Omega/pyproject.toml at main · jam-sudo/Omega · GitHub

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
[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "omega-pbpk"
version = "0.9.0"
description = "Whole-body PBPK simulation platform — 35-state ODE engine with ADME prediction, DDI, population PK, and clinical tools"
readme = "README.md"
requires-python = ">=3.10"
license = {text = "MIT"}
keywords = ["pbpk", "pharmacokinetics", "drug-development", "simulation"]
dependencies = [
  "numpy~=1.26",
  "scipy~=1.11",
  "pydantic~=2.0",
  "pyyaml~=6.0",
  "typer~=0.9",
  "pandas~=2.0",
]

[project.urls]
Repository = "https://github.com/jam-sudo/Omega"

[project.optional-dependencies]
ml   = ["torch~=2.0", "rdkit>=2023.0"]
api  = ["fastapi~=0.100", "uvicorn~=0.20", "httpx~=0.24", "python-multipart>=0.0.7"]
auth = ["python-jose[cryptography]>=3.3", "passlib[bcrypt]>=1.7", "bcrypt>=3.0,<4.0", "python-multipart>=0.0.7"]
llm  = ["openai>=1.0"]
viz  = ["matplotlib~=3.7"]
dev = [
  "pytest~=8.0",
  "pytest-cov~=5.0",
  "pytest-timeout>=2.2",
  "ruff~=0.6",
  "mypy~=1.8",
  "types-PyYAML",
  "httpx~=0.24",
  "xgboost>=2.0",
  "rdkit>=2023.0",
  "scikit-learn>=1.3",
  "pint>=0.24",
  "pytest-benchmark~=5.0",
  "beautifulsoup4>=4.12",
  "lxml>=5.0",
]
ml-new = [
    "admet-ai>=1.0",
    "chemprop>=1.0",
    "torchdiffeq>=0.2",
    "xgboost>=2.0",
    "optuna>=3.0",
    "PyTDC>=1.0",
    "torch-geometric>=2.4",
    "requests>=2.28",
]
all = ["omega-pbpk[ml,api,auth,viz,dev]"]

[project.scripts]
omega = "omega_pbpk.cli:main"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
"omega_pbpk" = ["static/*"]

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "B"]
ignore = ["B008", "B017", "B905", "E501"]

[tool.ruff.lint.per-file-ignores]
"src/omega_pbpk/api/app.py" = ["E402"]

[tool.ruff.lint.isort]
known-first-party = ["omega_pbpk"]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"

[tool.mypy]
python_version = "3.10"
strict = true
warn_unused_ignores = true
warn_redundant_casts = true
warn_return_any = true
disallow_untyped_defs = true
ignore_missing_imports = true
disable_error_code = ["import-untyped"]

[tool.pytest.ini_options]
pythonpath = ["src"]
markers = [
    "unit: fast unit tests (< 5ms each, mock externals)",
    "integration: real logic + short simulations (< 2s each)",
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
    "benchmark: marks tests as benchmark (run only in benchmark CI)",
    "regression: marks tests as regression tests",
]

[[tool.mypy.overrides]]
module = [
  "omega_pbpk._compat",
  "omega_pbpk.api.app",
  "omega_pbpk.api.server",
  "omega_pbpk.cli",
  "omega_pbpk.clinical.allometry",
  "omega_pbpk.clinical.dose_optimization",
  "omega_pbpk.clinical.nca",
  "omega_pbpk.clinical.ontogeny",
  "omega_pbpk.clinical.pgx_pbpk",
  "omega_pbpk.clinical.report",
  "omega_pbpk.core.body",
  "omega_pbpk.core.heuristics",
  "omega_pbpk.in_vitro.receptor",
  "omega_pbpk.ml_models.gnn_adme",
  "omega_pbpk.pipeline",
  "omega_pbpk.population.physiology",
  "omega_pbpk.population.pop_simulator",
  "omega_pbpk.prediction.adme_predictor",
  "omega_pbpk.qsp.pd_models",
  "omega_pbpk.sensitivity",
  "omega_pbpk.surrogate.train",
  "omega_pbpk.uncertainty",
  "omega_pbpk.validation.adme_benchmark",
  "omega_pbpk.validation.benchmarks",
  "omega_pbpk.visualization.vpc",
]
ignore_errors = true

[[tool.mypy.overrides]]
module = ["yaml", "torch", "torch.*", "rdkit", "rdkit.*", "fastapi", "uvicorn"]
ignore_missing_imports = true