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pyproject.toml
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[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"
[tool.poetry]
name = "bop"
version = "0.0.1"
description = ""
authors = ["Geometric Intelligence Lab"]
readme = "README.md"
repository = "https://github.com/geometry-intelligence/bop"
[tool.poetry.dependencies]
python = "^3.11"
numpy = ">=1.26.4,<1.27.0"
click = "<9.0"
aioboto3 = ">=10.0.0"
aiobotocore = {extras = ["boto3"], version = "^2.4.0"}
boto3 = ">=1.24.0"
timm = "^0.9.12"
einops = "^0.7.0"
fsspec = {extras = ["s3"], version = "^2022.11.0"}
joblib = "^1.2.0"
matplotlib = "^3.7.1"
pandas = "^2.0"
tqdm = "^4.65.0"
rich = "^13.3.4"
zarr = "^2.14.2"
pydantic = "^1.10.7"
s3fs = ">=2021.08.0"
bokeh = "^3.1.0"
pytorch-lightning = "^2.1.2"
wandb = "^0.17.5"
pyyaml = "^6.0"
cdsapi = "^0.6.1"
mypy = "^1.4.1"
torch-geometric = "^2.4.0"
six = "^1.16.0"
ogb = "^1.3.6"
scikit-learn = "^1.3.2"
gudhi = "^3.9.0"
opencv-python = "^4.0"
openpyxl = "^3.1.5"
PyWGCNA = "^2.0"
captum = "^0.7.0"
ray = {extras = ["tune"], version = "^2.24.0"}
focal-loss-torch = "^0.1.2"
ucimlrepo = "^0.0.7"
config_utils = "^0.3"
pingouin = "^0.5.5"
plotly = "^5.24.1"
xgboost = "^1.7.5"
imblearn = "^0.0"
import_ipynb = "^0.1.3"
ipywidgets = "^8.0.0"
pytorch_pretrained_bert = "^0.6.2"
[[tool.poetry.source]]
name = "torch-gpu"
url = "https://download.pytorch.org/whl/cu121"
priority = "explicit"
[[tool.poetry.source]]
name = "torch-geometric-gpu"
url = "https://pytorch-geometric.com/whl/torch-2.1.0+cu121.html"
priority = "explicit"
[tool.poetry.group.gpu.dependencies]
torch = {version = "^2.1.0+cu121", source = "torch-gpu"}
torchvision = {version = "^0.16.1+cu121", source = "torch-gpu"}
torch-cluster = {version = "^1.6.3+pt21cu121", source = "torch-geometric-gpu"}
torch-scatter = {version = "^2.1.2+pt21cu121", source = "torch-geometric-gpu"}
torch-sparse = {version = "^0.6.18+pt21cu121", source = "torch-geometric-gpu"}
torch-spline-conv = {version = "^1.2.2+pt21cu121", source = "torch-geometric-gpu"}
[tool.poetry.group.dev.dependencies]
black = "^23.3.0"
isort = "^5.12.0"
pytest = "^7.3.1"
pytest-cov = "^4.0.0"
flake8 = "^6.0.0"
autoflake8 = "^0.4.0"
ipython = "^8.12.0"
jupyter = "^1.0.0"
jupyterlab = "^4.0"
jupyter-server-proxy = "^4.0.0"
[tool.black]
line-length = 100
target-version = ['py39']
skip-string-normalization = true
include = '\.pyi?$'
[tool.coverage]
run.omit = ["*_test.py"]
[tool.bandit]
skips = ['B101']
assert_used.skips = ['test_*.py', '*_test.py']
[tool.isort]
py_version = 39
profile = "black" # be nice with black
line_length = 100
skip = ['.gitignore', '.dockerignore']
[tool.pytest.ini_options]
python_files = "*_test.py"
filterwarnings = [
"ignore::DeprecationWarning:pkg_resources.*:",
]
[tool.mypy]
python_version = "3.9"
show_error_codes = true
show_column_numbers = true
show_error_context = true
ignore_missing_imports = true # prefer explicit ignores