pyproject.toml

[tool.poetry]
name = "trident"
version = "0.1.1"
description = "A package for preprocessing whole-slide images."
authors = [
    "Andrew Zhang <andrewzh@mit.edu>",
    "Guillaume Jaume <gjaume@bwh.harvard.edu>",
    "Paul Doucet <homedoucetpaul@gmail.com>"
]
license = "CC BY-NC-ND 4.0"  # Specify your package's license if different.
repository = "https://github.com/mahmoodlab/TRIDENT"

[tool.poetry.dependencies]
python = "^3.10"  # Specify the Python version compatibility.
ipywidgets = "*"
torch = "*"
transformers = "*"
tqdm = "*"
h5py = "*"
matplotlib = "*"
segmentation-models-pytorch = "*"
opencv-python = "*"
openslide-python = "*"
Pillow = "*"
timm = "0.9.16"
einops_exts = "*"
geopandas = "*"
huggingface_hub = "*"
openslide-bin = "*"
scipy = "*"

[tool.poetry.dev-dependencies]
# Optional development dependencies 

[tool.poetry.scripts]
run_batch_of_slides = "run_batch_of_slides:main"
run_single_slide = "run_single_slide:main"

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

[tool.poetry.package]
include = [
    { format = "file", path = "trident/slide_encoder_models/local_ckpts.json" },
    { format = "file", path = "trident/patch_encoder_models/local_ckpts.json" },
    { format = "file", path = "trident/segmentation_models/local_ckpts.json" },
]
include_package_data = true