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pyproject.toml
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pyproject.toml
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[build-system]
build-backend = "hatchling.build"
requires = ["hatchling"]
[project]
name = "sincei"
description = "A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data "
readme = "README.md"
requires-python = ">=3.8"
dynamic = ["version"]
license = {file = "LICENCE.txt"}
authors = [
{name = "Vivek Bhardwaj"},
]
maintainers = [
{name = "Vivek Bhardwaj", email = "[email protected]"},
]
classifiers = [
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Programming Language :: Python :: 3",
]
urls.Documentation = "https://sincei.readthedocs.io/"
urls.Source = "https://github.com/vivekbhr/sincei"
urls.Home-page = "https://github.com/vivekbhr/sincei"
dependencies = [
"anndata",
"scanpy",
"loompy",
"umap-learn",
"pandas",
"deeptools",
"leidenalg",
"networkx",
"python-igraph",
# for debug logging (referenced from the issue template)
"session-info",
"torch",
"mctorch-lib",
"gensim"
]
[project.scripts]
scBulkCoverage = "sincei.scBulkCoverage:main"
scClusterCells = "sincei.scClusterCells:main"
scCombineCounts = "sincei.scCombineCounts:main"
scCountQC = "sincei.scCountQC:main"
scCountReads = "sincei.scCountReads:main"
scFilterBarcodes = "sincei.scFilterBarcodes:main"
scFilterStats = "sincei.scFilterStats:main"
scJSD = "sincei.scJSD:main"
sincei = "sincei.sincei:main"
[project.optional-dependencies]
dev = [
# CLI for bumping the version number
"bump2version",
"pre-commit",
"twine>=4.0.2"
]
doc = [
"sphinx>=4",
"sphinx-book-theme>=0.3.3",
"myst-nb",
"sphinxcontrib-bibtex>=1.0.0",
"sphinx-autodoc-typehints",
"readthedocs-sphinx-ext",
"sphinx-argparse",
"sphinx_toolbox"
# For notebooks
# "ipykernel",
# "ipython",
# "sphinx-copybutton",
]
test = [
"pytest"
]
[tool.hatch.build.targets.sdist]
include = [
"/sincei",
]
[tool.hatch.build.targets.wheel]
packages = ['sincei']
[tool.hatch.version]
path = "sincei/_version.py"
[tool.pytest.ini_options]
testpaths = ["sincei/test"]
xfail_strict = true
addopts = [
"--import-mode=importlib", # allow using test files with same name
]
[tool.isort]
include_trailing_comma = true
multi_line_output = 3
profile = "black"
skip_glob = ["docs/*"]
[tool.black]
line-length = 120
target-version = ['py38']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
)
'''