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pyproject.toml
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[tool.black]
line-length = 80
target-version = ['py312']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs # exclude a few common directories in the
| \.git # root of the project
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
| foo.py # also separately exclude a file named foo.py in
# the root of the project
)
'''
[tool.interrogate]
ignore-init-method = true
ignore-init-module = false
ignore-magic = false
ignore-semiprivate = false
ignore-private = false
ignore-property-decorators = false
ignore-module = true
fail-under = 100
exclude = [
"setup.py",
"docs",
"build",
"data",
"bin",
"dandelion/external",
"tests",
]
ignore-regex = ["^get$", "^mock_.*", ".*BaseClass.*"]
verbose = 2
quiet = false
whitelist-regex = []
color = true
[tool.pytest.ini_options]
filterwarnings = [
"ignore::DeprecationWarning",
"ignore::PendingDeprecationWarning",
"ignore::FutureWarning",
]
addopts = "--cov src/dandelion --cov-report=xml -rP"
testpaths = ["tests"]
[tool.coverage.run]
omit = ["containter/*", "src/dandelion/external/*"]
[build-system]
requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
build-backend = "setuptools.build_meta"
[project]
name = "sc-dandelion"
dynamic = ["version"]
authors = [{ name = "zktuong", email = "[email protected]" }]
description = "sc-TCR/BCR-seq analysis tool"
readme = { file = "README.md", content-type = "text/markdown" }
license = { text = "GNU Affero General Public License v3 or later (AGPLv3+)" }
classifiers = [
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)",
]
keywords = ["dandelion", "single-cell", "immune", "TCR", "BCR"]
dependencies = [
"airr",
"setuptools_scm[toml]>=6.0",
"numpy>=1.18.4,<2.2.3",
"pandas>=1.0.3,<2.2.4",
"changeo>=1.0.0,<1.3.1",
"anndata>=0.7.1,<0.11.4",
"scanpy>=1.4.6,<1.10.5",
"scikit-learn>=0.23.0,<1.6.2",
"scipy>=1.4.1,<1.15.2",
"numba>=0.48.0,<0.61.1",
"seaborn>=0.10.1,<0.13.3",
"networkx>=2.4,<3.4.3",
"leidenalg>=0.8.0,<0.10.3",
"polyleven>=0.5,<0.8.1",
"h5py>=3.1.0,<3.12.2",
"adjustText>=0.7,<1.3.1",
"distance>=0.1.3,<0.1.4",
"plotnine>=0.6.0,<0.14.6",
"palettable>=3.3.0,<3.3.4",
"mizani>=0.9.0,<0.13.2",
]
[project.urls]
homepage = "https://github.com/zktuong/dandelion/"
documentation = "https://sc-dandelion.readthedocs.io/"
[project.optional-dependencies]
docs = [
"airr>=1.1.0,<1.5.2",
"ipykernel",
"biopython>=1.76,<1.86",
"changeo>=1.0.0,<1.3.1",
"presto>=0.5.0,<0.7.3",
"pyyaml",
"yamlordereddictloader",
"nbsphinx<=0.9.2",
"sphinx-autodoc-typehints<=3.0.1",
"sphinx_rtd_theme<=3.0.2",
"readthedocs-sphinx-ext<=2.2.5",
"recommonmark<=0.7.1",
]
scirpy = ["scirpy<=0.20.1", "awkward<=2.7.4", "mudata<=0.3.1"]
[tool.setuptools]
include-package-data = true
package-data = { "dandelion" = [
"bin/tigger-genotype.R",
"bin/MakeDb_gentle.py",
] }
# Use data-files for extra files, if required
data-files = { bin = ["bin/tigger-genotype.R", "bin/MakeDb_gentle.py"] }
[tool.setuptools.packages.find]
where = ["src"]
[tool.setuptools_scm]
version_scheme = "guess-next-dev"
local_scheme = "dirty-tag"