setup.py

import os
import subprocess as sp
from io import open

from setuptools import Extension, find_packages, setup

import versioneer
from compile_externals import compile_all

CONFIG_NAME = "gimmemotifs.cfg"
DESCRIPTION = "GimmeMotifs is a motif prediction pipeline."

with open("README.md", encoding="utf-8") as f:
    long_description = f.read().strip("\n")

# are we in the conda build environment?
conda_build = os.environ.get("CONDA_BUILD")

module1 = Extension("gimmemotifs.c_metrics", sources=["gimmemotifs/c_metrics.c"])

MOTIF_BINS = {
    "AMD": ["src/AMD/AMD.bin"],
    "BioProspector": ["src/BioProspector/BioProspector"],
    "MDmodule": ["src/MDmodule/MDmodule"],
    "Posmo": ["src/posmo/posmo", "src/posmo/clusterwd"],
}


cmdclass = versioneer.get_cmdclass()
my_build_py = cmdclass["build_py"]


class build_tools(my_build_py):
    user_options = []

    def initialize_options(self):
        my_build_py.initialize_options(self)
        self.build_base = None
        self.build_lib = None

    def finalize_options(self):
        my_build_py.finalize_options(self)
        self.set_undefined_options("build", ("build_base", "build_base"))
        self.set_undefined_options("build", ("build_lib", "build_lib"))

    def run(self):
        if not self.dry_run:
            src_dir = os.path.join(self.build_base, "src")
            target_dir = os.path.join(self.build_lib, "gimmemotifs/included_tools")
            # package_data={'gimmemotifs.data':['data/cfg/*']},

            self.copy_tree("src/", src_dir)
            # mkpath is a distutils helper to create directories
            self.mkpath(target_dir)

            compile_all(src_dir)

            for exes in MOTIF_BINS.values():
                for exe in exes:
                    if os.path.exists(exe):
                        self.copy_file(exe, target_dir)
                    exe = os.path.join(self.build_base, exe)
                    if os.path.exists(exe):
                        self.copy_file(exe, target_dir)

            self.copy_tree(
                os.path.join(src_dir, "ChIPMunk"), os.path.join(target_dir, "ChIPMunk")
            )
            self.copy_tree(
                os.path.join(src_dir, "HMS"), os.path.join(target_dir, "HMS")
            )

            arch = "x86_64"
            try:
                sp.check_call(f"src/MotifSampler/MotifSampler_{arch}")
            except (sp.CalledProcessError, OSError) as e:
                if "died" in str(e):
                    arch = "i386"

            self.copy_file(
                os.path.join(src_dir, f"MotifSampler/MotifSampler_{arch}"),
                os.path.join(target_dir, "MotifSampler"),
            )
            self.copy_file(
                os.path.join(src_dir, f"MotifSampler/CreateBackgroundModel_{arch}"),
                os.path.join(target_dir, "CreateBackgroundModel"),
            )
            self.copy_file(
                os.path.join(src_dir, "Improbizer/ameme_x86_64"),
                os.path.join(target_dir, "ameme"),
            )

        my_build_py.run(self)


cmdclass["build_py"] = build_tools
version = versioneer.get_version()

setup(
    name="gimmemotifs",
    version=version,
    long_description=long_description,
    long_description_content_type="text/markdown",
    description=DESCRIPTION,
    author="Simon van Heeringen",
    author_email="simon.vanheeringen@gmail.com",
    url="https://github.com/vanheeringen-lab/gimmemotifs/",
    download_url="https://github.com/vanheeringen-lab/gimmemotifs/tarball/" + version,
    license="MIT",
    packages=find_packages(),
    scripts=["scripts/gimme", "scripts/combine_peaks", "scripts/coverage_table"],
    package_data={"gimmemotifs.data": ["data/"]},
    include_package_data=True,
    ext_modules=[module1],
    cmdclass=cmdclass,
    classifiers=[
        "Development Status :: 4 - Beta",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: MIT License",
        "Operating System :: MacOS :: MacOS X",
        "Operating System :: POSIX :: Linux",
        "Programming Language :: Python :: 3",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
    ],
    install_requires=[
        "setuptools >=0.7",
        # copied from the requirements.yaml
        "biofluff >=3.0.4",
        "configparser",
        "diskcache",
        "feather-format",
        "genomepy >=0.13.0",
        # "ipywidgets",
        "iteround",
        "jinja2",
        "logomaker",
        "loguru",
        "matplotlib >=3.3",  # matplotlib-base
        "numpy >=1.18",
        "pandas >=1.3.0",
        "pybedtools >=0.9.0",
        "pysam >=0.16",
        # "python",
        "xxhash",  # "python-xxhash"
        "qnorm  >=0.8.1",
        "scikit-learn >=0.23.2",
        "scipy >=1.5",
        "seaborn >=0.10.1",
        "statsmodels",
        "tqdm >=4.46.1",
        "xdg",
        # "xgboost >=1.0.2",
    ],
    extras_require={
        "ete3": ["ete3"],
        "notebook": ["ipywidgets"],
        "xgboost": ["xgboost >=1.0.2"],
    },
)