pyproject.toml

[build-system]
requires = [
    "setuptools", "wheel", "Cython", "numpy>1.20.0"
]
build-backend = "setuptools.build_meta"


[project]
name = "pymantra"
version = "1.0.2"
license = {text = "AGPLv3"}
description = "Reaction-Centred Metabolic Network Analysis"
readme = "README.md"
authors = [
    {name="Nikolai Koehler", email="nikolai.koehler@tum.de"},
    {name="Josch Konstantin Pauling"}
]
maintainers = [
    {name="Nikolai Koehler", email="nikolai.koehler@tum.de"},
    {name="Josch Konstantin Pauling"}
]
keywords = [
	"Bioinformatics", "Computational Metabolomics", "Metabolic Network"
]
classifiers = [
    "License :: OSI Approved :: GNU Affero General Public License v3",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Intended Audience :: Science/Research",
    "Natural Language :: English",
    "Operating System :: MacOS",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX :: Linux",
    "Programming Language :: Python :: 3"
]
dependencies = [
	# pandas <= 1.4.2 contains a bug that prevents from debugging
	# in certain cases
    "pandas>=1.4.3",
    "scipy>=1.8.0",
    "scikit-learn>=1.0.2",
    "networkx>=2.8.0",
    "tqdm>=4.62.1",
    "matplotlib>=3.3.0",
    "seaborn>=0.9.0",
    "neo4j>=4.4.0",
    "pingouin>=0.5.2",
    "statsmodels>=0.13.5",
    # these are dependencies of pingouin that seems to not install
    # automatically
    "pandas-flavor",
    "seaborn",
    "outdated"
]

[project.optional-dependencies]
experiments = ["scikit-bio", "openpyxl", "scikit-optimize"]
dev = ["pytest", "pytest-cov", "flake8", "coverage"]
docs = [
    "Sphinx", "furo", "sphinxcontrib-bibtex", "sphinx-copybutton",
    "sphinxcontrib-mermaid>=0.8.1"
]


[project.urls]
Source = "https://www.github.com/lipitum/pymantra"
Documentation = "https://pymantra.readthedocs.io"
Publication = "https://doi.org/10.1101/2023.05.15.540613"


[tool.flake8]
max-line-length = 80


[tool.pytest.ini_options]
testpaths = ["tests"]


[tool.coverage.run]
source = ["pymantra"]
omit = [
    "*/__init__.py",
    "pymantra/network/exceptions.py",
    "pymantra/network/io_estimation.py",
    # namemapping is excluded due to the high bandwidth
    # => we only test it locally
    "pymantra/namemapping/*",
    "pymantra/database/query.py"
]

[tool.coverage.xml]
output = "coverage/coverage.xml"

[tool.coverage.html]
show_contexts = true
directory = "coverage/html"