.github/ISSUE_TEMPLATE/issues.md

@@ -0,0 +1,58 @@
+---
+name: Issues
+about: 'Create a bug report '
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+** DO NOT IGNORE **
+
+READ THESE INSTRUCTIONS FULLY.    If you have not submitted a GitHub Issue to lmfit before, read [this](https://github.com/lmfit/lmfit-py/blob/master/.github/CONTRIBUTING.md) first.
+
+***DO NOT USE GitHub Issues for questions, it is only for bug reports***
+
+Issues here should be concerned with errors or problems in the lmfit code.  There are other places to get support and help with using lmfit or to discuss ideas about the library. 
+
+If you **think** something is an Issue, it probably is not an Issue. If the behavior you
+want to report involves a fit that runs to completion without raising an exception but
+that gives a result that you think is incorrect, that is almost certainly not an Issue.
+
+Use the [mailing list](https://groups.google.com/group/lmfit-py) or [GitHub discussions
+page](https://github.com/lmfit/lmfit-py/discussions) for questions about lmfit or things
+you think might be problems.  We don't feel obligated to spend our free time helping
+people who do not respect our chosen work processes, so if you ignore this advice and post
+a question as a GitHub Issue anyway, it is quite likely that your Issue will be closed and
+not answered. If you have any doubt at all, do NOT submit an Issue.
+
+To submit an Issue, you MUST provide ALL of the following information.  If you delete any
+of these sections, your Issue may be closed. If you think one of the sections does not
+apply to your Issue, state that explicitly. We will probably disagree with you and insist
+that you provide that information. If we have to ask for it twice, we will expect it to be
+correct and prompt.
+
+** Description **
+Provide a short description of the issue, describe the expected outcome, and give the actual result
+
+** A Minimal, Complete, and Verifiable example **
+See, for example, https://stackoverflow.com/help/mcve on how to do this 
+
+** Fit report: **
+Paste the *full* fit report here 
+
+** Error message: **
+If any, paste the *full* error message inside a code block (starting from line Traceback) 
+
+
+
+** Version information: **
+Generate version information with this command in the Python shell and copy the output here:
+```
+import sys, lmfit, numpy, scipy, asteval, uncertainties
+print(f"Python: {sys.version}\n\nlmfit: {lmfit.__version__}, scipy: {scipy.__version__}, numpy: {numpy.__version__},"
+      f"asteval: {asteval.__version__}, uncertainties: {uncertainties.__version__}")
+```
+
+** Link(s): **
+If you started a discussion on the lmfit mailing list, discussion page, or Stack Overflow, please provide the relevant link(s)

.pre-commit-config.yaml

@@ -2,28 +2,28 @@ exclude: 'doc/conf.py'
 
 repos:
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.16.0
+    rev: v3.19.1
     hooks:
     -   id: pyupgrade
-        args: [--py38-plus]
+        args: [--py39-plus]
 
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     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]

AUTHORS.txt

@@ -55,7 +55,8 @@ Roam, Alexander Stark, Alexandre Beelen, Andrey Aristov, Nicholas Zobrist,
 Ethan Welty, Julius Zimmermann, Mark Dean, Arun Persaud, Ray Osborn, @lneuhaus,
 Marcel Stimberg, Yoshiera Huang, Leon Foks, Sebastian Weigand, Florian LB,
 Michael Hudson-Doyle, Ruben Verweij, @jedzill4, @spalato, Jens Hedegaard Nielsen,
-Martin Majli, Kristian Meyer, @azelcer, Ivan Usov, and many others.
+Martin Majli, Kristian Meyer, @azelcer, Ivan Usov, Ville Yrjänä, Timothy Warner
+and many others.
 
 The lmfit code obviously depends on, and owes a very large debt to the code
 in scipy.optimize. Several discussions on the SciPy-user and lmfit mailing

azure-pipelines.yml

@@ -14,7 +14,7 @@ stages:
       steps:
         - task: UsePythonVersion@0
           inputs:
-            versionSpec: '3.12'
+            versionSpec: '3.13'
         - script: |
             python -m pip install --upgrade build pip setuptools wheel
           displayName: 'Install Python build tools and dependencies'
@@ -43,7 +43,7 @@ stages:
       steps:
         - task: UsePythonVersion@0
           inputs:
-            versionSpec: '3.12'
+            versionSpec: '3.13'
         - script: |
             python -m pip install --upgrade build pip setuptools wheel
           displayName: 'Install Python build tools'
@@ -67,8 +67,8 @@ stages:
         vmImage: 'ubuntu-latest'
       strategy:
         matrix:
-          Python38:
-            python.version: '3.8'
+          Python39:
+            python.version: '3.9'
 
       steps:
         - task: UsePythonVersion@0
@@ -82,7 +82,7 @@ stages:
           displayName: 'Install dependencies'
         - script: |
             python -m pip install --upgrade build pip wheel
-            python -m pip install asteval==1.0 numpy==1.23.0 scipy==1.8.0 uncertainties==3.2.2
+            python -m pip install asteval==1.0 numpy==1.24.0 scipy==1.10.0 uncertainties==3.2.2
           displayName: 'Install minimum required version of dependencies'
         - script: |
             python -m build
@@ -117,8 +117,6 @@ stages:
         vmImage: 'ubuntu-latest'
       strategy:
         matrix:
-          Python38:
-            python.version: '3.8'
           Python39:
             python.version: '3.9'
           Python310:
@@ -127,6 +125,8 @@ stages:
             python.version: '3.11'
           Python312:
             python.version: '3.12'
+          Python313:
+            python.version: '3.13'
 
