setup.py

#!/usr/bin/env python

# This file is part of PyPop

# Copyright (C) 2003-2007.
# The Regents of the University of California (Regents)
# All Rights Reserved.

# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.

# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.

# IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT,
# INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
# LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS
# DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY
# OF SUCH DAMAGE.

# REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
# FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING
# DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS
# IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
# UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

import sys, os
from glob import glob
from setuptools import setup
from setuptools.extension import Extension
from setuptools.command.build_py import build_py as _build_py
from setuptools.command.install import install as _install
from distutils.command import clean
from sysconfig import _PREFIX, get_config_vars, get_config_var
from src.PyPop import __pkgname__, __version_scheme__

src_dir = "src"
pkg_dir = "PyPop"

# distutils doesn't currently have an explicit way of setting CFLAGS,
# it takes CFLAGS from the environment variable of the same name, so
# we set the environment to emulate that.
#os.environ['CFLAGS'] = '-funroll-loops'

class CleanCommand(clean.clean):
    """Customized clean command - removes in_place extension files if they exist"""
    def run(self):
        DIR = os.path.join(os.path.dirname(__file__), src_dir)
        # generate glob pattern from extension name and suffix
        ext_files = [os.path.join(DIR, pkg_dir, ext.name.split(pkg_dir + '.').pop() + ("*.pyd" if sys.platform == "win32" else "*.so")) for ext in extensions]
        for ext_file in ext_files:
            for ext_file in glob(ext_file):
                if os.path.exists(ext_file):
                    print("Removing in-place extension {}".format(ext_file))
                    os.unlink(ext_file)
        clean.clean.run(self)

# look for libraries in _PREFIX
library_dirs = [os.path.join(_PREFIX, "lib")]
include_dirs = [os.path.join(_PREFIX, "include")]
# also look in LIBRARY_PATH, CPATH (needed for macports etc.)
if "LIBRARY_PATH" in os.environ:
    library_dirs += os.environ["LIBRARY_PATH"].rstrip(os.pathsep).split(os.pathsep)
if "CPATH" in os.environ:
    include_dirs += os.environ["CPATH"].rstrip(os.pathsep).split(os.pathsep)

# generate the appropriate relative path to source directory, given
# paths within that source directory (this means we need to define
# this directory in just one place
def path_to_src(source_path_list):
    new_source_list = []
    for file_path in source_path_list:
        new_source_list.append(os.path.join(src_dir, file_path))
    return new_source_list

    
swig_opts = ["-I%s" % os.path.join(src_dir, "SWIG"), "-I%s" % os.path.join(src_dir)]

# define each extension
ext_Emhaplofreq = Extension("PyPop._Emhaplofreq",
                            path_to_src(["emhaplofreq/emhaplofreq_wrap.i",
                                         "emhaplofreq/emhaplofreq.c"
                                         ]),
                            swig_opts = swig_opts,
                            include_dirs=include_dirs + path_to_src(["emhaplofreq"]),
                            define_macros=[('__SWIG__', '1'),
                                           ('DEBUG', '0'),
                                           ('EXTERNAL_MODE', '1'),
                                           ('XML_OUTPUT', '1')]
                            )
ext_EWSlatkinExact = Extension("PyPop._EWSlatkinExact",
                               path_to_src(["slatkin-exact/monte-carlo_wrap.i",
                                "slatkin-exact/monte-carlo.c"]),
                               swig_opts = swig_opts,
                               include_dirs=include_dirs,
                               )

ext_Pvalue = Extension("PyPop._Pvalue",
                       path_to_src(["pval/pval_wrap.i",
                        "pval/pval.c",
                        "pval/pchisq.c",
                        "pval/chebyshev.c",
                        "pval/ftrunc.c",
                        "pval/lgamma.c",
                        "pval/mlutils.c",
                        "pval/pgamma.c",
                        "pval/fmin2.c",
                        "pval/fmax2.c",
                        "pval/dnorm.c",
                        "pval/dpois.c",
                        "pval/gamma.c",
                        "pval/bd0.c",
                        "pval/stirlerr.c",
                        "pval/lgammacor.c",
                        "pval/pnorm.c"]),
                       swig_opts = swig_opts,
                       include_dirs=include_dirs + path_to_src(["pval"]),
                       define_macros=[('MATHLIB_STANDALONE', '1')]
                       )

