lightcone-cli/pyproject.toml at main · LightconeResearch/lightcone-cli · 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
[project]
name = "lightcone-cli"
dynamic = ["version"]
description = "Lightcone command-line toolchain"
readme = "README.md"
license = { text = "BSD-3-Clause" }
requires-python = ">=3.11"
authors = [
    { name = "Lightcone Research" }
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: Python :: 3 :: Only",
    "Topic :: Scientific/Engineering",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Human Machine Interfaces",
]

dependencies = [
    "astra-tools>=0.2.5",
    "click>=8.0",
    "pyyaml>=6.0",
    "rich>=13.0",
    "jinja2>=3.0",
    "snakemake>=9.0",
    "snakemake-interface-executor-plugins>=9.0",
    "snakemake-interface-common>=1.14",
    "dask>=2024.1",
    "distributed>=2024.1",
    "rocrate>=0.11",
]

[dependency-groups]
eval = [
    "anthropic>=0.90",
    "build>=1.0",
    "daytona-sdk>=0.140",
    "pydantic>=2.0",
    "python-dotenv>=1.0",
]
dev = [
    "pytest>=8.0",
    "pytest-cov",
    "ruff",
    "mypy",
    "types-PyYAML",
]
docs = [
    "zensical>=0.0.33",
]


[project.scripts]
lc = "lightcone.cli:main"

[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[tool.hatch.version]
source = "vcs"

[tool.hatch.build.targets.wheel]
packages = [
    "src/lightcone",
    "src/snakemake_executor_plugin_dask",
]

[tool.hatch.build.targets.wheel.force-include]
"claude/lightcone" = "lightcone/cli/claude/lightcone"

[tool.hatch.build.targets.sdist]
include = [
    "src/lightcone",
    "src/snakemake_executor_plugin_dask",
    "claude/lightcone",
]

[tool.ruff]
target-version = "py311"
line-length = 100

[tool.ruff.lint]
select = ["E", "F", "I", "N", "W", "UP"]

[tool.mypy]
python_version = "3.11"
strict = true
namespace_packages = true
explicit_package_bases = true
mypy_path = "src"

[[tool.mypy.overrides]]
module = ["dask.*", "distributed.*"]
ignore_missing_imports = true
follow_untyped_imports = true

[[tool.mypy.overrides]]
module = ["rocrate.*"]
ignore_missing_imports = true

[[tool.mypy.overrides]]
module = ["astra.*"]
ignore_missing_imports = true
follow_untyped_imports = true

[[tool.mypy.overrides]]
module = ["daytona_sdk", "daytona_sdk.*", "dotenv", "dotenv.*"]
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
markers = [
    "slow: tests that spin up real subsystems (dask cluster, etc.) — opt-in via -m slow",
]