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pyproject.toml
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# Copyright (C) 2024 Roberto Rossini <[email protected]>
#
# SPDX-License-Identifier: MIT
[build-system]
requires = [
"hatchling",
"hatch-vcs",
]
build-backend = "hatchling.build"
[project]
name = "stripepy-hic"
description = "StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning"
dynamic = ["version"]
authors = [
{name="Andrea Raffo", email="[email protected]"},
{name="Bendik Berg", email="[email protected]"},
{name="Roberto Rossini", email="[email protected]"},
]
maintainers = [
{name="Andrea Raffo", email="[email protected]"},
{name="Roberto Rossini", email="[email protected]"},
]
readme = "README.md"
classifiers = [
"Development Status :: 4 - Beta",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
keywords = [
"hi-c",
"hic",
"stripe",
"stripes",
"architectural stripe",
"contact map",
"cooler",
"stripe recognition",
]
requires-python = ">=3.9"
dependencies = [
"h5py >3, <4",
"hictkpy[scipy] >=1, <2",
"numpy >=2, <3",
"pandas >=2.0, <3",
"scipy >=1.10, <2",
"structlog >=24, <25"
]
[project.optional-dependencies]
all = [
"stripepy-hic",
"colorama >=0.4, <0.5",
"matplotlib >=3.8, <4",
"rich >=13.9, <14",
]
test = [
"stripepy-hic[all]",
"pytest",
"pytest-cov",
]
dev = [
"stripepy-hic[all,test]",
"black[jupyter]",
"build",
"isort",
"pre-commit",
]
[project.scripts]
stripepy = "stripepy.main:main"
[project.urls]
Homepage = "https://github.com/paulsengroup/StripePy"
Issues = "https://github.com/paulsengroup/StripePy/issues"
Repository = "https://github.com/paulsengroup/StripePy.git"
Source = "https://github.com/paulsengroup/StripePy"
[tool.pytest.ini_options]
minversion = "8.0"
addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
xfail_strict = true
markers = ["end2end", "unit"]
python_files = [
"test/unit/test*.py",
"test/integration/test*.py",
]
testpaths = [
"test/integration",
"test/unit",
]
[tool.coverage.run]
branch = true
concurrency = ["multiprocessing", "thread"]
data_file = "coverage/data/stripepy.cov"
# debug = ["callers", "config", "pytest"]
# debug_file = "coverage/debug.txt"
parallel = true
source_pkgs = ["stripepy"]
[tool.coverage.html]
directory = "coverage/html/"
title = "StripePy coverage report"
[tool.coverage.json]
output = "coverage/stripepy.json"
[tool.coverage.lcov]
output = "coverage/stripepy.lcov"
[tool.coverage.xml]
output = "coverage/stripepy.xml"
[tool.hatch.version]
source = "vcs"
fallback-version = "unknown"
[tool.hatch.build.targets.wheel]
packages = ["src/stripepy"]
[[tool.hatch.envs.test.matrix]]
python = ["3.9", "3.10", "3.11", "3.12", "3.13"]