ext_Gthwe_files = path_to_src(["gthwe/gthwe_wrap.i",
                   "gthwe/hwe.c",
                   "gthwe/cal_const.c",
                   "gthwe/cal_n.c",
                   "gthwe/cal_prob.c",
                   "gthwe/check_file.c",
                   "gthwe/do_switch.c", 
                   "gthwe/new_rand.c",
                   "gthwe/ln_p_value.c",
                   "gthwe/to_calculate_log.c",
                   "gthwe/print_data.c",
                   "gthwe/random_choose.c",
                   "gthwe/read_data.c",
                   "gthwe/select_index.c",
                   "gthwe/stamp_time.c",
                   "gthwe/test_switch.c",
                   "gthwe/statistics.c"])


ext_Gthwe_macros = [('__SWIG__', '1'),
                    ('DEBUG', '0'),
                    ('XML_OUTPUT', '1'),
                    ('SUPPRESS_ALLELE_TABLE', '1'),
                    ('INDIVID_GENOTYPES', '1')] 

ext_Gthwe = Extension("PyPop._Gthwe",
                      ext_Gthwe_files,
                      swig_opts = swig_opts,
                      include_dirs=include_dirs + path_to_src(["gthwe"]),
                      library_dirs=library_dirs,
                      libraries=["gsl", "gslcblas"],
                      define_macros=ext_Gthwe_macros
                      )

ext_Haplostats = Extension("PyPop._Haplostats",
                       path_to_src(["haplo-stats/haplostats_wrap.i",
                        "haplo-stats/haplo_em_pin.c"]),
                       swig_opts = swig_opts,
                       include_dirs=include_dirs + path_to_src(["haplo-stats", "pval"]),
                       define_macros=[('MATHLIB_STANDALONE', '1'),
                                      ('__SWIG__', '1'),
                                      ('DEBUG', '0'),
                                      ('R_NO_REMAP', '1')]
                       )

ext_HweEnum = Extension("PyPop._HweEnum",
                      path_to_src(["hwe-enumeration/src/hwe_enum_wrap.i",
                        "hwe-enumeration/src/hwe_enum.c",
                        "hwe-enumeration/src/factorial.c",
                        "hwe-enumeration/src/main.c",
                        "hwe-enumeration/src/common.c",
                        "hwe-enumeration/src/statistics.c",
                        "hwe-enumeration/src/external.c"
                        ]),
                        swig_opts = swig_opts,
                        include_dirs=include_dirs + [path_to_src(["hwe-enumeration/src/include"]),
                                                     "/usr/include/glib-2.0",
                                                     "/usr/include/glib-2.0/include",
                                                     "/usr/lib/glib-2.0/include",
                                                     "/usr/lib64/glib-2.0/include/",
                                                     "/usr/include/libxml2",
                                                     "/usr/include/gsl",
                                                     ],
                        libraries=["glib-2.0", "xml2", "popt",
                                   "m", "gsl", "gslcblas"],
                        define_macros=[('__SORT_TABLE__', '1'),
                                       ('g_fprintf', 'pyfprintf'),
                                       ('VERSION', '"internal"'),
                                       ('PACKAGE_NAME','"hwe-enumeration"'),
                                       ('INDIVID_GENOTYPES', '1'),
                                       ('HAVE_LIBGSL', '1')]
                        )

ext_Emhaplofreq.depends=path_to_src(["SWIG/typemap.i", "emhaplofreq/emhaplofreq.h", "emhaplofreq/drand48.c"])
ext_Pvalue.depends=path_to_src(["SWIG/typemap.i", "pval/Rconfig.h", "pval/Rmath.h", "pval/dpq.h", "pval/nmath.h"])
ext_Gthwe.depends=path_to_src(["SWIG/typemap.i", "gthwe/func.h", "gthwe/hwe.h"])
ext_Haplostats.depends=path_to_src(["SWIG/typemap.i", "haplo-stats/haplo_em_pin.h"])
    
