pip install fixed

MANIFEST.in

@@ -1,4 +1,2 @@
-include sphae/sphae.LICENSE
-include sphae/sphae.CITATION
-include sphae/sphae.VERSION
-recursive-include sphae *
+graft sphae
+

setup.py

@@ -1,5 +1,5 @@
 import os
-from setuptools import find_packages, setup
+from setuptools import setup, find_packages
 
 
 def get_version():
@@ -12,6 +12,12 @@ def get_description():
         long_description = fh.read()
     return long_description
 
+def get_requirements():
+    reqs = []
+    with open('requirements.txt', 'r') as f:
+        for l in f:
+            reqs.append(l.strip())
+    return reqs
 
 def get_data_files():
     data_files = [(".", ["README.md"])]
@@ -22,38 +28,47 @@ def get_data_files():
     "Environment :: Console",
     "Environment :: MacOS X",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT license",
+    "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
     "Operating System :: POSIX :: Linux",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
 ]
 
-setup(
-    name='sphae',
-    description="Assembling pure culture phages from both Illumina and Nanopore sequencing technology",
-    long_description=get_description(),
-    long_description_content_type="text/markdown",
-    version=get_version(),
-    author="Bhavya Papudeshi",
-    author_email="[email protected]",
-    data_files=get_data_files(),
-    py_modules=['sphae'],
-    install_requires=[
-        "snaketool-utils>=0.0.4",
-        "snakemake>=7.14.0",
-        "pyyaml>=6.0",
-        "Click==8.1.3",
-        "metasnek>=0.0.4",
-        "attrmap>=0.0.7",
-        "biopython>=1.8.1",
-        "pandas"
-    ],
-    entry_points={
-        'console_scripts': [
-            'sphae=sphae.__main__:main'
-        ]
-    },
-    include_package_data=True,
-)
+def main():
+    setup(
+        name='sphae',
+        description="Assembling pure culture phages from both Illumina and Nanopore sequencing technology",
+        long_description=get_description(),
+        long_description_content_type="text/markdown",
+        version=get_version(),
+        author="Bhavya Papudeshi",
+        author_email="[email protected]",
+        platforms='any',
+        keywords="phage 'phage therapy' bioinformatics microbiology bacteria genome genomics",
+        data_files=get_data_files(),
+        license='The MIT License (MIT)',
+        url='https://github.com/linsalrob/sphae',
+        packages=find_packages(),
+        include_package_data=True,
+        classifiers=CLASSIFIERS,
+        install_requires=[
+            "snaketool-utils>=0.0.4",
+            "snakemake>=7.14.0",
+            "pyyaml>=6.0",
+            "Click==8.1.3",
+            "metasnek>=0.0.4",
+            "attrmap>=0.0.7",
+            "biopython>=1.8.1",
+            "pandas"
+        ],
+        entry_points={
+            'console_scripts': [
+                'sphae=sphae.__main__:main'
+            ]
+        },
+    )
+
+if __name__ == "__main__":
+    main()