Merge pull request #928 from reneeotten/switch-to-pyproject.toml

lmfit · Dec 1, 2023 · caf0930 · caf0930
2 parents e21a6aa + af16a01
commit caf0930
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Showing 5 changed files with 161 additions and 121 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -26,7 +26,7 @@ repos:
     rev: 6.1.0
     hooks:
     -   id: flake8
-        additional_dependencies: [flake8-deprecated, flake8-mutable]
+        additional_dependencies: [flake8-deprecated, flake8-mutable, Flake8-pyproject]
 
 -   repo: https://github.com/PyCQA/isort/
     rev: 5.12.0
@@ -64,3 +64,4 @@ repos:
     rev: v1.5.0
     hooks:
     -   id: yesqa
+        additional_dependencies: [flake8-deprecated, flake8-mutable, Flake8-pyproject]
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -14,7 +14,7 @@ stages:
       steps:
         - task: UsePythonVersion@0
           inputs:
-            versionSpec: '3.11'
+            versionSpec: '3.12'
         - 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: '3.11'
+            versionSpec: '3.12'
         - script: |
             python -m pip install --upgrade build pip setuptools wheel
           displayName: 'Install Python build tools'
@@ -125,6 +125,8 @@ stages:
             python.version: '3.10'
           Python311:
             python.version: '3.11'
+          Python312:
+            python.version: '3.12'
 
       steps:
         - task: UsePythonVersion@0
@@ -163,7 +165,6 @@ stages:
             ./codecov -v -f "coverage.xml"
           displayName: 'Upload to codecov.io'
 
-# Python 3.11 on Windows currently fails to build pycairo
 - stage: test_Windows_latest
   dependsOn: check_codestyle
   condition: succeededOrFailed()
@@ -173,8 +174,8 @@ stages:
         vmImage: 'windows-latest'
       strategy:
         matrix:
-          Python310:
-            python.version: '3.10'
+          Python312:
+            python.version: '3.12'
 
       steps:
         - task: UsePythonVersion@0
@@ -208,8 +209,8 @@ stages:
         vmImage: 'macos-latest'
       strategy:
         matrix:
-          Python311:
-            python.version: '3.11'
+          Python312:
+            python.version: '3.12'
 
       steps:
         - task: UsePythonVersion@0
@@ -235,13 +236,13 @@ stages:
   dependsOn: check_codestyle
   condition: succeededOrFailed()
   jobs:
-    - job: Python312_dev
+    - job: Python313_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 python3.12-dev python3.12-venv
+            sudo apt-get update && sudo apt-get install -y --no-install-recommends python3.13-dev python3.13-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 \
@@ -250,47 +251,47 @@ stages:
           displayName: 'Install dependencies'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            ##curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
-            ##python3.12 get-pip.py --user
-            python3.12 -m ensurepip --upgrade
-            pip3.12 install -U build pip setuptools wheel pybind11 cython || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.13 -m ensurepip --upgrade
+            pip3.13 install -U build pip setuptools wheel pybind11 cython || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install build, pip, setuptools, wheel, pybind11, and cython'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
             export numpy_version=1.26.2
             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}
-            python3.12 setup.py install --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development 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!!"
           displayName: 'Install latest available version of NumPy'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            pip3.12 install -U pythran || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            pip3.13 install -U pythran || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install pythran'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
             export scipy_version=1.11.3
             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}
-            python3.12 setup.py install --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development 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!!"
           displayName: 'Install latest available version of SciPy'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
             # remove numdifftools for now as it pulls in statsmodels, that wants to build with NumPy 1.14.5
-            pip3.12 install asteval uncertainties dill emcee flaky pytest pytest-cov || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            pip3.13 install asteval uncertainties dill emcee flaky pytest pytest-cov || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Install latest available version of Python dependencies'
         - script: |
-            python3.12 -m build
-            python3.12 -m pip install '.[test]' --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            python3.13 -m build
+            python3.13 -m pip install '.[test]' --user || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
           displayName: 'Build wheel/sdist and install lmfit'
         - script: |
             export PATH=/home/vsts/.local/bin:$PATH
-            pip3.12 list || echo -e "\043#vso[task.logissue type=warning;] Allowed failure for development version!!"
+            pip3.13 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
-            pip3.12 install pytest-azurepipelines
+            pip3.13 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'
diff --git a/doc/installation.rst b/doc/installation.rst
@@ -57,7 +57,7 @@ the Python packages `sphinxcontrib-svg2pdfconverter`_ and `cairosvg`_ are also r
 as well as the LaTex package `Latexmk`_ (which is included by default in some
 LaTex distributions).
 
