setup.py

from setuptools import setup, Extension
from setuptools.command.build_py import build_py as _build_py
from setuptools.command.build_ext import build_ext
from distutils.errors import CCompilerError, DistutilsExecError, DistutilsPlatformError
import subprocess
import os
import itertools
import warnings
import logging

logging.basicConfig()
log = logging.getLogger(__file__)

ext_errors = (CCompilerError, DistutilsExecError, DistutilsPlatformError, IOError)



class CustomBuildExtCommand(build_ext):
    """
    build_ext command for use when numpy headers are needed.
    See: https://stackoverflow.com/a/42163080/5069869
    """
    def run(self):

        # Import numpy here, only when headers are needed
        import numpy

        # Add numpy headers to include_dirs
        self.include_dirs.append(numpy.get_include())

        # Call original build_ext command
        build_ext.run(self)

try: #If we are in a git-repo, get git-describe version.
    path = os.path.abspath(os.path.dirname(__file__))
    forgi_version = subprocess.check_output(["git", "describe", "--always"], universal_newlines=True).strip()
    try:
        subprocess.check_call(['git', 'diff-index', '--quiet', 'HEAD', '--'], universal_newlines=True)
    except subprocess.CalledProcessError:
        forgi_version+="+uncommited_changes"
    #Use a subclass of build_py from distutils to costumize the build.
    class build_py(_build_py):
        def run(self):
            """
            During building, adds a variable with the complete version (from git describe)
            to forgi/__init__.py.
            """
            outfile = self.get_module_outfile(self.build_lib, ["forgi"], "__init__")
            try:
                os.remove(outfile) #If we have an old version, delete it, so _build_py will copy the original version into the build directory.
            except:
                pass
            # Superclass build
            _build_py.run(self)
            # Apped the version number to init.py
            with open(outfile, "a") as of:
                of.write('\n__complete_version__ = "{}"'.format(forgi_version))
except: #Outside of a git repo, do nothing.
    build_py = _build_py

class BuildFailed(Exception):
    pass



extras = {"forgi.visual":["matplotlib>=2.0"],
          "development":["cython"],
          "classification":["scikit-learn"],
          "pdbechem":['beautifulsoup4>=4.6'],
          "tests":["ddt", "hypothesis", "nose2"]
         }
extras["all"]=list(itertools.chain(extras.values()))
setup_args = {
      "zip_safe":False,
      "cmdclass":{'build_py': build_py, 'build_ext': CustomBuildExtCommand},
      "name":'forgi',
      "version":'2.2.3',
      "description":'RNA Graph Library',
      "author":'Bernhard Thiel, Peter Kerpedjiev',
      "author_email":'thiel@tbi.univie.ac.at',
      "license":'GNU GPL 3.0',
      "url":'http://www.tbi.univie.ac.at/~pkerp/forgi/',
      "ext_modules": [Extension("forgi.threedee.utilities.cytvec",
                                sources=["forgi/threedee/utilities/cytvec.pyx",
                                         "forgi/threedee/utilities/broken_ml_core.cpp",
                                        ],
                                extra_compile_args=['-O3', "-std=c++11"],
                                language='c++' )],
      "packages":['forgi', 'forgi.graph', 'forgi.threedee',
                'forgi.threedee.model', 'forgi.utilities',
                'forgi.threedee.utilities',
                'forgi.threedee.classification',
                'forgi.threedee.classification._training',
                'forgi._k2n_standalone', 'forgi.threedee.visual',
                'forgi.visual', 'forgi.projection'],
      "package_data":{'forgi.threedee': ['data/*.pdb', 'data/stats/temp.stats', 'data/average_atom_positions.json', 'data/aminor_geometries.csv', 'data/aminor_params.json']},
      "data_files":[("", ["CREDITS", "LICENSE"])],
      "scripts":['examples/rnaConvert.py',
               'examples/describe_cg.py',
               'examples/compare_RNA.py',
               'examples/visualize_rna.py',
               'examples/pseudoknot_analyzer.py',
               'examples/forgi_config.py'],
      "install_requires":[
		'numpy>=1.10.0',
                'scipy>=0.19.1',
                'pandas>=0.20',
                'future',
                'networkx>=2.0',
                'biopython',
                'appdirs>=1.4',
                'logging_exceptions>=0.1.9',
                'cython'
	],
      "setup_requires":[
        'numpy>=1.10.0',
        'cython',
        'setuptools>=18'
      ],
      "extras_require":extras,
    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
    "classifiers":[
        # How mature is this project? Common values are
        #   3 - Alpha
        #   4 - Beta
        #   5 - Production/Stable
        'Development Status :: 5 - Production/Stable',
        # Indicate who your project is intended for
        'Intended Audience :: Science/Research',
        'Operating System :: POSIX :: Linux',
        'Topic :: Scientific/Engineering :: Bio-Informatics',
        'Topic :: Scientific/Engineering :: Chemistry',

        # Pick your license as you wish (should match "license" above)
        'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',

        # Specify the Python versions you support here. In particular, ensure
        # that you indicate whether you support Python 2, Python 3 or both.
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.10',
        'Programming Language :: Python :: 3.11',
         ],
     }

setup(**setup_args)