/
pyproject.toml
130 lines (123 loc) · 3.15 KB
/
pyproject.toml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
[build-system]
requires = ["poetry_core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "pypath-omnipath"
version = "0.16.15"
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"