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539
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1 from setuptools import setup, find_packages
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542
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2 import os
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3
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4 # Get the path to README.md in the parent directory
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5 readme_path = os.path.join(os.path.dirname(__file__), '..', 'README.md')
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6
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7 setup(
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8 name='cobraxy',
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9 version='0.1.0',
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10 description='A collection of tools for metabolic flux analysis in Galaxy.',
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542
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11 long_description=open(readme_path, encoding="utf-8").read(),
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539
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12 long_description_content_type='text/markdown',
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542
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13 author='Francesco Lapi',
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14 author_email='f.lapi@campus.unimib.it',
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539
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15 url='https://github.com/CompBtBs/COBRAxy.git',
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16 license='',
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542
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17 package_dir={'cobraxy': '.'}, # Mappa il package 'cobraxy' alla directory corrente
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18 packages=['cobraxy', 'cobraxy.utils', 'cobraxy.local'], # Solo packages sotto cobraxy
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19 package_data={
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20 'cobraxy': ['*.py'], # Include i moduli Python principali
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21 'cobraxy.local': ['**/*'], # Include all files in local directory
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22 'cobraxy.utils': ['**/*'], # Include all files in utils directory
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23 },
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539
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24 include_package_data=True,
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25 install_requires=[
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542
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26 'cairosvg>=2.7.0',
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27 'cobra>=0.29.0',
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28 'joblib>=1.3.0',
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29 'lxml>=5.0.0',
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30 'matplotlib>=3.7.0',
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31 'numpy>=1.24.0',
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32 'pandas>=2.0.0',
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33 'pyvips>=2.2.0',
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34 'scikit-learn>=1.3.0',
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35 'scipy>=1.11.0',
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36 'seaborn>=0.13.0',
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37 'svglib>=1.5.0',
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38 'anndata>=0.8.0',
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39 'pydeseq2>=0.4.0'
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539
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40 ],
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41 entry_points={
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42 'console_scripts': [
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542
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43 'importMetabolicModel=cobraxy.importMetabolicModel:main',
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44 'exportMetabolicModel=cobraxy.exportMetabolicModel:main',
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45 'ras_generator=cobraxy.ras_generator:main',
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46 'rps_generator=cobraxy.rps_generator:main',
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47 'marea_cluster=cobraxy.marea_cluster:main',
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48 'marea=cobraxy.marea:main',
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49 'ras_to_bounds=cobraxy.ras_to_bounds:main',
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50 'flux_simulation=cobraxy.flux_simulation:main',
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51 'flux_to_map=cobraxy.flux_to_map:main'
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539
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52 ],
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53 },
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54 classifiers=[
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55 'Programming Language :: Python :: 3',
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542
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56 'Programming Language :: Python :: 3.8',
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57 'Programming Language :: Python :: 3.9',
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58 'Programming Language :: Python :: 3.10',
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59 'Programming Language :: Python :: 3.11',
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60 'Programming Language :: Python :: 3.12',
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61 'Programming Language :: Python :: 3.13',
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539
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62 'License :: OSI Approved :: MIT License',
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63 'Operating System :: OS Independent',
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64 ],
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65 python_requires='>=3.8,<3.14',
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66 )
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