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setup.py
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setup.py
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#!/usr/bin/env python
# -*- encoding: utf-8 -*-
"""Setup dot py."""
import os
import platform
import subprocess
import sys
import urllib.request
from os.path import dirname, join
from pathlib import Path
from setuptools import Extension, find_packages, setup
from setuptools.command.build_ext import build_ext
from setuptools.command.develop import develop
from setuptools.command.install import install
CNS_BINARIES = {
"x86_64-linux": "https://surfdrive.surf.nl/files/index.php/s/BWa5OimzbNliTi6/download",
"x86_64-darwin": "https://surfdrive.surf.nl/files/index.php/s/3Fzzte0Zx0L8GTY/download",
"arm64-darwin": "https://surfdrive.surf.nl/files/index.php/s/bYB3xPWf7iwo07X/download",
"aarch64-linux": "https://surfdrive.surf.nl/files/index.php/s/3rHpxcufHGrntHn/download",
}
cpp_extensions = [
Extension(
"haddock.bin.contact_fcc",
sources=["src/haddock/deps/contact_fcc.cpp"],
extra_compile_args=["-O2"],
),
Extension(
"haddock.bin.fast_rmsdmatrix",
sources=["src/haddock/deps/fast-rmsdmatrix.c"],
extra_compile_args=["-Wall", "-O3", "-march=native", "-std=c99"],
extra_link_args=["-lm"],
),
]
class CustomBuild(build_ext):
"""Custom build handles the C/C++ dependencies"""
def run(self):
print("Building HADDOCK3 C/C++ binary dependencies...")
self.build_executable(
name="contact_fcc",
cmd=["g++", "-O2", "-o", "contact_fcc", "src/haddock/deps/contact_fcc.cpp"],
)
self.build_executable(
name="fast-rmsdmatrix",
cmd=[
"gcc",
"-Wall",
"-O3",
"-march=native",
"-std=c99",
"-o",
"fast-rmsdmatrix",
"src/haddock/deps/fast-rmsdmatrix.c",
"-lm",
],
)
# Run the standard build_ext
build_ext.run(self)
def build_executable(self, name, cmd):
"""Helper function to execute the build command"""
try:
subprocess.check_call(cmd)
# Ensure the source bin directory exists
src_bin_dir = Path("src", "haddock", "bin")
src_bin_dir.mkdir(exist_ok=True, parents=True)
# Move the built executable to the source bin directory
src_bin_exec = Path(src_bin_dir, name)
if src_bin_exec.exists():
src_bin_exec.unlink()
self.move_file(name, src_bin_exec)
# If build_lib exists, also copy to there
if hasattr(self, "build_lib"):
build_bin_dir = Path(self.build_lib, "haddock", "bin")
build_bin_dir.mkdir(exist_ok=True, parents=True)
self.copy_file(Path(src_bin_dir, name), Path(build_bin_dir, name))
print(f"Successfully built and moved {name}")
except subprocess.CalledProcessError as e:
print(f"Error building {name}: {e}")
raise
class CustomInstall(install):
"""Custom class to handle the download of the CNS binary"""
def run(self):
install.run(self)
if self.install_lib is None:
print("Something went wrong during installation")
sys.exit(1)
arch = self.get_arch()
if arch not in CNS_BINARIES:
print(f"Unknown architecture: {arch}")
sys.exit(1)
cns_binary_url = CNS_BINARIES[arch]
src_bin_dir = Path("src", "haddock", "bin")
src_bin_dir.mkdir(exist_ok=True, parents=True)
cns_exec = Path(src_bin_dir, "cns")
status, msg = self.download_file(cns_binary_url, cns_exec)
if not status:
print(msg)
sys.exit(1)
# Make it executable
os.chmod(cns_exec, 0o755)
# check if this is being done via `pip install .`
if hasattr(self, "install_lib"):
install_bin_dir = Path(self.install_lib, "haddock", "bin")
install_bin_dir.mkdir(exist_ok=True, parents=True)
self.copy_file(cns_exec, Path(install_bin_dir, "cns"))
@staticmethod
def download_file(url, dest) -> tuple[bool, str]:
"""Download a file from a URL"""
try:
urllib.request.urlretrieve(url, dest)
return True, "Download successful"
except Exception as e: # pylint: disable=broad-except
return False, f"Download failed: {e}"
@staticmethod
def get_arch():
"""Helper function to figure out the architetchure"""
system = platform.system().lower()
machine = platform.machine().lower()
return f"{machine}-{system}"
class CustomDevelop(develop):
def run(self):
"""Wrapper class to run the installation also when using `python setup.py develop`"""
self.run_command("install")
develop.run(self)
with open("requirements.txt", "r", encoding="utf-8") as f:
requirements = f.read().splitlines()
def read_description(*names, **kwargs) -> str:
"""Read description files."""
path = join(dirname(__file__), *names)
with open(path, encoding=kwargs.get("encoding", "utf8")) as fh:
return fh.read()
readme = read_description("README.md")
changelog = read_description("CHANGELOG.md")
long_description = f"{readme}{os.linesep}{changelog}"
setup(
name="haddock3",
version="3.0.0",
description="HADDOCK3",
long_description=long_description,
long_description_content_type="text/markdown",
license="Apache License 2.0",
author="BonvinLab",
author_email="bonvinlab.support@uu.nl",
url="https://github.com/haddocking/haddock3",
packages=find_packages("src"),
package_dir={"": "src"},
package_data={"haddock": ["bin/*"]},
include_package_data=True,
zip_safe=False,
classifiers=[
# TODO: Update the classifiers - http://pypi.python.org/pypi?%3Aaction=list_classifiers
"Development Status :: 4 - Beta",
"License :: OSI Approved :: Apache Software License",
"Natural Language :: English",
"Operating System :: POSIX",
"Operating System :: POSIX :: Linux",
"Operating System :: MacOS",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Chemistry",
"Topic :: Scientific/Engineering :: Physics",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
],
project_urls={
"webpage": "https://bonvinlab.org/haddock3",
"Documentation": "https://github.com/haddocking/haddock3#readme",
"Changelog": "",
"Issue Tracker": "https://github.com/haddocking/haddock3/issues",
"Discussion Forum": "https://github.com/haddocking/haddock3/issues",
},
keywords=[
"Structural Biology",
"Biochemistry",
"Docking",
"Protein docking",
"Proteins",
],
python_requires=">=3.9, <3.11",
install_requires=[requirements],
extras_require={},
setup_requires=[],
entry_points={
"console_scripts": [
"haddock3 = haddock.clis.cli:maincli",
"haddock3-mpitask = haddock.clis.cli_mpi:maincli",
"haddock3-bm = haddock.clis.cli_bm:maincli",
"haddock3-cfg = haddock.clis.cli_cfg:maincli",
"haddock3-clean = haddock.clis.cli_clean:maincli",
"haddock3-copy = haddock.clis.cli_cp:maincli",
"haddock3-dmn = haddock.clis.cli_dmn:maincli",
"haddock3-pp = haddock.clis.cli_pp:maincli",
"haddock3-score = haddock.clis.cli_score:maincli",
"haddock3-unpack = haddock.clis.cli_unpack:maincli",
"haddock3-analyse = haddock.clis.cli_analyse:maincli",
"haddock3-traceback = haddock.clis.cli_traceback:maincli",
"haddock3-re = haddock.clis.cli_re:maincli",
"haddock3-restraints = haddock.clis.cli_restraints:maincli",
]
},
cmdclass={
"build_ext": CustomBuild,
"install": CustomInstall,
"develop": CustomDevelop,
},
ext_modules=cpp_extensions,
)