# default list of extensions to build
extensions = [ext_Emhaplofreq, ext_EWSlatkinExact, ext_Pvalue, ext_Haplostats, ext_Gthwe]

# don't include HWEEnum 
# extensions.append(ext_HweEnum)

xslt_data_file_paths = []
# xslt files are in a subdirectory
xslt_files = [f + '.xsl' for f in ['text', 'html', 'lib', 'common', 'filter', 'hardyweinberg', 'homozygosity', 'emhaplofreq', 'meta-to-tsv', 'sort-by-locus', 'haplolist-by-group', 'phylip-allele', 'phylip-haplo']]
xslt_data_file_paths.extend(xslt_files)

citation_data_file_paths = []
# citation files are in a subdirectory of PyPop, but not a separate module
from src.PyPop.citation import citation_output_formats, convert_citation_formats
citation_files = [os.path.join("citation", 'CITATION.' + suffix) for suffix in citation_output_formats]
citation_data_file_paths.extend(citation_files)

# currently disabled (these are built in a github action)
class CustomBuildPy(_build_py):
    def run(self):

        # do standard build process
        super().run()

        # if not running from a CIBUILDWHEEL environment variable
        # we need to create the citations
        if os.environ.get('CIBUILDWHEEL') != '1':
            
            # source citation path (single-source of truth)
            citation_path = "CITATION.cff"
        
            # then copy CITATION.cff to temp build directory
            # use setuptools' temp build directory
            build_lib = self.get_finalized_command('build').build_lib

            convert_citation_formats(build_lib, citation_path)

# read the contents of your README file
from pathlib import Path
this_directory = Path(__file__).parent
long_description = (this_directory / "README.rst").read_text()

setup (name = __pkgname__,
       use_scm_version={
           'write_to': os.path.join(src_dir, pkg_dir, "_version.py"),
           'version_scheme': __version_scheme__,
       },
       description = "PyPop: Python for Population Genomics",
       long_description=long_description,
       long_description_content_type='text/x-rst',
       url = "http://www.pypop.org/",
       project_urls={
           'Documentation': 'http://pypop.org/docs/',
           'Changelog': 'https://github.com/alexlancaster/pypop/blob/main/NEWS.md',
           'Source': 'https://github.com/alexlancaster/pypop/',
           'Tracker': 'https://github.com/alexlancaster/pypop/issues',
       },
       author = "Alex Lancaster",
       maintainer = "PyPop team",
       license = "GNU GPL",
       platforms = ["GNU/Linux", "Windows", "MacOS"],
       keywords = ["bioinformatics", "population-genomics", "evolutionary-biology", "population-genetics"],
       classifiers = ["Programming Language :: Python :: 3",
                      "Intended Audience :: Science/Research",
                      "Topic :: Scientific/Engineering :: Bio-Informatics",
                      "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
                      "Operating System :: MacOS :: MacOS X",
                      "Operating System :: Microsoft :: Windows",
                      "Operating System :: POSIX :: Linux",
                      ],
       package_dir = {"": src_dir},
       packages = ["PyPop", "PyPop.xslt"],
       package_data = {"PyPop.xslt": xslt_data_file_paths,
                       "PyPop": citation_data_file_paths},
       install_requires = ["numpy <= 2.1.3",
                           "lxml <= 5.3.0",
                           "importlib-resources; python_version <= '3.8'",
                           "importlib-metadata; python_version <= '3.8'"],
       extras_require={
           "test": ['pytest']
           # FIXME:  "psutil <= 5.9.5", not currently used, 5.9.6 and later had problems with building on Windows PyPy
           },
       entry_points = {
           'console_scripts': ['pypop=PyPop.pypop:main',
                               'popmeta=PyPop.popmeta:main',
                               'pypop-interactive=PyPop.pypop:main_interactive']
       },
       ext_modules=extensions,
       cmdclass={'clean': CleanCommand,
                 # enable the custom build
                 'build_py': CustomBuildPy,
                 },
       )