DeepRBP/pyproject.toml at main · ML4BM-Lab/DeepRBP · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "deeprbp"
version = "1.0.0"
description = "Deep learning model for inferring RBP-Gene regulations"
readme = "README.md"
requires-python = ">=3.9,<3.12"
authors = [{ name = "Joseba Sancho Zamora" }]

dependencies = [
    "numpy<2",
    "scipy<1.14",
    "h5py",
    "matplotlib",
    "pandas",
    "scanpy",
    "scikit-learn",
    "seaborn",
    "statsmodels",
    "tornado",
    "tqdm",
    "plotly",
    "openpyxl",
    "captum",
    "optuna",
    "joblib",
    "pydeseq2",
    "sanbomics",
    "colorama",
    "torchinfo",
    "psutil",
    "lightning",
    "optuna-integration[pytorch_lightning]",
    "tabulate",
    "xgboost",
    "lightgbm",
]

[project.optional-dependencies]
gpu = [
    "torch>=2.0",
    "torchvision>=0.15",
    "GPUtil"
]
dev = [
    "notebook",
    "ipykernel"
]

[project.urls]
Homepage = "https://github.com/ML4BM-Lab/DeepRBP"

[project.scripts]
preprocess-data = "deeprbp.data_preprocessing.preprocess_data:main"
split-and-save = "deeprbp.data_preprocessing.split_data_and_save:main"
create-optuna-study = "deeprbp.training_module.hyperparameter_optimization.create_optuna_study:main"
analyze-optuna-results = "deeprbp.training_module.hyperparameter_optimization.analyze_results_optuna:main"
run-deeprbp-predictor = "deeprbp.training_module.main_predictor:main"
run-deeprbp-evaluator = "deeprbp.training_module.evaluate_predictor:main"
run-deeprbp-explainer = "deeprbp.explainability_module.main_explainer:main"
run-postar-validator = "deeprbp.explainability_module.postar_validation.postar_validator:main"
preprocess-realkd-data = "deeprbp.explainability_module.real_knockdowns.preprocess_data.preprocess_realkd_data:main"
preprocess-user-data = "deeprbp.data_preprocessing.preprocess_data_user:main"
run-deeprbp-realkd = "deeprbp.explainability_module.real_knockdowns.main_real_knockdowns:main"
run-deeprbp-differential-regulation-scores = "deeprbp.explainability_module.differential_regulation.compute_scores_per_condition:main"
run-deeprbp-differential-expression = "deeprbp.explainability_module.differential_regulation.de_expression_conditions:main"

[tool.setuptools]
package-dir = {"" = "src"}
include-package-data = true

[tool.setuptools.packages.find]
where = ["src"]