| [tool.poetry] |
| name = "scprint" |
| version = "0.1.0" |
| license = "MIT" |
| description = "" |
| authors = ["jeremie kalfon"] |
| readme = ["README.md", "LICENSE"] |
| repository = "https://github.com/jkobject/scPrint" |
| keywords = [ |
| "scRNAseq", |
| "transformer", |
| "GRN", |
| "gene regulatory network", |
| "scPrint", |
| ] |
|
|
| [tool.poetry.dependencies] |
| lamindb = "*" |
| python = "3.10" |
| cellxgene-census = "*" |
| torch = ">=2.0.0" |
| anndata = "*" |
| matplotlib = "*" |
| seaborn = "*" |
| gseapy = "*" |
| ipykernel = "*" |
| owlready2 = "*" |
| torchdata = "*" |
| biomart = "*" |
| scib = "*" |
| scikit-learn = "*" |
| scipy = "*" |
| pandas = ">=2.0.0" |
| numpy = "*" |
| leidenalg = "*" |
| decoupler = "*" |
| Bio = "*" |
| attridict = "*" |
| gget = "*" |
| torchvision = "*" |
| fair-esm = { git = "https://github.com/facebookresearch/esm.git", branch = "main" } |
| hydra-core = "*" |
| lightning = "*" |
| |
| |
| pynndescent = ">=0.5.11" |
| scDataLoader = "*" |
| einops = "*" |
| rich = "*" |
| typeshed-client = "*" |
| tensorboardX = "*" |
| jsonargparse = "*" |
| docstring-parser = "*" |
| lnschema-bionty = "*" |
| bionty = "*" |
| wandb = "*" |
| wandb-core = "*" |
| pykeops = "*" |
| louvain = "*" |
| hdbscan = "*" |
| scib-metrics = "*" |
| scikit-misc = "*" |
| zarr = "*" |
| galore-torch = { git = "https://github.com/jiaweizzhao/GaLore", branch = "master" } |
| tensorly = "*3 |
| |
| [tool.poetry.group.flashattention.dependencies] |
| # C_INCLUDE_PATH=$CONDA_HOME/envs/scprint/include |
| torchtext = "0.15.1" |
| triton = "2.0.0.dev20221202" #no deps |
| torch = "2.0.0" |
| torchvision = "0.15.0" |
| torchaudio = "2.0.0" |
| pytorch-fast-transformers = "*" |
| |
| [tool.poetry.group.dev.dependencies] |
| pytest = "^7.4.3" |
| coverage = "^7.3.2" |
| flake8 = "^6.1.0" |
| black = "^23.10.1" |
| isort = "^5.12.0" |
| pytest-cov = "^4.1.0" |
| mypy = "^1.6.1" |
| gitchangelog = "^3.0.4" |
| mkdocs = "^1.5.3" |
| mkdocs-git-revision-date-localized-plugin = "*" |
| mkdocstrings = "*" |
| mkdocs-git-authors-plugin = "*" |
| mkdocs-jupyter = "*" |
| mkdocstrings-python = "*" |
| |
| [build-system] |
| requires = ["poetry-core"] |
| build-backend = "poetry.core.masonry.api" |
| |
| [tool.poetry.scripts] |
| scprint = 'scprint.__main__:main' |
| |
