setup.py

#
# setup.py
#
# The MIT License (MIT)
#
# Copyright (c) 2023-2025 dātma, inc™
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
# the Software, and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
# FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
# COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
# IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
#
# Description: setup script to build the GenomicsDB python package
#

import glob
import os
import shutil
import sys

import numpy
from setuptools import Extension, find_packages, setup

# Directory where a copy of the CPP compiled object is found.
GENOMICSDB_LOCAL_DATA_DIR = "genomicsdb"

# Specify genomicsdb install location via
#     "--with-genomicsdb=<genomicsdb_install_path>" command line arg
GENOMICSDB_INSTALL_PATH = os.getenv("GENOMICSDB_HOME", default="genomicsdb")
copy_genomicsdb_libs = False
copy_protobuf_definitions = False
with_version = "0.0.9.14"

args = sys.argv[:]
for arg in args:
    if arg.find("--with-genomicsdb=") == 0:
        GENOMICSDB_INSTALL_PATH = os.path.expanduser(arg.split("=")[1])
        sys.argv.remove(arg)
    if arg.find("--with-libs") == 0:
        copy_genomicsdb_libs = True
        sys.argv.remove(arg)
    if arg.find("--with-protobuf") == 0:
        copy_protobuf_definitions = True
        sys.argv.remove(arg)
    if arg.find("--with-version=") == 0 and len(arg.split("=")[1]) > 0:
        with_version = arg.split("=")[1]
        sys.argv.remove(arg)

print("Compiled GenomicsDB Install Path: {}".format(GENOMICSDB_INSTALL_PATH))

GENOMICSDB_INCLUDE_DIR = os.path.join(GENOMICSDB_INSTALL_PATH, "include")
GENOMICSDB_LIB_DIR = os.path.join(GENOMICSDB_INSTALL_PATH, "lib")
GENOMICSDB_PROTOBUF_DIR = os.path.join(GENOMICSDB_INSTALL_PATH, "genomicsdb/protobuf/python")

if GENOMICSDB_INSTALL_PATH == "genomicsdb":
    copy_genomicsdb_libs = False
    copy_protobuf_definitions = False

rpath = []
link_args = []
dst = os.path.join("genomicsdb/lib")
if copy_genomicsdb_libs:
    os.makedirs(dst, exist_ok=True)
    glob_paths = [os.path.join(GENOMICSDB_LIB_DIR, e) for e in ["lib*genomicsdb*.so*", "lib*genomicsdb*.dylib"]]
    lib_paths = []
    for paths in glob_paths:
        lib_paths.extend(glob.glob(paths))
    print("Adding the following libraries to the GenomicsDB Package :")
    print(lib_paths, sep="\n")

    for lib_path in lib_paths:
        print("Copying {0} to {1}".format(lib_path, dst))
        shutil.copy(lib_path, dst)

    if sys.platform == "darwin":
        link_args = ["-Wl,-rpath," + dst]
    else:
        rpath = ["$ORIGIN/lib"]

dst = os.path.join("genomicsdb/protobuf")
if copy_protobuf_definitions:
    shutil.copytree(GENOMICSDB_PROTOBUF_DIR, dst, dirs_exist_ok=True)
    for file in os.listdir(dst):
        if file.endswith(".py"):
            # Read in the file
            filename = os.path.join(dst, file)
            with open(filename, "r") as file:
                replaced_contents = file.read().replace("import genomicsdb_", "from . import genomicsdb_")
            # Write out the file
            with open(filename, "w") as file:
                file.write(replaced_contents)

os.environ["CFLAGS"] = "-DUSE_NANOARROW=1"
os.environ["CXXFLAGS"] = "-DUSE_NANOARROW=1"

if "OSX_ARCH" in os.environ:
    os.environ["CFLAGS"] = "-arch " + os.environ["OSX_ARCH"]
    os.environ["CXXFLAGS"] = "-arch " + os.environ["OSX_ARCH"]

EXTRA_COMPILE_ARGS = ["-std=c++20"]
if "CXX" in os.environ and os.environ["CXX"].find("devtoolset-11") > 0:
    EXTRA_COMPILE_ARGS = ["-std=c++2a"]


def run_cythonize(src):
    from Cython.Build.Dependencies import cythonize

    cythonize(src, include_path=[GENOMICSDB_INCLUDE_DIR, numpy.get_include()], force=True)
    return os.path.splitext(src)[0] + ".cpp"


genomicsdb_extension = Extension(
    "genomicsdb.genomicsdb",
    language="c++",
    include_dirs=[GENOMICSDB_INCLUDE_DIR, numpy.get_include()],
    sources=[
        run_cythonize("src/genomicsdb.pyx"),
        "src/genomicsdb_processor.cpp",
        "src/genomicsdb_processor_columnar.cpp",
        "src/genomicsdb_arrow_utils.cpp",
    ],
    libraries=["tiledbgenomicsdb"],
    library_dirs=[GENOMICSDB_LIB_DIR],
    runtime_library_dirs=rpath,
    extra_link_args=link_args,
    extra_compile_args=EXTRA_COMPILE_ARGS,
)

with open("README.md") as f:
    long_description = f.read()

with open("requirements.txt") as f:
    install_requirements = f.readlines()

setup(
    name="genomicsdb",
    description="Python Bindings for querying GenomicsDB",
    long_description=long_description,
    long_description_content_type="text/markdown",
    author="GenomicsDB.org",
    author_email="support@genomicsdb.org",
    maintainer="GenomicsDB.org",
    maintainer_email="support@genomicsdb.org",
    license="MIT",
    ext_modules=[genomicsdb_extension],
    zip_safe=False,
    setup_requires=["cython>=0.27"],
    install_requires=install_requirements,
    python_requires=">=3.9",
    packages=find_packages(include=["genomicsdb", "genomicsdb.*"], exclude=["package", "test"]),
    keywords=["genomics", "genomicsdb", "variant", "vcf", "variant calls"],
    include_package_data=True,
    version=with_version,
    entry_points={
        "console_scripts": [
            "genomicsdb_query=genomicsdb.scripts.genomicsdb_query:main",
            "genomicsdb_cache=genomicsdb.scripts.genomicsdb_cache:main",
        ],
    },
    classifiers=[
        "Development Status :: 5 - Production/Stable",
        "Intended Audience :: Developers",
        "Intended Audience :: Information Technology",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: MIT License",
        "Topic :: Software Development :: Libraries :: Python Modules",
        "Operating System :: POSIX :: Linux",
        "Operating System :: MacOS :: MacOS X",
        "Programming Language :: Python :: 3.9",
        "Programming Language :: Python :: 3.10",
        "Programming Language :: Python :: 3.11",
        "Programming Language :: Python :: 3.12",
    ],
)