-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathpyproject.toml
199 lines (194 loc) · 4.14 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
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "omnipath"
version = "1.0.9"
description = "Python client for the OmniPath web service"
license = "MIT"
authors = [
{ name = "Michal Klein", email = "[email protected]" },
{ name = "Dénes Türei", email = "[email protected]" },
]
maintainers = [
{ name = "Dénes Türei", email = "[email protected]" },
]
readme = "README.rst"
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Natural Language :: English",
"Typing :: Typed",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
keywords = [
"protein",
"mRNA",
"miRNA",
"DNA",
"signaling",
"SignaLink",
"SIGNOR",
"InnateDB",
"IntAct",
"Reactome",
"MPPI",
"NCI-PID",
"DIP",
"MatrixDB",
"PANTHER",
"PhosphoSite",
"PhosphoPoint",
"DEPOD",
"SPIKE",
"KEGG",
"Autophagy",
"ARN",
"NRF2ome",
"Guide to Pharmacology",
"UniProt",
"BioPAX",
"Ensembl",
"Surfaceome",
"Exocarta",
"Vesiclepedia",
"Matrisome",
"Human Protein Atlas",
"Compleat",
"CORUM",
"ComplexPortal",
"BioGRID",
"STRING",
"ICELLNET",
"Cell Surface Protein Atlas",
"COSMIC",
"Cancer Gene Census",
"IntOGen",
"TopDB",
"iTALK",
"Human Plasma Membrane Receptome",
"EMBRACE",
"ELM",
"phospho.ELM",
"CancerSEA",
"ComPPI",
"CellPhoneDB",
"DGIdb",
"DisGeNet",
"PAZAR",
"ORegAnno",
"TRED",
"DoRothEA",
"TRRD",
"CPAD",
"regulation",
"phosphorylation",
"kinase",
"phosphatase",
"dephosphorylation",
"directed graph",
"annotations",
"cancer",
"complexes",
"intercellular communication",
"HGNC",
"GPCRdb",
"MSigDB",
"GSEA",
"Phobius",
"Phosphatome",
"NetPath",
"gene",
"gene symbol",
"mouse",
"rat",
"HomoloGene",
"integrin",
"adhesion",
"receptor",
"ligand",
"transporter",
"ion channel",
"disease",
"activity flow",
"transcription",
"PPI",
"subcellular localization",
"pathway",
"signaling pathway",
]
requires-python = ">=3.9"
dependencies = [
"attrs>=20.2.0",
"docrep>=0.3.1",
"inflect>=4.1.0",
"packaging>=24.2",
"pandas>=1.2.0",
"requests>=2.24.0",
"tqdm>=4.51.0",
"typing-extensions>=3.7.4.3",
"urllib3>=1.26.0",
"wrapt>=1.12.0",
]
[project.optional-dependencies]
docs = [
"attrs>=20.2.0",
"docrep>=0.3.1",
"inflect>=4.1.0",
"packaging>=24.2",
"pandas>=1.2.0",
"requests>=2.24.0",
"sphinx>=4",
"sphinx-autodoc-annotation>=1.0.post1",
"sphinx-autodoc-typehints>=1.10.3",
"sphinx-copybutton>=0.5.2",
"sphinx-last-updated-by-git>=0.3.8",
"sphinx-paramlinks>=0.6.0",
"sphinx-rtd-theme>=3.0.2",
"sphinx-toolbox>=3.9.0",
"tqdm>=4.51.0",
"typing-extensions>=3.7.4.3",
"urllib3>=1.26.0",
"wrapt>=1.12.0",
]
tests = [
"tox>=3.20.1",
]
graph = [
"networkx>=2.3.0",
]
[dependency-groups]
dev = [
"bump2version>=1.0.1",
"codecov-cli>=10.2.0",
"pre-commit>=2.7.1",
"tox-gh>=1.5.0",
]
[project.urls]
Homepage = "https://omnipathdb.org/"
Documentation = "https://omnipath.readthedocs.io/"
Repository = "https://github.com/saezlab/omnipath"
Issues = "https://github.com/saezlab/omnipath/issues"
[tool.isort]
from_first = true
line_length = 88
multi_line_output = 3
include_trailing_comma = true
use_parentheses = true
known_num="numpy,pandas"
sections = "FUTURE,STDLIB,THIRDPARTY,NUM,FIRSTPARTY,LOCALFOLDER"
no_lines_before="LOCALFOLDER"
balanced_wrapping = true
force_grid_wrap = 0
length_sort = "1"
indent = " "
skip_glob = "docs/source/conf.py"