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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "bioimage_embed"
version = "0.0.0"
description = ""
authors = ["Craig <[email protected]>"]
packages = [{ include = "bioimage_embed" }]
[tool.poetry.scripts]
bioimage_embed = "bioimage_embed:app"
bie = "bioimage_embed.cli:app"
bie_train = "bioimage_embed.cli:train"
bie_infer = "bioimage_embed.cli:infer"
bie_finetune = "bioimage_embed.cli:finetune"
[tool.poetry.dependencies]
python = "^3.9,<3.11"
umap-learn = { extras = ["plot"], version = "^0.5.3" }
jsonargparse = { extras = ["signatures"], version = "^4.21.0" }
llvmlite = "0.40.1"
pytorch-lightning = "1.*.*"
torchinfo = "^1.8.0"
matplotlib = "^3.7.2"
pyro-ppl = "^1.8.6"
scikit-image = "^0.21.0"
iteround = "^1.0.4"
ipykernel = "^6.25.1"
nonechucks = "^0.4.2"
pythae = { git = "https://github.com/clementchadebec/benchmark_VAE.git", branch = "main" }
pandas = "^2.1.0"
bokeh = "^3.2.2"
colorcet = "^3.0.1"
holoviews = "^1.17.1"
tensorboard = "^2.14.0"
albumentations = "^1.3.1"
timm = "^0.9.6"
pip = "^23.2.1"
hydra-core = "^1.3.2"
# pyqt5 = "^5.15.9"
requests = "^2.31.0"
shapely = "^2.0.1"
pyefd = "^1.6.0"
tikzplotlib = "^0.10.1"
# torchmetrics = "^1.1.1"
torchmetrics = "0.11.4"
# pytorch-lightning-bolts = "^0.3.2.post1"
lightning-bolts = "^0.7.0"
Pillow = "9.5.0"
onnx = "^1.15.0"
typer = "^0.9.0"
ray = { extras = ["all"], version = "^2.8.1" }
pydantic = "^2.6.4"
numpy = "1.23"
monai = "^1.3.2"
transformers = "^4.42.4"
torch = "^2.3.1"
torchvision = "^0.18.1"
wandb = "^0.17.4"
jupytext = "^1.16.4"
jupyter = "^1.0.0"
[tool.poetry.group.dev.dependencies]
black = "^24.4.2"
mypy = "^1.10.0"
pytest = "^8.2.0"
pytest-cov = "^5.0.0"
flake8 = "^7.0.0"
pre-commit = "^3.7.1"
isort = "^5.13.2"
poetry-dynamic-versioning = "^1.0.0"
# torch = {version = "^2.3.1+cpu", source = "pytorch-cpu"}
# torchvision="0.18.1+cpu"
jupytext = "^1.16.2"
[build-system]
requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning>=1.0.0,<2.0.0"]
build-backend = "poetry_dynamic_versioning.backend"
[tool.pytest.ini_options]
minversion = "6.0"
addopts = "-ra -q --ignore=env"
pythonpath = ["bioimage_embed"]
timeout = 180
# [flake8]
# max-line-length = 80
[tool.black]
line-length = 80
# [[tool.poetry.source]]
# name = "pytorch-cpu"
# url = "https://download.pytorch.org/whl/cpu"
# default = false
# secondary = true