mavedb-api/pyproject.toml at main · VariantEffect/mavedb-api · 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
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "mavedb"
version = "2026.2.6"
description = "API for MaveDB, the database of Multiplexed Assays of Variant Effect."
license = "AGPL-3.0-only"
readme = "README.md"
authors = []
homepage = "https://mavedb.org"
repository = "https://github.com/VariantEffect/mavedb-api"
documentation = "https://mavedb.org/docs/mavedb/"
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: GNU Affero General Public License v3",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

[tool.poetry.dependencies]
python = "^3.11"

fqfa = "~1.3.0"
pyhumps = "~3.8.0"
pyyaml = "~6.0.1"
IDUtils = "~1.2.0"
mavehgvs = "~0.7.0"
eutils = "~0.6.0"
email_validator = "~2.1.1"
numpy = "~1.26"
httpx = "~0.26.0"
pandas = ">=2.2.0,<3.0.0"
pydantic = "~2.10.0"
python-dotenv = "^1.2"
python-json-logger = "~2.0.7"
SQLAlchemy = "~2.0.29"
ga4gh-va-spec = "~0.4.2"
setuptools = "~81.0.0"

# Optional dependencies for running this application as a server
aiocache = { extras = ["redis"], version = "~0.12.2", optional = true }
alembic = { version = "~1.14.0", optional = true }
alembic-utils = { version = "0.8.1", optional = true }
arq = { version = "~0.25.0", optional = true }
authlib = { version = "~1.6.6", optional = true }
boto3 = { version = "~1.34.97", optional = true }
biocommons = { version = "~0.0.0", optional = true }
cryptography = { version = "~46.0.5", optional = true }
cdot = { version = "~0.2.21", optional = true }
fastapi = { version = "~0.121.0", optional = true }
hgvs = { version = "~1.5.4", optional = true }
orcid = { version = "~1.0.3", optional = true }
pyathena = { version = "~3.14.1", optional = true }
psycopg2 = { version = "~2.9.3", optional = true }
python-jose = { extras = ["cryptography"], version = "~3.5.0", optional = true }
python-multipart = { version = "~0.0.22", optional = true }
requests = { version = "^2.33", optional = true }
starlette = { version = "~0.49.0", optional = true }
starlette-context = { version = "^0.3.6", optional = true }
slack-sdk = { version = "~3.21.3", optional = true }
uvicorn = { extras = ["standard"], version = "*", optional = true }
watchtower = { version = "~3.2.0", optional = true }
asyncclick = "^8.3.0.7"
filelock = "^3.29.0"

[tool.poetry.group.dev]
optional = true

[tool.poetry.group.dev.dependencies]
boto3-stubs = { extras = ["s3"], version = "~1.42.33" }
mypy = "~1.20.0"
pre-commit = "*"
jsonschema = "*"
fakeredis = "~2.21.1"
pytest = "~9.0.0"
pytest-cov = "~7.1.0"
pytest-postgresql = "~8.0.0"
pytest-asyncio = "~1.3.0"
pytest-socket = "~0.6.0"
pandas-stubs = "~3.0.0"
types-requests = "~2.31.0"
types-python-jose = "~3.3.4"
types-PyYAML = "~6.0.12.20240808"
redis = "~5.0.2"
requests-mock = "~1.11.0"
ruff = "~0.15.0"
SQLAlchemy = { extras = ["mypy"], version = "~2.0.0" }


[tool.poetry.extras]
server = ["aiocache", "alembic", "alembic-utils", "arq", "authlib", "biocommons", "boto3", "cdot", "cryptography", "fastapi", "hgvs", "orcid", "psycopg2", "python-jose", "python-multipart", "pyathena", "requests", "starlette", "starlette-context", "slack-sdk", "uvicorn", "watchtower"]


[tool.mypy]
plugins = [
    "sqlalchemy.ext.mypy.plugin",
    "numpy.typing.mypy_plugin",
    "pydantic.mypy",
]
mypy_path = "mypy_stubs"

[tool.pytest.ini_options]
addopts = "-v --import-mode=importlib"
asyncio_mode = 'strict'
testpaths = "tests/"
pythonpath = "."
norecursedirs = "tests/helpers/"
markers = """
    integration: tests that exercise multi-component flows and/or database interactions.
    unit: fast unit tests with isolated dependencies.
    network: tests which interact with external services over a network connection.
    slow: tests which are slow running.
"""
# Uncomment the following lines to include application log output in Pytest logs.
# log_cli = true
# log_cli_level = "DEBUG"

[tool.ruff]
# target python 3.11 and above
target-version = "py311"

# max line length for linting is 120 characters
line-length = 120

# Exclude these files from linting/formatting
exclude = ["alembic/manual_migrations"]