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Merge pull request #206 from stefdoerr/pyproject
Modernized package by using pyproject.toml instead of setup.py
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‎LONG_DESCRIPTION.md‎

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# PROPKA3
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PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and
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protein-ligand complexes (version 3.1 and later) based on the 3D structure.
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For proteins without ligands both versions should produce the same result.
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The method is described in the following papers, which you should cite
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in publications:
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* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan
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H. Jensen. "Improved Treatment of Ligands and Coupling Effects in
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Empirical Calculation and Rationalization of pKa Values." Journal of
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Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
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* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan
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H. Jensen. "PROPKA3: consistent treatment of internal and surface
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residues in empirical pKa predictions." Journal of Chemical Theory
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and Computation 7, no. 2 (2011): 525-537.
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See http://propka.org/ for the PROPKA web server.

‎MANIFEST.in‎

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include README.md INSTALL
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include setup.py setup.cfg
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include README.md LONG_DESCRIPTION.md INSTALL
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include setup.py
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include propka.cfg
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include versioneer.py
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include propka/_version.py
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# Python type annotation declarations, see PEP-561
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include propka/py.typed
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prune docs
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prune tests

‎pyproject.toml‎

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[project]
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name = "propka"
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description = "Heuristic pKa calculations with ligands"
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authors = [{ name = "Jan H. Jensen", email = "jhjensen@chem.ku.dk" }]
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maintainers = [{ name = "Nathan Baker", email = "nathanandrewbaker@gmail.com" }]
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license = { text = "LGPL v2.1" }
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readme = "LONG_DESCRIPTION.md"
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requires-python = ">=3.10"
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keywords = ["science", "chemistry", "bioinformatics", "pKa", "proteins"]
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classifiers = [
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"Development Status :: 6 - Mature",
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"Environment :: Console",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)",
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"Operating System :: POSIX",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: Microsoft :: Windows",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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"Topic :: Scientific/Engineering :: Chemistry",
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]
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dynamic = ["version"]
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dependencies = ["numpy"]
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[project.urls]
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Homepage = "http://propka.org"
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Repository = "https://github.com/jensengroup/propka"
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Documentation = "https://propka.readthedocs.io"
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[project.scripts]
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propka3 = "propka.run:main"
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[project.optional-dependencies]
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test = ["pytest", "numpy"]
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docs = ["sphinx>=3.1", "sphinx_rtd_theme", "sphinx_sitemap"]
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dev = [
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"pytest",
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"numpy",
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"sphinx>=3.1",
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"sphinx_rtd_theme",
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"sphinx_sitemap",
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"mypy",
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"coverage",
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"yapf",
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]
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[build-system]
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requires = ["setuptools>=61.0", "versioneer[toml]==0.29"]
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build-backend = "setuptools.build_meta"
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[tool.setuptools]
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zip-safe = true
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[tool.setuptools.packages.find]
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exclude = ["scripts*", "tests*"]
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[tool.setuptools.package-data]
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propka = ["*.dat", "*.cfg", "*.json", "py.typed"]
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[tool.versioneer]
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VCS = "git"
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style = "pep440"
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versionfile_source = "propka/_version.py"
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versionfile_build = "propka/_version.py"
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tag_prefix = "v"
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parentdir_prefix = "propka-"
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[tool.coverage.run]
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source = ["propka"]
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omit = [
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# exclude versioneer generated file
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"propka/_version.py",
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# do not cover tests (already covered with source = propka)
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"tests/*",
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]
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[tool.coverage.report]
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exclude_lines = ["pragma: no cover"]
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[tool.yapf]
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column_limit = 88
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based_on_style = "pep8"
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allow_split_before_dict_value = false
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[tool.mypy]
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files = ["propka", "tests"]
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exclude = ["_version\\.py$"]
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explicit_package_bases = true
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ignore_missing_imports = true

‎setup.cfg‎

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‎setup.py‎

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#! /usr/bin/python
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# PROPKA 3
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from setuptools import setup, find_packages
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from setuptools import setup
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import versioneer
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setup(
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name="propka",
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version=versioneer.get_version(),
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cmdclass=versioneer.get_cmdclass(),
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description="Heuristic pKa calculations with ligands", long_description="""
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PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and
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protein-ligand complexes (version 3.1 and later) based on the 3D structure.
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For proteins without ligands both version should produce the same result.
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The method is described in the following papers, which you should cite
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in publications:
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* Sondergaard, Chresten R., Mats HM Olsson, Michal Rostkowski, and Jan
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H. Jensen. "Improved Treatment of Ligands and Coupling Effects in
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Empirical Calculation and Rationalization of pKa Values." Journal of
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Chemical Theory and Computation 7, no. 7 (2011): 2284-2295.
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* Olsson, Mats HM, Chresten R. Sondergaard, Michal Rostkowski, and Jan
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H. Jensen. "PROPKA3: consistent treatment of internal and surface
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residues in empirical pKa predictions." Journal of Chemical Theory
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and Computation 7, no. 2 (2011): 525-537.
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See http://propka.org/ for the PROPKA web server.
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""",
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author="Jan H. Jensen",
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author_email="jhjensen@chem.ku.dk",
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maintainer="Nathan Baker",
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maintainer_email="nathanandrewbaker@gmail.com",
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license="LGPL v2.1",
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url="http://propka.org",
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keywords="science",
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classifiers=[
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'Development Status :: 6 - Mature',
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'Environment :: Console',
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'Intended Audience :: Science/Research',
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'License :: OSI Approved :: GNU Lesser General Public License v2 (LGPLv2)',
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'Operating System :: POSIX',
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'Operating System :: MacOS :: MacOS X',
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'Operating System :: Microsoft :: Windows',
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'Programming Language :: Python',
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'Programming Language :: Python :: 3.10',
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'Programming Language :: Python :: 3.11',
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'Programming Language :: Python :: 3.12',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Scientific/Engineering :: Chemistry',
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],
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packages=find_packages(exclude=['scripts']),
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package_data={'propka': ['*.dat', '*.cfg', '*.json']},
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entry_points={'console_scripts': ['propka3 = propka.run:main', ]},
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zip_safe=True,
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python_requires='>=3.10',
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tests_require=["numpy", "pytest"],
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test_suite="tests",
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)
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setup(version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass())

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