setup.py

"""A setuptools based setup module.

See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""

# Always prefer setuptools over distutils
from setuptools import setup, find_packages
from os import listdir, path

# io.open is needed for projects that support Python 2.7
# It ensures open() defaults to text mode with universal newlines,
# and accepts an argument to specify the text encoding
# Python 3 only projects can skip this import
from io import open

here = path.abspath(path.dirname(__file__))

# Get the long description from the README file
with open(path.join(here, "README.md"), encoding="utf-8") as f:
    long_description = f.read()

# Collect names of bin/*py scripts
# e.g. 'pdb_intersect=bin.pdb_intersect:main',
binfiles = listdir(path.join(here, "pdbtools"))
bin_py = [
    f[:-3] + "=pdbtools." + f[:-3] + ":main" for f in binfiles if f.endswith(".py")
]

setup(
    name="pdb-tools",  # Required
    version="2.6.1",  # Required
    description="A swiss army knife for PDB files.",  # Optional
    long_description=long_description,  # Optional
    long_description_content_type="text/markdown",  # Optional (see note above)
    url="http://bonvinlab.org/pdb-tools",  # Optional
    author="Joao Rodrigues",  # Optional
    author_email="j.p.g.l.m.rodrigues@gmail.com",  # Optional
    license="Apache Software License, version 2",
    classifiers=[
        "Development Status :: 5 - Production/Stable",
        "Intended Audience :: Science/Research",
        "Topic :: Scientific/Engineering",
        "Topic :: Scientific/Engineering :: Chemistry",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Programming Language :: Python :: 3.12",
        "Programming Language :: Python :: 3.13",
        "Programming Language :: Python :: 3.14",
    ],
    keywords="bioinformatics protein structural-biology pdb",  # Optional
    # You can just specify package directories manually here if your project is
    # simple. Or you can use find_packages().
    #
    # Alternatively, if you just want to distribute a single Python file, use
    # the `py_modules` argument instead as follows, which will expect a file
    # called `my_module.py` to exist:
    #
    #   py_modules=["my_module"],
    #
    packages=find_packages(),  # Required
    # To provide executable scripts, use entry points in preference to the
    # "scripts" keyword. Entry points provide cross-platform support and allow
    # `pip` to create the appropriate form of executable for the target
    # platform.
    #
    # For example, the following would provide a command called `sample` which
    # executes the function `main` from this package when invoked:
    entry_points={  # Optional
        "console_scripts": bin_py,
    },
    # scripts=[path.join('bin', f) for f in listdir(path.join(here, 'bin'))],
    # List additional URLs that are relevant to your project as a dict.
    #
    # This field corresponds to the "Project-URL" metadata fields:
    # https://packaging.python.org/specifications/core-metadata/#project-url-multiple-use
    #
    # Examples listed include a pattern for specifying where the package tracks
    # issues, where the source is hosted, where to say thanks to the package
    # maintainers, and where to support the project financially. The key is
    # what's used to render the link text on PyPI.
    project_urls={  # Optional
        "Bug Reports": "https://github.com/haddocking/pdb-tools/issues",
        "Source": "https://github.com/haddocking/pdb-tools",
    },
    # Test Suite
    test_suite="tests.test_all",
)