Merge pull request #959 from lmfit/numpy2_fixes

Numpy2 fixes

Author: newville

.pre-commit-config.yaml

@@ -2,13 +2,13 @@ exclude: 'doc/conf.py'
 
 repos:
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.2
+    rev: v3.16.0
     hooks:
     -   id: pyupgrade
         args: [--py38-plus]
 
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: check-ast
     -   id: check-builtin-literals
@@ -23,7 +23,7 @@ repos:
         args: [--remove]
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.0
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-deprecated, flake8-mutable, Flake8-pyproject]
@@ -51,14 +51,14 @@ repos:
     -   id: python-check-blanket-noqa
 
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
     -   id: codespell
         files: '.py|.rst'
         exclude: 'doc/doc_examples_to_gallery.py|.ipynb'
         # escaped characters currently do not work correctly
         # so \nnumber is considered a spelling error....
-        args: ["-L nnumber", "-L mone"]
+        args: ["-L nnumber", "-L mone", "-L assertIn", "-L efine",]
 
 -   repo: https://github.com/asottile/yesqa
     rev: v1.5.0

azure-pipelines.yml

@@ -82,7 +82,7 @@ stages:
           displayName: 'Install dependencies'
         - script: |
             python -m pip install --upgrade build pip wheel
-            python -m pip install asteval==0.9.28 numpy==1.23.0 scipy==1.8.0 uncertainties==3.1.4
+            python -m pip install asteval==1.0 numpy==1.23.0 scipy==1.8.0 uncertainties==3.2.2
           displayName: 'Install minimum required version of dependencies'
         - script: |
             python -m build
@@ -256,7 +256,7 @@ stages:
           displayName: 'Install build, pip, setuptools, wheel, pybind11, and cython'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            export numpy_version=1.26.4
+            export numpy_version=2.0.0
             wget https://github.com/numpy/numpy/releases/download/v${numpy_version}/numpy-${numpy_version}.tar.gz
             tar xzvf numpy-${numpy_version}.tar.gz
             cd numpy-${numpy_version}
@@ -269,7 +269,7 @@ stages:
           displayName: 'Install pythran'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            export scipy_version=1.13.0
+            export scipy_version=1.14.0
             wget https://github.com/scipy/scipy/releases/download/v${scipy_version}/scipy-${scipy_version}.tar.gz
             tar xzvf scipy-${scipy_version}.tar.gz
             cd scipy-${scipy_version}

doc/installation.rst

@@ -38,8 +38,8 @@ Lmfit works with `Python`_ versions 3.8 and higher. Version
 Lmfit requires the following Python packages, with versions given:
    * `NumPy`_ version 1.23 or higher.
    * `SciPy`_ version 1.8 or higher.
-   * `asteval`_ version 0.9.28 or higher.
-   * `uncertainties`_ version 3.1.4 or higher.
+   * `asteval`_ version 1.0 or higher.
+   * `uncertainties`_ version 3.2.2 or higher.
    * `dill`_ version 0.3.4 or higher.
 
 All of these are readily available on PyPI, and are installed

lmfit/parameter.py

@@ -181,9 +181,8 @@ 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()
         unique_symbols = {key: deepcopy(self._asteval.symtable[key])
-                          for key in sym_unique}
+                          for key in self._asteval.user_defined_symbols()}
 
         return self.__class__, (), {'unique_symbols': unique_symbols,
                                     'params': params}
@@ -567,9 +566,8 @@ def dumps(self, **kws):
 
         """
         params = [p.__getstate__() for p in self.values()]
-        sym_unique = self._asteval.user_defined_symbols()
         unique_symbols = {key: encode4js(deepcopy(self._asteval.symtable[key]))
-                          for key in sym_unique}
+                          for key in self._asteval.user_defined_symbols()}
         return json.dumps({'unique_symbols': unique_symbols,
                            'params': params}, **kws)
 

pyproject.toml

@@ -6,11 +6,11 @@ build-backend = "setuptools.build_meta"
 name = "lmfit"
 dynamic = ["version"]
 dependencies = [
-    "asteval>=0.9.28",
+    "asteval>=1.0",
     "numpy>=1.19",
     "scipy>=1.6",
-    "uncertainties>=3.1.4",
-    "dill>=0.3.4"
+    "uncertainties>=3.2.2",
+    "dill>=0.3.4",
 ]
 requires-python = ">= 3.8"
 authors = [
@@ -110,7 +110,7 @@ force_sort_within_sections = "True"
 [tool.rstcheck]
 report_level = "WARNING"
 ignore_substitutions = [
-    "release"
+    "release",
 ]
 ignore_roles = [
     "scipydoc",

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