pyproject.toml

[project]
name = "spras"
version = "0.2.0"
description = "Signaling Pathway Reconstruction Analysis Streamliner"
authors = [
  { name = "Anthony Gitter", email = "gitter@biostat.wisc.edu" },
  { name = "Anna Ritz", email = "aritz@reed.edu"},
]
license = { file = "LICENSE" }
readme = "README.md"
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.11"
dependencies = [
    "adjusttext==0.7.3",
    # A bug was introduced in older versions of snakemake that prevent it from running. Update to fix
    "snakemake==8.16.0",
    "docker==5.0.3", # Switched from docker-py to docker because docker-py is not maintained in pypi. This appears to have no effect
    "matplotlib==3.6",
    "networkx==2.8",
    "pandas==1.5",
    "numpy==1.26.4",
    "pip==22.1",
    "requests==2.28",
    "scikit-learn==1.2",
    "seaborn==0.12",
    "spython==0.2",
    # Only required for GraphSpace
    "commonmark==0.9",
    "docutils==0.19",
    "jinja2==3.1",
    "mock==4.0",
    "recommonmark==0.7",
    "sphinx==6.0",
    "graphspace_python==1.3.1",
    "sphinx-rtd-theme==2.0.0",
]

[project.optional-dependencies]
dev = [
   # Only required for development
    "pre-commit==2.20",
    "pytest==8.0",
]

[project.urls]
"Homepage" = "https://github.com/Reed-CompBio/spras"
"Issues" = "https://github.com/Reed-CompBio/spras/issues"

[build-system]
requires = ["setuptools>=64.0"]
build-backend = "setuptools.build_meta"

[tool.ruff]
target-version = "py311"
# Autofix errors when possible
fix = true
# Select categories or specific rules from https://beta.ruff.rs/docs/rules/
select = [
    "B", # flake8-bugbear
    "D300", # docstring triple-single-quotes
    "E101", # mixed-spaces-and-tabs
    "E711", # none-comparison
    "E713", # not-in-test
    "E714" , # not-is-test
    "F821", # undefined-name
    "F823", # undefined-local
    "F841", # unused-variable
    "I", # isort
    "W292", # missing-newline-at-end-of-file
]

[tool.setuptools]
# py-modules tells setuptools which directory is our actual module
py-modules = ["spras"]
# packages tells setuptools what the exported package is called (ie allows import spras)
packages = ["spras", "spras.analysis"]