pyproject.toml

[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"

[project]
name = "harissa"
authors = [
    { name="Ulysse Herbach", email="ulysse.herbach@inria.fr" },
]
description = "Tools for mechanistic gene network inference from single-cell data"
readme = "README.md"
classifiers = [
    "Development Status :: 4 - Beta",
    "License :: OSI Approved :: BSD License",
    "Programming Language :: Python :: 3",
    "Operating System :: OS Independent",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
license = { file = "LICENSE.txt" }
# license-files = { paths = ["LICENSE"] }
keywords = [
    "stochastic gene expression",
    "gene regulatory networks",
    "single-cell transcriptomics",
]
requires-python = ">=3.8"
dependencies = [
    "numpy>=1.24",
    "scipy>=1.7",
    "numba>=0.55",
    "matplotlib>=3.4",
    "networkx>=2.6",
    "scikit-learn"
]
dynamic = ["version"]

[project.optional-dependencies]
extra = ["alive-progress>=3.0", "umap-learn", "anndata"]

[project.urls]
Repository = "https://github.com/harissa-framework/harissa"
Documentation = "https://harissa-framework.github.io/harissa"
"Repository (legacy)" = "https://github.com/ulysseherbach/harissa"

[project.scripts]
harissa = "harissa.utils.cli:main"

# Tools config

# Hatch

[tool.hatch.build.targets.sdist]
only-include = ["src"]
# core-metadata-version = "2.1" # force it to 2.1 it seems to put 2.3 by default

# [tool.hatch.build.targets.wheel]
# core-metadata-version = "2.1" # force it to 2.1 it seems to put 2.3 by default

[tool.hatch.version]
source = "vcs"
raw-options = { local_scheme = "no-local-version" }

# Ruff

[tool.ruff]
select = ["E", "F", "W"]
line-length = 79

[tool.ruff.format]
quote-style = "single"
indent-style = "space"

# Pytest

[tool.pytest.ini_options]
minversion = "6.0"
required_plugins = ["pytest-cov"]
addopts = [
    "--junit-xml=report.xml",
    "--cov",
    "--cov-append",
    "--cov-report=lcov",
    "--cov-report=html",
    "--cov-report=term"
]
testpaths = ["tests"]

[tool.coverage.run]
source = ['harissa']
branch = true
omit = [
    '*/harissa/plot/*', 
    '*/harissa/utils/cli/*', 
    '*/harissa/benchmark/*'
]

[tool.coverage.report]
fail_under = 80

[tool.coverage.html]
directory = "coverage"