BLD: transition to pyproject.toml and setup.cfg

- rename THANKS.txt to AUTHORS.txt; so that it automatically gets
  included
- remove MANIFEST.in/requirements{-dev}.txt; now all covered in
  setup.cfg
- update installation documentation

Fixes: lmfit#769

Author: reneeotten

.github/CONTRIBUTING.md

@@ -6,7 +6,7 @@ the Python coding style conventions (i.e., [PEP 8](https://www.python.org/dev/pe
 closely. Additionally, we really want comprehensive docstrings that follow
 [PEP 257](https://www.python.org/dev/peps/pep-0257/) using the
 [numpydoc style](https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard),
-usable offline documentation, and good unit tests for the pytest framework. A
+usable offline documentation, and good unit tests for the ``pytest`` framework. A
 good contribution includes all of these. To ensure compliance with our coding
 style, we make use of the [pre-commit](https://pre-commit.com/) framework to run
 several *hooks* when committing code. Please follow the instructions below if
@@ -16,16 +16,16 @@ you intend to contribute to the lmfit repository:
 - clone your forked GitHub repository:
   ``git clone https://github.com/<your-name>/lmfit-py.git``
 - install all (optional) dependencies either using ``pip`` or ``conda``:
-  ``pip install -U -r requirements-dev.txt`` or
-  ``conda install <packages in requirements-dev.txt>``
+  ``pip install lmfit[all]`` or
+  ``conda install <all packages listed in setup.cfg>``
 - initialize ``pre-commit`` by running ``pre-commit install`` in the lmfit directory
 - create a new branch: ``git checkout -b <awesome_new_feature>``
 - start coding
-- install the latest version of your code using one of the usual ``python setup.py`` commands (e.g., ``python setup.py install --user``)
+- install the latest version of your code using the PEP517/PEP518 way (``python -m build && pip install .``)
 - make sure the test-suite passes locally: run ``pytest`` in the lmfit directory
 - make sure the documentation builds locally: run ``make`` in the doc directory
 - push to your fork: ``git push origin``
-- open a Pull Request on https://github.com/lmfit/lmfit-py/pulls
+- open a Pull Request on [the lmfit GitHub repository](https://github.com/lmfit/lmfit-py/pulls)
 
 If you need any additional help, please send a message to the
 [mailing list](https://groups.google.com/group/lmfit-py) or use the
@@ -55,7 +55,6 @@ inappropriate for the mailing list, but many questions are not Issues. We
 will try our best to engage in all discussions, but we may simply close
 GitHub Issues that are actually questions.
 
-
 ## Providing an Example with GitHub Issues
 
 If you are reporting a bug with GitHub Issues, we do expect a small, complete,
@@ -89,7 +88,6 @@ and are a good way to demonstrate a question or raise an issue. Please
 see the above about providing examples. The notebook you provide will be
 *read*, but will probably not be run.
 
-
 ## Secret Code for First Time Issues
 
 If you have not done so in the past, and are going to submit a GitHub Issue,

.pre-commit-config.yaml

@@ -14,11 +14,11 @@ repos:
     -   id: check-builtin-literals
     -   id: check-case-conflict
     -   id: check-merge-conflict
+    -   id: check-toml
     -   id: debug-statements
     -   id: end-of-file-fixer
     -   id: mixed-line-ending
     -   id: trailing-whitespace
-    -   id: requirements-txt-fixer
     -   id: fix-encoding-pragma
         args: [--remove]
 

THANKS.txt renamed to AUTHORS.txt

@@ -40,7 +40,7 @@ Lmfit requires the following Python packages, with versions given:
    * `asteval`_ version 0.9.22 or higher.
    * `uncertainties`_ version 3.0.1 or higher.
 
-All of these are readily available on PyPI, and should be installed
+All of these are readily available on PyPI, and are installed
 automatically if installing with ``pip install lmfit``.
 
 In order to run the test suite, the `pytest`_, `pytest-cov`_, and `flaky`_
@@ -56,8 +56,14 @@ packages `sphinxcontrib-svg2pdfconverter`_ and `cairosvg`_ are also required,
 as well as the LaTex package `Latexmk`_ (which is included by default in some
 LaTex distributions).
 
