bedhost/pyproject.toml at master · databio/bedhost · 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
[project]
name = "bedhost"
dynamic = ["version"]
description = "A database server application that provides both a RESTful API and GUI for access to BED files and related basic statistics"
readme = "README.md"
license = "BSD-2-Clause"
requires-python = ">=3.10"
authors = [
    { name = "Oleksandr Khoroshevskyi" },
    { name = "Michal Stolarczyk" },
    { name = "Ognen Duzlevski" },
    { name = "Bingjie Xue" },
    { name = "Nathan Sheffield" },
]
keywords = [
    "project",
    "bioinformatics",
    "sequencing",
    "ngs",
    "workflow",
    "GUI",
    "bed",
    "server",
]
classifiers = [
    "Development Status :: 4 - Beta",
    "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",
]
dependencies = [
    "bbconf>=0.15.0",
    "fastapi>=0.103.0",
    "sentence_transformers>=5.0",
    "logmuse>=0.3.1",
    "markdown",
    "requests",
    "uvicorn",
    "yacman>=1.0.0",
    "pephubclient>=0.4.1",
    "psycopg[binary,pool]",
    "python-multipart>=0.0.9",
    "APScheduler>=3.11.0",
    "cachetools>=4.2.4",
    "bedboss>=0.12.0",
    "Pillow>=10.0.0",
]

[project.urls]
Homepage = "https://github.com/databio/bedhost"

[project.scripts]
bedhost = "bedhost.__main__:main"

[project.optional-dependencies]
test = [
    "pytest",
    "httpx",
]

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

# bedhost is NOT installed as a distribution in production: the Docker image runs
# `uvicorn bedhost.main:app` from the copied source tree (see Dockerfile). The
# version is therefore kept in an importable source module (bedhost/_version.py)
# and read via `import`, never via importlib.metadata. hatchling reads the same
# file so PyPI wheels are versioned correctly too.
[tool.hatch.version]
path = "bedhost/_version.py"

[tool.hatch.build.targets.wheel]
packages = ["bedhost"]

[tool.pytest.ini_options]
addopts = "-rfE"
testpaths = ["tests"]
markers = [
    "require_service: marks test as requiring a running bedhost service (deselect with '-m \"not require_service\"')",
]

[tool.ruff]
line-length = 88
# Root-level experimentation script, not part of the package.
extend-exclude = ["interactive.py"]

[tool.ruff.lint]
select = ["E", "F", "I"]
ignore = ["F403", "F405", "E501"]

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