pyproject.toml

[build-system]
requires = ["setuptools>=61"]
build-backend = "setuptools.build_meta"

[project]
name = "nephroq"
version = "0.11.0"
description = "A mechanistic digital twin for type 2 diabetes -> chronic kidney disease progression"
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
authors = [{ name = "Daniel Pérez-Calixto" }]
keywords = ["nephrology", "digital twin", "mechanistic model", "CKD", "type 2 diabetes"]

# Lower bounds only: the model is plain numpy/scipy and does not depend on any
# recent API. For a MANUSCRIPT, freeze the exact environment instead --
# see requirements-lock.txt and the note below.
dependencies = [
    "numpy>=1.24",
    "scipy>=1.10",
    "matplotlib>=3.7",
    "scikit-learn>=1.3",
    "joblib>=1.3",
    "pandas>=2.0",
    "streamlit>=1.35",
]

[project.urls]
Repository = "https://github.com/Danpc11/nephroq"

[tool.pytest.ini_options]
# Lets the tests import from src/ without each file doing its own sys.path
# surgery, and without installing the package.
pythonpath = ["src"]
testpaths = ["tests"]
addopts = "-q"

# src/ is a flat collection of research modules rather than a package tree, so
# they are installed as top-level modules from src/ (package-dir maps the empty
# package to src/). With py-modules = [] a `pip install .` installed only
# metadata + dependencies and NONE of the code. The list is kept in sync with
# src/*.py by test_pyproject_lists_all_src_modules, so it cannot silently drift.
[tool.setuptools]
package-dir = { "" = "src" }
py-modules = [
    "acute_events", "audit_calibration", "calibrate_mimic", "clinical_data",
    "clinical_outputs", "clinical_safety", "digital_twin", "egfr_measurement",
    "external_validation", "i18n", "insilico_trial", "measurement_strategy",
    "mimic_loader", "model_core", "mvp_calibration", "patient_state",
    "personalize", "plot_cric_validation", "plot_key_results", "treatment_engine",
    "uncertainty",
]