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pyproject.toml
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75 lines (70 loc) · 1.64 KB
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[tool.poetry]
name = "pyeed"
version = "0.4.3"
description = "Toolkit to create, annotate, and analyze sequence data"
authors = ["haeussma <[email protected]>"]
license = "MIT"
readme = "README.md"
packages = [{ include = "pyeed", from = "src" }]
[tool.poetry.dependencies]
python = ">=3.10,<3.13"
biopython = ">=1.81,<1.84"
networkx = "^3.2.1"
plotly = "^5.18.0"
scipy = "^1.11.3"
httpx = "^0.27.0"
nest-asyncio = "^1.6.0"
rich = "^13.0.0"
aiometer = "^0.5.0"
joblib = "^1.4.0"
requests = "^2.31.0"
matplotlib = "^3.9.0"
pymsaviz = "^0.4.2"
tenacity = "^8.3.0"
neo4j = "5.19.*"
bio = "^1.7.1"
loguru = "^0.7.0"
neomodel = "^5.3.3"
shapely = "^2.0.6"
torch = "^2.4.1"
transformers = "^4.45.2"
scikit-learn = "^1.5.2"
openai = "^1.52.2"
esm = "^3.1.3"
rdflib = "^6.0.0"
docker = "5.0.0"
absl-py = "1.0.0"
crc64iso = "0.0.2"
SPARQLWrapper = "2.0.0"
pysam = "0.23.0"
types-requests = "2.32.0.20250328"
ipywidgets = "^8.1.7"
sentencepiece = "^0.2.0"
umap-learn = "^0.5.7"
[tool.poetry.group.dev.dependencies]
mkdocstrings = {extras = ["python"], version = "^0.26.2"}
mkdocs-material = "^9.5.9"
pytest = "^8.0.1"
python-dotenv = "^1.0.1"
pytest-mock = "^3.12.0"
ruff = "^0.4.1"
mkdocs-jupyter = "^0.24.7"
jupyter-contrib-nbextensions = "^0.7.0"
notebook = "^6"
pytest-loguru = "^0.4.0"
fastapi = "^0.115.6"
uvicorn = "^0.34.0"
devtools = "^0.12.2"
mypy = "^1.14.1"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.mypy]
ignore_missing_imports = true
disallow_untyped_defs = true
disallow_incomplete_defs = true
warn_return_any = true
check_untyped_defs = true
strict = true
[tool.ruff.lint]
extend-select = ["I"]