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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["poetry_core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "pypath-omnipath"
version = "0.16.19"
description = "Molecular signaling prior knowledge processing"
license = "GPL-3.0-only"
authors = [
"Denes Turei <turei.denes@gmail.com>",
"Nicolàs Palacio",
"Sebastian Lobentanzer",
"Olga Ivanova",
"Melih Darcan",
"Erva Ulusoy",
"Tennur Kilic",
"Omer Kaan Vural",
"Ahmet Rifaioglu",
"Charles Tapley Hoyt"
]
packages = [
{ include = "pypath" }
]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Natural Language :: English",
"Topic :: Software Development :: Libraries :: Python Modules",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Topic :: Scientific/Engineering :: Information Analysis",
"Topic :: Scientific/Engineering :: Mathematics"
]
repository = "https://github.com/saezlab/pypath"
homepage = "https://omnipathdb.org/"
readme = "README.rst"
keywords = [
"systems biology",
"molecular biology",
"omics",
"network",
"signaling"
]
[tool.poetry.urls]
"Bug Tracker" = "https://github.com/saezlab/pypath/issues"
[tool.poetry.dependencies]
python = "^3.9"
beautifulsoup4 = "*"
dill = "*"
future = "*"
glom = "*"
lxml = "*"
matplotlib = "*"
numpy = "*"
openpyxl = "*"
pandas = "*"
psutil = "*"
pycurl = "*"
pypath-common = ">=0.2.0"
pyreadr = "*"
PyYAML = "*"
rdata = "*"
requests = "*"
scipy = ">=1.9.0"
sqlparse = "*"
tabulate = "*"
timeloop = "*"
toml = "*"
tqdm = "*"
xlrd = "*"
# pybel = { version = "*", optional = true, extras = [] }
# bio2bel = { version = "*", optional = true, extras = [] }
# click = { version = "*", optional = true }
python-igraph = { version = "*", optional = true }
sparqlwrapper = { version = "*", optional = true }
openbabel = { version = "*", optional = true }
rdkit = { version = "*", optional = true }
"epam.indigo" = { version = "*", optional = true }
pysftp = "^0.2.9"
typing_extensions = "*"
tornado = ">=3.6.6"
cryptography = ">=41.0.4"
certifi = ">=2023.7.22"
[tool.poetry.extras]
# bel = [
# "pybel",
# "bio2bel",
# "click",
# ]
graph = [
"python-igraph",
]
pathophenodb = [
"sparqlwrapper",
]
metabo = [
"epam.indigo",
"openbabel",
"rdkit",
]
[tool.poetry.dev-dependencies]
bump2version = "*"
sphinx = ">=5.0.0"
insipid-sphinx-theme = ">=0.3.6"
sphinx-last-updated-by-git = ">=0.3"
sphinx-autodoc-typehints = ">=1.18.0"
sphinxcontrib-fulltoc = ">=1.2.0"
sphinx_copybutton = "*"
jupyterlab = "*"
notebook = "6.4.12"
pydata-sphinx-theme = "*"
sphinx_remove_toctrees = "*"
jupyter-contrib-nbextensions = { git = "https://github.com/deeenes/jupyter_contrib_nbextensions.git", branch = "master" }
nbsphinx = { git = "https://github.com/deeenes/nbsphinx.git", branch = "timings" }
jupyter-server = ">=2.7.2"
traitlets = "5.9.0"
[tool.poetry.scripts]
bio2bel_omnipath = "pypath.omnipath.bel:main"
[tool.poetry.plugins."bio2bel"]
omnipath = "pypath.omnipath.bel"