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setup.py
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setup.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""The setup script."""
from setuptools import setup, find_packages
with open('README.rst') as readme_file:
readme = readme_file.read()
requirements = [
"reframed>=1.5.3",
"pandas>=1.0",
]
included_files = {
'carveme': [
'config.cfg',
'data/input/bigg_models.csv',
'data/input/biomass_db.tsv',
'data/input/manually_curated.csv',
'data/input/media_db.tsv',
'data/input/metabolomics_park2016.csv',
'data/input/unbalanced_metabolites.csv',
'data/input/bigg_proteins.faa',
'data/input/equilibrator_compounds.tsv.gz',
'data/input/refseq_release_201.tsv.gz',
'data/generated/bigg_gibbs.csv',
'data/generated/bigg_gprs.csv.gz',
'data/generated/model_specific_data.csv.gz',
'data/generated/universe_draft.xml.gz',
'data/generated/universe_bacteria.xml.gz',
'data/generated/universe_grampos.xml.gz',
'data/generated/universe_gramneg.xml.gz',
'data/generated/universe_archaea.xml.gz',
'data/benchmark/media_db.tsv',
'data/benchmark/biolog/bsub/biolog_carbon.tsv',
'data/benchmark/biolog/bsub/biolog_phosphorus.tsv',
'data/benchmark/biolog/bsub/biolog_nitrogen.tsv',
'data/benchmark/biolog/bsub/biolog_sulfur.tsv',
'data/benchmark/biolog/ecol/biolog_carbon.tsv',
'data/benchmark/biolog/ecol/biolog_phosphorus.tsv',
'data/benchmark/biolog/ecol/biolog_nitrogen.tsv',
'data/benchmark/biolog/ecol/biolog_sulfur.tsv',
'data/benchmark/biolog/paer/biolog_carbon.tsv',
'data/benchmark/biolog/rsol/biolog_carbon.tsv',
'data/benchmark/biolog/rsol/biolog_phosphorus.tsv',
'data/benchmark/biolog/rsol/biolog_nitrogen.tsv',
'data/benchmark/biolog/rsol/biolog_sulfur.tsv',
'data/benchmark/biolog/sone/biolog_carbon.tsv',
'data/benchmark/biolog/sone/biolog_nitrogen.tsv',
'data/benchmark/essentiality/bsub.tsv',
'data/benchmark/essentiality/ecol.tsv',
'data/benchmark/essentiality/mgen.tsv',
'data/benchmark/essentiality/paer.tsv',
'data/benchmark/essentiality/sone.tsv',
'data/benchmark/fasta/Bsubtilis_168.faa',
'data/benchmark/fasta/Paeruginosa_PAO1.faa',
'data/benchmark/fasta/Ecoli_K12_MG1655.faa',
'data/benchmark/fasta/M_genitalium_G37.faa',
'data/benchmark/fasta/Rsolanacearum_GMI1000.faa',
'data/benchmark/fasta/Soneidensis_MR1.faa',
'data/benchmark/models/bsub.xml',
'data/benchmark/models/rsol.xml',
'data/benchmark/models/ecol.xml',
'data/benchmark/models/paer.xml',
'data/benchmark/models/sone.xml',
'data/benchmark/models/mgen.xml',
'data/benchmark/results/biolog.tsv',
'data/benchmark/results/essentiality.tsv',
]
}
setup(
name='carveme',
version='1.6.2',
description="CarveMe: automated metabolic model reconstruction",
long_description=readme,
author="Daniel Machado",
author_email='cdanielmachado@gmail.com',
url='https://github.com/cdanielmachado/carveme',
entry_points={
'console_scripts': [
'build_universe=carveme.cli.build_universe:main',
'curate_universe=carveme.cli.curate_universe:main',
'carve=carveme.cli.carve:main',
'gapfill=carveme.cli.gapfill:main',
'merge_community=carveme.cli.merge_community:main',
'benchmark=carveme.cli.benchmark:main',
],
},
# package_dir={'':'src'},
packages=find_packages(),
include_package_data=True,
package_data=included_files,
install_requires=requirements,
license="Apache Software License 2.0",
zip_safe=False,
keywords='carveme',
classifiers=[
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
'License :: OSI Approved :: Apache Software License',
],
setup_requires=['setuptools_scm']
# test_suite='tests',
# tests_require=test_requirements,
)