-Please refer to ``setup.cfg`` under ``options.extras_require`` for a list of all
+Please refer to ``pyproject.toml`` under ``project.optional-dependencies`` for a list of all
 dependencies that are needed if you want to participate in the development of lmfit.
 You can install all these dependencies automatically by doing ``pip install lmfit[all]``,
 or select only a subset (e.g., ``dev```, ``doc``, or ``test``).

diff --git a/pyproject.toml b/pyproject.toml
@@ -2,6 +2,142 @@
 requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
 build-backend = "setuptools.build_meta"
 
+[project]
+name = "lmfit"
+dynamic = ["version"]
+dependencies = [
+    "asteval>=0.9.28",
+    "numpy>=1.19",
+    "scipy>=1.6",
+    "uncertainties>=3.1.4",
+]
+requires-python = ">= 3.8"
+authors = [
+    {name = "LMFit Development Team", email = "matt.newville@gmail.com"},
+]
+description = "Least-Squares Minimization with Bounds and Constraints"
+readme = "README.rst"
+license = {file = "LICENSE"}
+keywords = ["curve-fitting, least-squares minimization"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Programming Language :: Python :: Implementation :: PyPy",
+]
+
+[project.urls]
+Homepage = "https://lmfit.github.io//lmfit-py/"
+Documentation = "https://lmfit.github.io/lmfit-py/"
+Changelog = "https://lmfit.github.io/lmfit-py/whatsnew.html"
+
+[project.optional-dependencies]
+dev = [
+    "build",
+    "check-wheel-contents",
+    "flake8-pyproject",
+    "pre-commit",
+    "twine",
+]
+doc = [
+    "cairosvg",
+    "corner",
+    "dill",
+    "emcee>=3.0.0",
+    "ipykernel",
+    "jupyter_sphinx>=0.2.4",
+    "matplotlib",
+    "numdifftools",
+    "pandas",
+    "Pillow",
+    "pycairo;platform_system=='Windows'",
+    "Sphinx",
+    "sphinx-gallery>=0.10",
+    "sphinxcontrib-svg2pdfconverter",
+    "sympy",
+]
+test = [
+    "coverage",
+    "flaky",
+    "pytest",
+    "pytest-cov",
+]
+all = ["lmfit[dev, doc, test]"]
+
+[tool.setuptools.packages.find]
+include = ["lmfit"]
+
 [tool.setuptools_scm]
 write_to = "lmfit/version.py"
 version_scheme = "post-release"
+
+[tool.isort]
+skip = [
+    "lmfit/__init__.py",
+    "doc/conf.py",
+]
+known_third_party = [
+    "asteval",
+    "dill" ,
+    "emcee",
+    "IPython",
+    "matplotlib",
+    "numdifftools",
+    "numpy",
+    "NISTModels",
+    "pandas",
+    "pytest",
+    "scipy",
+    "uncertainties",
+]
+known_first_party = [
+    "lmfit",
+    "lmfit_testutils",
+]
+force_sort_within_sections = "True"
+
+[tool.rstcheck]
+report_level = "WARNING"
+ignore_substitutions = [
+    "release"
+]
+ignore_roles = [
+    "scipydoc",
+    "numpydoc",
+]
+ignore_directives = [
+    "autoclass",
+    "autodoc",
+    "autofunction",
+    "automethod",
+    "jupyter-execute",
+    "math",
+]
+
+[tool.coverage.run]
+omit = [
+    "tests/*",
+]
+
+[tool.pytest.ini_options]
+addopts = "--cov=lmfit --cov-report html"
+
+[tool.flake8]
+ignore = [
+    "E121", "E123", "E126", "E226",
+    "W503", "W504", "E501", "E731",
+]
+exclude = [
+    "doc/conf.py",
+    "lmfit/__init__.py",
+]
diff --git a/setup.cfg b/setup.cfg