| | [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 = [] |
| |
|
