| [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] |
| |
| line-length = 120 |
| exclude = ["jupyter_notebook_config.py"] |
| select = [ |
| "E", |
| "W", |
| "F", |
| "I", |
| "C", |
| "B", |
| ] |
| ignore = [ |
| "E501", |
| "C901", |
| ] |
|
|
| [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 = [] |
|
|
