--- a/COBRAxy/src/setup.py	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/src/setup.py	Sun Oct 26 19:27:41 2025 +0000
@@ -1,59 +1,66 @@
 from setuptools import setup, find_packages
+import os
+
+# Get the path to README.md in the parent directory
+readme_path = os.path.join(os.path.dirname(__file__), '..', 'README.md')
 
 setup(
     name='cobraxy',
     version='0.1.0',
     description='A collection of tools for metabolic flux analysis in Galaxy.',
-    long_description=open('README.md',encoding="utf-8").read(),
+    long_description=open(readme_path, encoding="utf-8").read(),
     long_description_content_type='text/markdown',
-    author='',  
-    author_email='',
+    author='Francesco Lapi',  
+    author_email='f.lapi@campus.unimib.it',
     url='https://github.com/CompBtBs/COBRAxy.git',
     license='',
-    packages=find_packages(include=["utils", "utils.*"]),  
-    py_modules=[
-        'ras_generator',
-        'rps_generator',
-        'marea_cluster',
-        'marea',
-        'metabolic_model_setting',
-        'ras_to_bounds',
-        'flux_simulation',
-        'flux_to_map'
-    ],
+    package_dir={'cobraxy': '.'},  # Mappa il package 'cobraxy' alla directory corrente
+    packages=['cobraxy', 'cobraxy.utils', 'cobraxy.local'],  # Solo packages sotto cobraxy
+    package_data={
+        'cobraxy': ['*.py'],  # Include i moduli Python principali
+        'cobraxy.local': ['**/*'],  # Include all files in local directory
+        'cobraxy.utils': ['**/*'],  # Include all files in utils directory
+    },
     include_package_data=True, 
     install_requires=[
-        'cairosvg==2.7.1',
-        'cobra==0.29.0',
-        'joblib==1.4.2',
-        'lxml==5.2.2',
-        'matplotlib==3.7.3',
-        'numpy==1.24.4',
-        'pandas==2.0.3',
-        'pyvips==2.2.3',
-        'scikit-learn==1.3.2',
-        'scipy==1.11',
-        'seaborn==0.13.0',
-        'svglib==1.5.1',
-        'anndata==0.8.0',
-        'pydeseq2==0.5.1'
+        'cairosvg>=2.7.0',
+        'cobra>=0.29.0',
+        'joblib>=1.3.0',
+        'lxml>=5.0.0',
+        'matplotlib>=3.7.0',
+        'numpy>=1.24.0',
+        'pandas>=2.0.0',
+        'pyvips>=2.2.0',
+        'scikit-learn>=1.3.0',
+        'scipy>=1.11.0',
+        'seaborn>=0.13.0',
+        'svglib>=1.5.0',
+        'anndata>=0.8.0',
+        'pydeseq2>=0.4.0'
     ],
     entry_points={
         'console_scripts': [
-            'metabolic_model_setting=metabolic_model_setting:main',
-            'ras_generator=ras_generator:main',
-            'rps_generator=rps_generator:main',
-            'marea_cluster=marea_cluster:main',
-            'marea=marea:main',
-            'ras_to_bounds=ras_to_bounds:main',
-            'flux_simulation=flux_simulation:main',
-            'flux_to_map=flux_to_map:main'
+            'importMetabolicModel=cobraxy.importMetabolicModel:main',
+            'exportMetabolicModel=cobraxy.exportMetabolicModel:main',
+            'ras_generator=cobraxy.ras_generator:main',
+            'rps_generator=cobraxy.rps_generator:main',
+            'marea_cluster=cobraxy.marea_cluster:main',
+            'marea=cobraxy.marea:main',
+            'ras_to_bounds=cobraxy.ras_to_bounds:main',
+            'flux_simulation=cobraxy.flux_simulation:main',
+            'flux_to_map=cobraxy.flux_to_map:main'
         ],
     },
     classifiers=[
         'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
         'License :: OSI Approved :: MIT License',
         'Operating System :: OS Independent',
     ],
-    python_requires='>=3.8.20,<3.12',
+    python_requires='>=3.8,<3.14',
 )