 17 00:00:00 2001
From: reneeotten <reneeotten@users.noreply.github.com>
Date: Fri, 16 Aug 2024 12:39:05 -0400
Subject: [PATCH 7/9] BLD: remove redundant wheel dependency

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e41e844b..9578466d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
+requires = ["setuptools>=45", "setuptools_scm>=6.2"]
 build-backend = "setuptools.build_meta"
 
 [project]

From d6810a558887956f598d58d9876be8fe96090d6d Mon Sep 17 00:00:00 2001
From: reneeotten <reneeotten@users.noreply.github.com>
Date: Fri, 16 Aug 2024 18:06:34 -0400
Subject: [PATCH 8/9] DOC: update names of the documentation examples in
 Gallery

- also rename the file doc_uvars_params.py to follow the usual naming
  conventions
---
 doc/doc_examples_to_gallery.py                      | 13 ++++++++-----
 doc/model.rst                                       |  2 +-
 ...{doc_uvars_params.py => doc_parameters_uvars.py} |  4 ++--
 3 files changed, 11 insertions(+), 8 deletions(-)
 rename examples/{doc_uvars_params.py => doc_parameters_uvars.py} (96%)

diff --git a/doc/doc_examples_to_gallery.py b/doc/doc_examples_to_gallery.py
index 4cfeb5bc..49695ffd 100755
--- a/doc/doc_examples_to_gallery.py
+++ b/doc/doc_examples_to_gallery.py
@@ -5,7 +5,7 @@
 
 - create a "documentation" directory within "examples"
 - add a README.txt file
-- copy the examples from the documentation, bu remove the "doc_" from the
+- copy the examples from the documentation, removing the "doc_" from the
    filename
 - add the required docstring to the files for proper rendering
 - copy the data files
@@ -46,12 +46,15 @@ def copy_data_files(src_dir, dest_dir):
 )
 
 for fn in files:
+    sname = fn.name[4:]
+    lmfit_class, *description = sname[:-3].split('_')
+    gallery_name = f"{lmfit_class.capitalize()} - {' '.join(description)}"
 
     script_text = fn.read_text()
 
-    gallery_file = examples_documentation_dir / fn.name[4:]
-    msg = ""  # add optional message f
-    gallery_file.write_text(f'"""\n{fn.name}\n{"=" * len(fn.name)}\n\n'
+    gallery_file = examples_documentation_dir / sname
+    msg = ""  # add optional message
+    gallery_file.write_text(f'"""\n{gallery_name}\n{"=" * len(gallery_name)}\n\n'
                             f'{msg}\n"""\n{script_text}')
 
     # make sure the saved Models and ModelResult are available
@@ -67,5 +70,5 @@ def copy_data_files(src_dir, dest_dir):
 
 os.chdir(doc_dir)
 
-# # data files for the other Gallery examples
+# data files for the other Gallery examples
 copy_data_files(examples_documentation_dir, doc_dir)
diff --git a/doc/model.rst b/doc/model.rst
index 5c8ae340..e5d6506a 100644
--- a/doc/model.rst
+++ b/doc/model.rst
@@ -1166,7 +1166,7 @@ that taking correlations between Parameters into account when performing
 calculations can have a noticeable influence on the resulting uncertainties.
 
 
-.. jupyter-execute:: ../examples/doc_uvars_params.py
+.. jupyter-execute:: ../examples/doc_parameters_uvars.py
 
 
 Note that the :meth:`Model.post_fit` does not need to be limited to this
diff --git a/examples/doc_uvars_params.py b/examples/doc_parameters_uvars.py
similarity index 96%
rename from examples/doc_uvars_params.py
rename to examples/doc_parameters_uvars.py
index 124c3024..1c4f2da8 100644
--- a/examples/doc_uvars_params.py
+++ b/examples/doc_parameters_uvars.py
@@ -1,4 +1,4 @@
-# <examples/doc_uvars_params.py>
+# <examples/doc_parameters_uvars.py>
 import numpy as np
 
 from lmfit.models import ExponentialModel, GaussianModel
@@ -67,4 +67,4 @@ def post_fit(result):
 
 out = mod.fit(y, pars, x=x)
 print(out.fit_report(min_correl=0.5))
-# <end examples/doc_uvars_params.py>
+# <end examples/doc_parameters_uvars.py>

From ff436c270d07433a7ae404fe76bc9c627b4edc3f Mon Sep 17 00:00:00 2001
From: reneeotten <reneeotten@users.noreply.github.com>
Date: Fri, 16 Aug 2024 22:02:40 -0400
Subject: [PATCH 9/9] BLD: remove numexpr dependency (again)

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9578466d..cacdb8a4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -59,7 +59,6 @@ doc = [
     "matplotlib",
     "numdifftools",
     "pandas",
-    "numexpr", # note: Pandas appears to need numexpr to build our docs
     "Pillow",
     "pycairo;platform_system=='Windows'",
     "Sphinx",

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File lmfit-pr965-asteval.patch of Package python-lmfit (Revision 37a1078cf69d592a519c9382024799dc)

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