pyproject.toml

[tool.logging]
version = 1
incremental = true

[tool.logging.formatters.formatter]
format = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
default_time_format = "%H:%M:%S"

[tool.logging.root]
# The root logger level holds for every module that doesn't have its own level.
level = "DEBUG"

[tool.logging.loggers."__main__"]
# The special module __main__ is the script currently being executed.
level = "DEBUG"

[tool.logging.loggers."jax"]
level = "INFO"

[tool.logging.loggers."matplotlib"]
level = "INFO"

[tool.ruff]
# Set the maximum line length to 79.
line-length = 127

[tool.ruff.format]
docstring-code-format = true  # code snippets in docstrings will be formatted

[tool.ruff.lint]
# Add the `line-too-long` rule to the enforced rule set.
extend-select = ["E501","F405","E402"]

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

[tool.setuptools]
packages = ["jaxkineticmodel"]

[tool.my_project]
project_root = "."

[project]
name = "jaxkineticmodel"
version = "0.0.1"
readme = "README.md"
requires-python = ">=3.9"
description = "A tool for building, training, and simulating metabolic kinetic models in Jax/Diffrax"

dependencies = [
    "diffrax>=0.6.0",
    "equinox>=0.11.8",
    "functions==0.7.0",
    "jax==0.4.35",
    "jaxlib==0.4.35",
    "matplotlib>=3.9.2",
    #"numpy>=2.0.2",
    "optax==0.2.3",
    "pandas>=1.1.4",
    "pytest>=8.3.4",
    "scikit_learn==1.5.2",
    "scipy>=1.11.1",
    "sympy>=1.13.3",
    "tomli>=2.1.0 ; python_version<'3.11'",
    "python-libsbml==5.20.4",
    "scikit-optimize>=0.10.2",
    "markdown-include>=0.8.1",
    "xgboost>=2.1.3"
]

authors = [
  {name="Paul van Lent", email="p.h.vanlent@tudelft.nl"},
  {name="Léon Planken",email="l.r.planken@tudelft.nl"},
  {name="Thomas Abeel", email="t.abeel@tudelft.nl"},
]

classifiers = [
    "Programming Language :: Python :: 3",
    "License :: OSI Approved :: Apache License",
    "Operating System :: OS Independent",
]

#[project.urls]
#Homepage = "https://github.com/pypa/sampleproject"
#Issues = "https://github.com/pypa/sampleproject/issues"

[project.optional-dependencies]
test = ["tellurium>=2.2.10"]