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pyproject.toml
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pyproject.toml
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# needed for installation of refinegems
[build-system]
requires = ["setuptools"]
build-backend = "setuptools.build_meta"
[project]
name = "refineGEMs"
version = "2.0.0-alpha.1"
requires-python = ">=3.10, <3.12"
authors = [
{name = "Famke Baeuerle", email = "[email protected]"},
{name = "Gwendolyn O. Döbel", email = "[email protected]"},
{name = "Carolin Brune", email = "[email protected]"}
]
maintainers = [
{name = "Tobias Fehrenbach"},
{name = "Nina Roßbach"},
]
description='refineGEMs: a python package intended to help with the curation of genome-scale metabolic models (GEMS)'
license = {text = "MIT"}
readme = 'README.md'
keywords = ['Systems Biology', 'GEM', 'Metabolic Modelling', 'Python Package']
classifiers = [
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Programming Language :: Python",
"Programming Language :: SQL",
"License :: OSI Approved :: MIT License",
]
# dynamic = ['version']
dependencies = [
# cobra changed model.add_reaction to model.add_reactions -> important in investigate.py
"biopython>=1.79",
"bioregistry>=0.10.132",
"bioservices>=1.11.2",
"click>=8.1.3",
"cloup>=3.0.5",
"cobra>=0.28.0",
"depinfo>=1.7.0",
"gffutils>=0.10.1",
"libchebipy>=1.0.10",
"markupsafe>=2.0.1",
'matplotlib >= 3.8.2',
"memote>=0.17.0",
"multiprocess>=0.70.16",
"numpy>=1.20.3,<2.0.0", # @TODO wait for update? >2.0.0 not working properly
"ols-client>=0.1.3",
"pandas>=1.2.4",
'pyyaml>=6.0.1',
"ratelimit>=2.2.1",
'requests>=2.32.2',
"sboannotator>=3.0.2",
"seaborn>=0.12.2",
"sortedcontainers>=2.4.0",
"sqlalchemy>=2.0.0",
"sqlite_dump>=0.1.1",
'tqdm>=4.66.1',
"venn>=0.1.3",
"z3-solver>=4.13.0.0",
]
[project.optional-dependencies]
# developer/docs installation dependancies
docs = ["accessible-pygments",
"sphinx",
"nbsphinx",
"sphinx_rtd_theme",
"pandoc",
"ipython",
"sphinxcontrib-bibtex",
"sphinx_copybutton",
"pip-tools"]
[project.urls]
# homepage
repository = 'https://github.com/draeger-lab/refinegems'
documentation = 'https://refinegems.readthedocs.io/en/latest/'
"Bug Tracker" = "https://github.com/draeger-lab/refinegems/issues"
[project.scripts]
refinegems = "refinegems.cmd_access:cli"
# [tool.setuptools.dynamic]
# version = {attr = "refinegems.VERSION"}
[tool.setuptools.packages.find]
where = ['src']
[tool.setuptools.package-data]
"refinegems.example.example_inputs" = ['*.xlsx','*.csv']
"refinegems.data.database" = ['*.txt', '*.sql', '*.db', '*.csv']
"refinegems.data.config" = ['*.yaml','*.yml']
"refinegems.data.pathway" = ['*.csv']