-Please refer to ``requirements-dev.txt`` for a list of all dependencies that
-are needed if you want to participate in the development of lmfit.
+Please refer to ``setup.cfg`` under ``options.extras_require`` 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``).
+
+Please note: the "original" ``python setup.py install`` is deprecated, but we will
+provide a shim ``setup.py`` file for as long as ``Python`` and/or ``setuptools``
+allow the use of this legacy command.
 
 Downloads
 ~~~~~~~~~
@@ -88,7 +94,14 @@ To get the latest development version from the `lmfit GitHub repository`_, use::
 
 and install using::
 
-   python setup.py install
+   pip install --upgrade build pip setuptools wheel
+
+to install the required build dependencies and then do::
+
+   python -m build
+   pip install ".[all]'
+
+to generate the wheel and install ``lmfit`` with all its dependencies.
 
 We welcome all contributions to lmfit! If you cloned the repository for this
 purpose, please read `CONTRIBUTING.md`_ for more detailed instructions.
@@ -109,7 +122,7 @@ that `matplotlib`_ has been installed and is working correctly.
 Acknowledgements
 ~~~~~~~~~~~~~~~~
 
-.. literalinclude:: ../THANKS.txt
+.. literalinclude:: ../AUTHORS.txt
   :language: none
 
 

MANIFEST.in

@@ -18,7 +18,9 @@ Version 1.0.4 Release Notes (unreleased)
 
 Bug fixes/enhancements:
 
-- make sure variable ``spercent`` is always defined in ``params_html_table`` functions (Issue #768, PR #770)
+- make sure variable ``spercent`` is always defined in ``params_html_table`` functions (reported by @MySlientWind; Issue #768, PR #770)
+- always initialize the variables ``success`` and ``covar`` the ``MinimizerResult`` (reported by Marc W. Pound; PR #771)
+- build package following PEP517/PEP518; use pyproject.toml and setup.cfg; leave setup.py for now (PR #777)
 
 
 .. _whatsnew_103_label:

doc/installation.rst

@@ -0,0 +1,7 @@
+[build-system]
+requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "lmfit/version.py"
+version_scheme = "post-release"

doc/whatsnew.rst

@@ -1,3 +1,81 @@
+[metadata]
+name = lmfit
+description = Least-Squares Minimization with Bounds and Constraints
+long_description = file: README.rst
+long_description_content_type = text/x-rst
+author = LMFit Development Team
+author_email = [email protected]
+url = https://lmfit.github.io//lmfit-py/
+license = BSD 3-Clause
+platforms = any
+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 :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: Implementation :: CPython
+    Programming Language :: Python :: Implementation :: PyPy
+keywords = curve-fitting, least-squares minimization
+project_urls =
+    Source = https://github.com/lmfit/lmfit-py
+    Changelog = https://lmfit.github.io/lmfit-py/whatsnew.html
+    Documentation = https://lmfit.github.io/lmfit-py/
+    Tracker = https://github.com/lmfit/lmfit-py/issues
+
+[options]
+packages = find:
+python_requires = >=3.6
+setup_requires = setuptools_scm
+install_requires =
+    asteval>=0.9.22
+    numpy>=1.18
+    scipy>=1.4
+    uncertainties>=3.0.1
+
+[options.packages.find]
+include =
+    lmfit
+
+[options.extras_require]
+dev =
+    build
+    check-wheel-contents
+    pre-commit
+    twine
+doc =
+    cairosvg
+    corner
+    dill
+    emcee>=3.0.0
+    jupyter_sphinx>=0.2.4
+    matplotlib
+    numdifftools
+    pandas
+    Pillow
+    pycairo;platform_system=="Windows"
+    Sphinx
+    sphinx-gallery>=0.10
+    sphinxcontrib-svg2pdfconverter
+    sympy
+test =
+    codecov
+    coverage
+    flaky
+    pytest
+    pytest-cov
+all =
+    %(dev)s
+    %(test)s
+    %(doc)s
+
 [isort]
 skip=lmfit/__init__.py,doc/conf.py
 known_third_party=asteval,dill,emcee,IPython,matplotlib,numdifftools,numpy,NISTModels,pandas,pytest,scipy,uncertainties