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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "momics"
version = "0.4.0"
description = "A package to create and manage genome-related TileDB arrays"
requires-python = ">=3.8"
license = {text = "CC BY-NC 4.0"}
readme = "README.md"
authors = [
{name = "Jacques Serizay", email = "[email protected]"}
]
keywords = [
"multi-omics",
"genomics",
"epigenomics",
"Tile-DB",
"bioinformatics",
"matrix",
"sparse",
"format"
]
classifiers = [
"Operating System :: OS Independent",
"Programming Language :: Python :: 3"
]
dependencies = [
"tiledb",
"pyBigWig",
"pyranges",
"pyfaidx",
"Biopython",
"numpy",
"pandas",
"pyarrow>=1.0",
"click>=7",
"cloup",
"packaging",
"psutil",
"setuptools",
"typing-extensions",
"tensorflow[and-cuda]",
]
[project.urls]
homepage = "https://js2264.github.io/momics"
documentation = "https://js2264.github.io/momics"
repository = "https://github.com/js2264/momics"
changelog = "https://github.com/js2264/momics/blob/devel/CHANGES.md"
[project.scripts]
momics = "momics.cli:cli"
[tool.hatch.version]
path = "src/momics/version.py"
[tool.hatch.metadata]
allow-direct-references = true
[project.optional-dependencies]
all = [
"biopython",
"dask[array,dataframe]",
"matplotlib",
"psutil",
]
test = [
"coverage[toml]",
"isort",
"python-dotenv",
"pytest",
"pytest-cov",
"pytest-order",
"ruff",
]
dev = [
"momics[all,test]",
"pre-commit",
"twine"
]
docs = [
'autodoc',
'sphinx-autoapi',
"autodocsumm",
"sphinxcontrib-napoleon",
"m2r",
"recommonmark",
"Sphinx>=1.6",
"sphinx-autobuild",
"sphinx-click",
"furo",
"pydata-sphinx-theme",
"sphinx-rtd-theme",
"myst-parser",
"nbsphinx",
"lxml[html_clean]",
]
[tool.black]
line-length = 130
target-version = ['py39']
[tool.ruff]
line-length = 130
src = ["src"]
exclude = [
"bench/*",
".venv",
"__main__.py",
]
lint.ignore = ["E402", "I001"]
lint.extend-select = [
"B", # bugbear
"E", # style errors
"F", # pyflakes
"I", # isort
"RUF", # ruff-specific rules
# "UP", # pyupgrade
"W", # style warnings
]
lint.isort.known-first-party = ["momics"]
[tool.pytest.ini_options]
markers = ["order: mark test to run in a specific order"]
minversion = "7"
log_cli_level = "INFO"
xfail_strict = true
addopts = [
"-ra",
"--strict-config",
"--strict-markers",
"--cov=momics",
"--cov-config=pyproject.toml",
"--cov-report=term-missing",
"--cov-report=html",
"--cov-report=xml",
]
filterwarnings = ["ignore::PendingDeprecationWarning"]
testpaths = ["tests"]
[tool.coverage.run]
source = ["momics"]
omit = []
[tool.coverage.report]
exclude_lines = [
"pragma: no cover",
"return NotImplemented",
"raise NotImplementedError"
]
[tool.hatch.envs.default.scripts]
fix = "ruff check --fix src tests"
lint = "ruff check src tests"
test = "pytest ."
docs = "sphinx-autobuild docs docs/_build/html"
[tool.hatch.envs.test]
features = ["dev"]
[[tool.hatch.envs.test.matrix]]
python = ["3.8", "3.9", "3.10", "3.11", "3.12"]
[tool.tox]
legacy_tox_ini = """
[tox]
envlist =
py38
[testenv]
install_command = pip install -U {opts} {packages}
deps =
.[dev,docs]
commands =
pytest ### Run unit tests
make -C docs html ### Compile docs
ruff check src tests --fix ### Compile docs
# sybil --check docs/ ### Execute code chunks in docs
allowlist_externals =
make
"""