       steps:
         - task: UsePythonVersion@0
@@ -174,8 +174,8 @@ stages:
         vmImage: 'windows-latest'
       strategy:
         matrix:
-          Python312:
-            python.version: '3.12'
+          Python313:
+            python.version: '3.13'
 
       steps:
         - task: UsePythonVersion@0
@@ -209,8 +209,8 @@ stages:
         vmImage: 'macos-latest'
       strategy:
         matrix:
-          Python312:
-            python.version: '3.12'
+          Python313:
+            python.version: '3.13'
 
       steps:
         - task: UsePythonVersion@0
@@ -236,13 +236,13 @@ stages:
   dependsOn: check_codestyle
   condition: succeededOrFailed()
   jobs:
-    - job: Python313_dev
+    - job: Python314_dev
       pool:
         vmImage: 'ubuntu-latest'
       steps:
         - script: |
             sudo add-apt-repository ppa:deadsnakes/nightly
-            sudo apt-get update && sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-venv
+            sudo apt-get update && sudo apt-get install -y --no-install-recommends python3.14-dev python3.14-venv
           displayName: Install Python development version from the deadsnakes PPA
         - script: |
             sudo apt-get update && sudo apt-get install -yq --no-install-suggests --no-install-recommends \
@@ -251,47 +251,47 @@ stages:
           displayName: 'Install dependencies'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            python3.13 -m ensurepip --upgrade
-            pip3.13 install -U build pip setuptools wheel pybind11 cython || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.14 -m ensurepip --upgrade
+            pip3.14 install -U build pip setuptools wheel pybind11 cython || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install build, pip, setuptools, wheel, pybind11, and cython'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            export numpy_version=2.0.0
+            export numpy_version=2.2.1
             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}
-            python3.13 -m build || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
-            python3.13 -m pip install . --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.14 -m build || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.14 -m pip install . --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install latest available version of NumPy'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            pip3.13 install -U pythran || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            pip3.14 install -U pythran || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install pythran'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            export scipy_version=1.14.0
+            export scipy_version=1.14.1
             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}
-            python3.13 -m build || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
-            python3.13 -m pip install . --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.14 -m build || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.14 -m pip install . --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install latest available version of SciPy'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
             # remove numdifftools for now as it pulls in statsmodels, that wants to build with NumPy 1.14.5
-            pip3.13 install asteval uncertainties dill emcee flaky pytest pytest-cov || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            pip3.14 install asteval uncertainties dill emcee flaky pytest pytest-cov || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install latest available version of Python dependencies'
         - script: |
-            python3.13 -m build
-            python3.13 -m pip install '.[test]' --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.14 -m build
+            python3.14 -m pip install '.[test]' --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Build wheel/sdist and install lmfit'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            pip3.13 list || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            pip3.14 list || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'List installed Python packages'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            pip3.13 install pytest-azurepipelines
+            pip3.14 install pytest-azurepipelines
             cd $(Agent.BuildDirectory)/s/tests
             pytest || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Run test-suite'

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"],
 }

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)

doc/faq.rst

@@ -92,7 +92,11 @@ class, which are also complex-aware.
 How should I cite LMFIT?
 ========================
 
-See https://dx.doi.org/10.5281/zenodo.11813
+For LMFIT 1.3.2, use https://doi.org/10.5281/zenodo.12785036.
+
+For other versions, see https://zenodo.org/records/12785036
+
+
 
 
 I get errors from NaN in my fit. What can I do?

doc/installation.rst

@@ -32,12 +32,12 @@ Downloading and Installation
 Prerequisites
 ~~~~~~~~~~~~~
 
-Lmfit works with `Python`_ versions 3.8 and higher. Version
+Lmfit works with `Python`_ versions 3.9 and higher. Version
 0.9.15 is the final version to support Python 2.7.
 
 Lmfit requires the following Python packages, with versions given:
-   * `NumPy`_ version 1.23 or higher.
-   * `SciPy`_ version 1.8 or higher.
+   * `NumPy`_ version 1.24 or higher.
+   * `SciPy`_ version 1.10 or higher.
    * `asteval`_ version 1.0 or higher.
    * `uncertainties`_ version 3.2.2 or higher.
    * `dill`_ version 0.3.4 or higher.

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

doc/whatsnew.rst

@@ -11,6 +11,15 @@ significant to the use and behavior of the library. This is not meant
 to be a comprehensive list of changes. For such a complete record,
 consult the `lmfit GitHub repository`_.
 
+.. _whatsnew_133_label:
+
+Version 1.3.3 Release Notes
+===========================
+
+Fixes:
+
+-  fix loading spline models with more than five knots (Issue #985)
+
 
 .. _whatsnew_132_label:
 

examples/doc_uvars_params.py → 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>