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comparison COBRAxy/src/setup.py @ 542:fcdbc81feb45 draft

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author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
parents 2fb97466e404
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541:fa93040a75af 542:fcdbc81feb45
1 from setuptools import setup, find_packages 1 from setuptools import setup, find_packages
2 import os
3
4 # Get the path to README.md in the parent directory
5 readme_path = os.path.join(os.path.dirname(__file__), '..', 'README.md')
2 6
3 setup( 7 setup(
4 name='cobraxy', 8 name='cobraxy',
5 version='0.1.0', 9 version='0.1.0',
6 description='A collection of tools for metabolic flux analysis in Galaxy.', 10 description='A collection of tools for metabolic flux analysis in Galaxy.',
7 long_description=open('README.md',encoding="utf-8").read(), 11 long_description=open(readme_path, encoding="utf-8").read(),
8 long_description_content_type='text/markdown', 12 long_description_content_type='text/markdown',
9 author='', 13 author='Francesco Lapi',
10 author_email='', 14 author_email='f.lapi@campus.unimib.it',
11 url='https://github.com/CompBtBs/COBRAxy.git', 15 url='https://github.com/CompBtBs/COBRAxy.git',
12 license='', 16 license='',
13 packages=find_packages(include=["utils", "utils.*"]), 17 package_dir={'cobraxy': '.'}, # Mappa il package 'cobraxy' alla directory corrente
14 py_modules=[ 18 packages=['cobraxy', 'cobraxy.utils', 'cobraxy.local'], # Solo packages sotto cobraxy
15 'ras_generator', 19 package_data={
16 'rps_generator', 20 'cobraxy': ['*.py'], # Include i moduli Python principali
17 'marea_cluster', 21 'cobraxy.local': ['**/*'], # Include all files in local directory
18 'marea', 22 'cobraxy.utils': ['**/*'], # Include all files in utils directory
19 'metabolic_model_setting', 23 },
20 'ras_to_bounds',
21 'flux_simulation',
22 'flux_to_map'
23 ],
24 include_package_data=True, 24 include_package_data=True,
25 install_requires=[ 25 install_requires=[
26 'cairosvg==2.7.1', 26 'cairosvg>=2.7.0',
27 'cobra==0.29.0', 27 'cobra>=0.29.0',
28 'joblib==1.4.2', 28 'joblib>=1.3.0',
29 'lxml==5.2.2', 29 'lxml>=5.0.0',
30 'matplotlib==3.7.3', 30 'matplotlib>=3.7.0',
31 'numpy==1.24.4', 31 'numpy>=1.24.0',
32 'pandas==2.0.3', 32 'pandas>=2.0.0',
33 'pyvips==2.2.3', 33 'pyvips>=2.2.0',
34 'scikit-learn==1.3.2', 34 'scikit-learn>=1.3.0',
35 'scipy==1.11', 35 'scipy>=1.11.0',
36 'seaborn==0.13.0', 36 'seaborn>=0.13.0',
37 'svglib==1.5.1', 37 'svglib>=1.5.0',
38 'anndata==0.8.0', 38 'anndata>=0.8.0',
39 'pydeseq2==0.5.1' 39 'pydeseq2>=0.4.0'
40 ], 40 ],
41 entry_points={ 41 entry_points={
42 'console_scripts': [ 42 'console_scripts': [
43 'metabolic_model_setting=metabolic_model_setting:main', 43 'importMetabolicModel=cobraxy.importMetabolicModel:main',
44 'ras_generator=ras_generator:main', 44 'exportMetabolicModel=cobraxy.exportMetabolicModel:main',
45 'rps_generator=rps_generator:main', 45 'ras_generator=cobraxy.ras_generator:main',
46 'marea_cluster=marea_cluster:main', 46 'rps_generator=cobraxy.rps_generator:main',
47 'marea=marea:main', 47 'marea_cluster=cobraxy.marea_cluster:main',
48 'ras_to_bounds=ras_to_bounds:main', 48 'marea=cobraxy.marea:main',
49 'flux_simulation=flux_simulation:main', 49 'ras_to_bounds=cobraxy.ras_to_bounds:main',
50 'flux_to_map=flux_to_map:main' 50 'flux_simulation=cobraxy.flux_simulation:main',
51 'flux_to_map=cobraxy.flux_to_map:main'
51 ], 52 ],
52 }, 53 },
53 classifiers=[ 54 classifiers=[
54 'Programming Language :: Python :: 3', 55 'Programming Language :: Python :: 3',
56 'Programming Language :: Python :: 3.8',
57 'Programming Language :: Python :: 3.9',
58 'Programming Language :: Python :: 3.10',
59 'Programming Language :: Python :: 3.11',
60 'Programming Language :: Python :: 3.12',
61 'Programming Language :: Python :: 3.13',
55 'License :: OSI Approved :: MIT License', 62 'License :: OSI Approved :: MIT License',
56 'Operating System :: OS Independent', 63 'Operating System :: OS Independent',
57 ], 64 ],
58 python_requires='>=3.8.20,<3.12', 65 python_requires='>=3.8,<3.14',
59 ) 66 )