--- a/SeqSero2/setup.py	Wed Mar 01 13:21:51 2023 -0500
+++ b/SeqSero2/setup.py	Tue Mar 25 23:22:38 2025 -0400
@@ -1,19 +1,30 @@
+import os, sys
+from distutils.core import setup
+from setuptools import find_packages
 
-from distutils.core import setup
+def readme():
+    with open('README.md') as f:
+        return f.read()
 
-setup(
-    name = "seqsero2",
-    version = "2.0",
-    author = "DengLab",
-    author_email = "seqsero@gmail.com",
-    description = ("Serotyping for Salmonella."),
-    license = "GPL-2.0",
-    keywords = "salmonella",
-    url = "https://github.com/CFSAN-Biostatistics/SeqSero2",
-    packages=['seqsero2'],
-    scripts=['scripts/SeqSero2.py'],
-     entry_points={
-        'console_scripts': ['SeqSero2 = seqsero2.SeqSero2:main']
-    },
-    package_dir = {'seqsero': 'scripts'}
+setup(name='SeqSero2',
+    version=open("version.py").readlines()[-1].split()[-1].strip("\"'"),
+    description='Salmonella serotyping',
+    long_description=readme(),
+    classifiers=[
+        'Development Status :: 3 - Alpha',
+        'License :: OSI Approved :: GNU General Public License v2 (GPLv2)',
+        'Programming Language :: Python :: 3',
+        'Topic :: Text Processing :: Linguistic',
+        ],
+    keywords='Salmonella serotyping bioinformatics WGS',
+    url='https://github.com/denglab/SeqSero2/',
+    author='Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng',
+    author_email='zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu',
+    license='GPLv2',
+    scripts=["bin/deinterleave_fastq.sh","bin/Initial_Conditions.py","bin/SeqSero2_package.py","bin/SeqSero2_update_kmer_database.py"],
+    packages=[""],
+    include_package_data = True,
+    install_requires=['biopython==1.73'],
+    data_files=[("seqsero2_db",["seqsero2_db/antigens.pickle","seqsero2_db/H_and_O_and_specific_genes.fasta","seqsero2_db/invA_mers_dict","seqsero2_db/special.pickle"])],
+    zip_safe=False,
 )