import codecs

import os.path

from setuptools import find_packages, setup

with open("README.md", encoding="UTF-8") as fh:

long_description = fh.read()

def read(rel_path):

here = os.path.abspath(os.path.dirname(__file__))

with codecs.open(os.path.join(str(here), rel_path), "r") as fp:

return fp.read()

def get_version(rel_path):

for line in read(rel_path).splitlines():

if line.startswith("__version__"):

delim = '"' if '"' in line else "'"

return line.split(delim)[1]

raise RuntimeError("Unable to find version string.")

setup(

name="mzidentml-reader",

version="0.4.24",

description="mzidentml-reader uses pyteomics (https://pyteomics.readthedocs.io/en/latest/index.html) to "

"parse mzIdentML files (v1.2.0 and v1.3.0) and extract crosslink information. Results are written to a "

"relational database (PostgreSQL or SQLite) using sqlalchemy.",

long_description_content_type="text/markdown",

long_description=long_description,

author="Colin Combe, Lars Kolbowski, Suresh Hewapathirana",

license="Apache 2.0",

url="https://github.com/PRIDE-Archive/mzidentml-reader",

packages=find_packages(),

include_package_data=True,

package_data={"config": ["logging.ini"], "schema": ["*.xsd"]},

install_requires=[

"lxml>=4.9.1",

"numpy>=1.14.3",

"pandas>=0.21.0",

"pymzml>=0.7.8",

"pyteomics>=5.0.0",

"psims",

"requests>=2.31.0",

"urllib3>=2.6.3",

"psycopg2-binary",

"sqlalchemy>=2.0.38",

"sqlalchemy-utils",

"obonet==1.1.0",

"orjson",

"virtualenv>=20.36.1",

"filelock>=3.20.3",

"certifi>=2023.7.22",

],

entry_points={

"console_scripts": ["process_dataset = parser.process_dataset:main"]

},

platforms=["any"],

classifiers=[

"Programming Language :: Python :: 3",

"License :: OSI Approved :: Apache Software License",

"Operating System :: OS Independent",

"Topic :: Scientific/Engineering :: Bio-Informatics",

],

keywords="crosslinking python proteomics",

python_requires=">=3.10",

)