atomica-mcp/pyproject.toml at main · longevity-genie/atomica-mcp · 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
[project]
name = "atomica-mcp"
version = "0.1.5"
description = "MCP server for PDB structure queries and protein resolution using AnAge database"
readme = "README.md"
authors = [
    { name = "Anton Kulaga", email = "antonkulaga@gmail.com" },
    { name = "Newton Winter" },
    { name = "Livia Zaharia" }
]
requires-python = ">=3.11"
dependencies = [
    "biotite>=1.5.0",
    "eliot>=1.17.5",
    "fastmcp>=2.12.5",
    "fsspec>=2025.9.0",
    "huggingface-hub>=0.35.3",
    "numpy>=2.3.4",
    "polars>=1.34.0",
    "pycomfort>=0.0.18",
    "requests>=2.32.5",
    "rich>=13.9.0",
    "tenacity>=9.1.2",
    "typer>=0.20.0",
    "urllib3>=2.5.0",
]

[project.scripts]
atomica-mcp = "atomica_mcp.__main__:cli_app_stdio_standalone"
atomica-stdio = "atomica_mcp.__main__:cli_app_stdio_standalone"
atomica-sse = "atomica_mcp.__main__:cli_app_sse_standalone"
atomica-run = "atomica_mcp.__main__:cli_app_run"
atomica-cli = "atomica_mcp.__main__:app"
dataset = "atomica_mcp.dataset:app"
pdb-mining = "atomica_mcp.mining.cli:main"
upload-to-hf = "atomica_mcp.upload_to_hf:app"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[dependency-groups]
dev = [
    "jupyter>=1.1.1",
    "jupyterlab>=4.4.10",
    "pytest>=8.4.2",
    "pytest-asyncio>=1.2.0",
    "pytest-timeout>=2.3.1",
]

[tool.hatch.build.targets.wheel]
packages = ["src/atomica_mcp"]

[tool.hatch.build.targets.sdist]
exclude = [
    "data/",
    "logs/",
    "notebooks/",
    "docs/",
    "tests/",
    "examples/",
    ".pytest_cache/",
    "*.log",
    "*.json",
    "mcp-config-*.json",
]

[tool.uv]
package = true

[tool.uv.sources]