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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "curategpt"
version = "0.2.2"
description = "CurateGPT"
authors = ["Chris Mungall <[email protected]>", "Carlo Kroll <[email protected]>", "Harshad Hegde <[email protected]>", "J. Harry Caufield <[email protected]>"]
license = "BSD-3"
readme = "README.md"
[tool.poetry.dependencies]
python = "^3.9, !=3.9.7"
click = "^8.1.7"
importlib-metadata = ">=6"
oaklib = "^0.6.9"
beautifulsoup4 = ">=4.8.0"
streamlit = ">=1.22.0"
openai = ">=0.27.7"
wikipedia = ">=1.4.0"
google-search-results = ">=2.4.2"
chromadb = "^0.5.0"
tiktoken = "^0.7.0"
inflection = ">=0.5.1"
sentence-transformers = ">=2.2.2"
pymongo = ">=4.4.1"
linkml-runtime = "^1.6.3"
python-ulid = "^1.1.0"
sqlite-utils = "^3.34"
gpt4all = {version = "^1.0.8", optional = true}
httpx = "^0.24.1"
eutils = "^0.6.0"
matplotlib = "^3.7.2"
seaborn = "^0.12.2"
bioc = {version = ">=2.0.0.post5", optional = true}
requests-cache = "^1.1.0"
jsonpatch = "^1.33"
scholarly = "^1.7.11"
pytrials = "^0.3.0"
xmltodict = "^0.13.0"
ratelimiter = "^1.2.0.post0"
google-api-python-client = "^2.97.0"
google-auth-oauthlib = "^1.0.0"
textract = "1.5.0"
jsonpath-ng = "^1.5.3"
pygithub = "^1.59.1"
jsonlines = "*"
llm = "^0.15"
llm-gpt4all = {version = "^0.1.1", optional = true}
gspread = "^5.10.0"
defusedxml = "^0.7.1"
click-default-group = "^1.2.4"
venomx = "^0.1.1"
duckdb = "~1.0.0"
python-dotenv = "^1.0.1"
onnxruntime = [
{version = "<=1.19.2", python = "<3.10"},
{version = "^1.20.0", python = ">=3.10"}
]
[tool.poetry.dev-dependencies]
pytest = ">=7.1.2"
tox = ">=3.25.1"
linkml = "^1.5.6"
jupyter = "^1.0.0"
sphinx = {version = ">=6.1.3", extras = ["docs"]}
sphinx-rtd-theme = {version = ">=1.0.0", extras = ["docs"]}
sphinx-autodoc-typehints = {version = ">=1.2.0", extras = ["docs"]}
sphinx-click = {version = ">=4.3.0", extras = ["docs"]}
sphinx-automodapi = {version = "*", extras = ["docs"]}
myst-parser = {version = ">=0.18.1", extras = ["docs"]}
[tool.poetry.group.docs]
optional = true
[tool.poetry.group.docs.dependencies]
sphinx = {version = ">=6.1.3"}
sphinx-rtd-theme = {version = ">=1.0.0"}
sphinx-autodoc-typehints = {version = ">=1.2.0"}
sphinx-click = {version = ">=4.3.0"}
myst-parser = {version = ">=0.18.1"}
[tool.poetry.scripts]
curategpt = "curategpt.cli:main"
gocampr = "curategpt.adhoc.gocam_predictor:main"
[tool.poetry.extras]
docs = [
"sphinx",
"sphinx-rtd-theme",
"sphinx-autodoc-typehints",
"sphinx-click",
"myst-parser"
]
bioc = [
"bioc"
]
gpt4all = [
"gpt4all",
"llm-gpt4all"
]
[tool.poetry-dynamic-versioning]
enable = false
vcs = "git"
style = "pep440"
[tool.black]
line-length = 100
target-version = ["py38", "py39", "py310"]
[tool.ruff]
line-length = 100
target-version = "py311"
[tool.ruff.lint] # New section for linter-specific settings
extend-ignore = [
"D211", # `no-blank-line-before-class`
"D212", # `multi-line-summary-first-line`
]
# Allow autofix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
# Select or ignore from https://beta.ruff.rs/docs/rules/
select = [
"B", # bugbear
# "D", # pydocstyle
# "E", # pycodestyle errors
"F", # Pyflakes
"I", # isort
# "S", # flake8-bandit
"W", # Warning
]
unfixable = []
# Unlike Flake8, default to a complexity level of 10.
[tool.ruff.lint.mccabe]
max-complexity = 10
[tool.ruff.lint.isort]
known-third-party = ["duckdb"]
[tool.codespell]
skip = "*.po,*.ts,.git,pyproject.toml"
count = ""
quiet-level = 3
# ignore-words-list = ""
[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]
build-backend = "poetry_dynamic_versioning.backend"