pyproject.toml

[tool.poetry]
name = "teddy"
version = "0.1.0"
description = "A module for fine-tuning and preprocessing foundational models."
authors = ["Olga Kotova <kotova.olga@bcg.com>"]
license = "MIT"
readme = "README.md"

[tool.poetry.dependencies]
python = "3.11.10"
accelerate = "0.30.1"
aiohttp = "3.9.5"
aiosignal = "1.3.1"
alembic = "1.13.2"
aniso8601 = "9.0.1"
anndata = "0.10.7"
attrs = "23.2.0"
azure-common = "1.1.28"
azure-core = "1.30.1"
azure-mgmt-core = "1.4.0"
azure-mgmt-storage = "21.1.0"
azure-storage-blob = "12.20.0"
beautifulsoup4 = "4.12.3"
blinker = "1.8.2"
boto3 = "1.34.112"
botocore = "1.34.112"
cachetools = "5.3.3"
certifi = "2024.7.4"
cffi = "1.16.0"
charset-normalizer = "3.3.2"
click = "8.1.7"
cloudpickle = "3.0.0"
contourpy = "1.2.1"
cryptography = "44.0.0"
cycler = "0.12.1"
datasets = "2.19.1"
deprecated = "1.2.14"
dill = "0.3.8"
docker = "7.1.0"
docker-pycreds = "0.4.0"
fabric = "3.2.2"
filelock = "3.14.0"
flask = "3.0.3"
fonttools = "4.51.0"
frozenlist = "1.4.1"
fsspec = "2024.3.1"
gdown = "5.2.0"
gitdb = "4.0.11"
gitpython = "3.1.43"
graphene = "3.3"
graphql-core = "3.2.3"
graphql-relay = "3.2.0"
greenlet = "3.0.3"
gunicorn = "22.0.0"
h5py = "3.11.0"
huggingface-hub = "0.23.1"
hyperopt = "0.1.2"
idna = "3.7"
igraph = "0.11.5"
isodate = "0.6.1"
itsdangerous = "2.2.0"
jinja2 = "3.1.4"
jmespath = "1.0.1"
joblib = "1.4.2"
kiwisolver = "1.4.5"
legacy-api-wrap = "1.4"
leidenalg = "0.10.2"
llvmlite = "0.42.0"
mako = "1.3.5"
markdown = "3.6"
markupsafe = "2.1.5"
matplotlib = "3.9.0"
mlflow = "2.16.0"
mpmath = "1.3.0"
multidict = "6.0.5"
multiprocess = "0.70.16"
natsort = "8.4.0"
networkx = "3.3"
numba = "0.59.1"
numpy = "1.26.4"
opentelemetry-api = "1.25.0"
opentelemetry-sdk = "1.25.0"
opentelemetry-semantic-conventions = "0.46b0"
pandas = "2.2.2"
patsy = "0.5.6"
pillow = "10.3.0"
protobuf = "4.25.3"
psutil = "5.9.8"
pyarrow = "15.0.2"
pycparser = "2.22"
pydot = "2.0.0"
pymongo = "4.7.2"
pynndescent = "0.5.12"
pyparsing = "3.1.2"
pysocks = "1.7.1"
python-box = "7.1.1"
python-dateutil = "2.9.0.post0"
pytz = "2024.1"
pyyaml = "6.0.1"
regex = "2024.5.15"
requests = "2.32.2"
s3transfer = "0.10.1"
safetensors = "0.4.3"
scanpy = "1.10.1"
scib = "1.1.5"
scikit-learn = "1.5.0"
scikit-misc = "0.3.1"
scipy = "1.13.0"
scvi = "0.6.8"
seaborn = "0.13.2"
sentry-sdk = "2.8.0"
session-info = "1.0.0"
setproctitle = "1.3.3"
smmap = "5.0.1"
soupsieve = "2.5"
sqlalchemy = "2.0.31"
sqlparse = "0.5.0"
statsmodels = "0.14.2"
sympy = "1.12"
texttable = "1.7.0"
threadpoolctl = "3.5.0"
tokenizers = "0.19.1"
torch = "^2.3.0 || >=2.0.1"
torchtext = "^0.18.0 || >=0.15.2"
torchvision = "^0.18.0 || >=0.15.2"
tqdm = "4.66.4"
transformers = "4.41.0"
tzdata = "2024.1"
umap-learn = "0.5.6"
urllib3 = "2.2.2"
wandb = "0.17.0"
werkzeug = "3.0.6"
wrapt = "1.16.0"
xxhash = "3.4.1"
yarl = "1.9.4"
jupyter = "^1.1.1"
ipykernel = "^6.29.5"
tensorboard = "^2.19.0"
pydantic = "^2.10.6"

[tool.poetry.group.dev.dependencies]
pytest = "^7.0"
black = "^24.3"
isort = "^5.0"
ruff = "^0.0.286"
pre-commit = "^4.0.1"

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.black]
skip-string-normalization = true
line-length = 120

[tool.ruff]
# Same as Black.
line-length = 120
exclude = ["jupyter_notebook_config.py"]
select = [
    "E",  # pycodestyle errors (settings from FastAPI, thanks, @tiangolo!)
    "W",  # pycodestyle warnings
    "F",  # pyflakes
    "I",  # isort
    "C",  # flake8-comprehensions
    "B",  # flake8-bugbear
]
ignore = [
    "E501",  # line too long, handled by black
    "C901",  # too complex
]

[tool.ruff.isort]
order-by-type = true
relative-imports-order = "closest-to-furthest"
extra-standard-library = ["typing"]
section-order = ["future", "standard-library", "third-party", "first-party", "local-folder"]
known-first-party = []