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pyproject.toml
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pyproject.toml
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[project]
name = "dcd-mapping"
description = "Map MaveDB scoresets to VRS objects"
authors = [
{name = "Jeremy Arbesfeld", email = "[email protected]"},
{name = "James Stevenson", email = "[email protected]"},
{name = "Alan Rubin", email = "[email protected]"},
{name = "Alex Handler Wagner", email = "[email protected]"},
]
readme = "README.md"
license = { file = "LICENSE" }
classifiers = [
"Development Status :: 3 - Alpha",
"Framework :: Pydantic",
"Framework :: Pydantic :: 2",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.10"
dependencies = [
"requests",
"biopython",
"tqdm",
"click",
"cool-seq-tool~=0.6.0",
"ga4gh.vrs==2.0.0-a10",
# probably easiest to just include pg dependency group even if it's not always necessary
"gene-normalizer[pg]~=0.4.1",
"pydantic~=2.0",
"python-dotenv",
"setuptools>=68.0", # tmp -- ensure 3.12 compatibility
"canonicaljson",
]
dynamic = ["version"]
[project.scripts]
dcd-map = "dcd_mapping.cli:cli"
[project.optional-dependencies]
tests = [
"pytest",
"pytest-mock",
"pytest-cov",
"pytest-asyncio",
"requests-mock"
]
dev = [
"ruff==0.5.0",
"pre-commit>=3.7.1"
]
[project.urls]
Homepage = "https://www.varianteffect.org/"
Documentation = "https://github.com/ave-dcd/dcd_mapping/README.md"
Source = "https://github.com/ave-dcd/dcd_mapping"
[build-system]
requires = ["setuptools>=64", "setuptools_scm>=8"]
build-backend = "setuptools.build_meta"
[tool.setuptools_scm]
[tool.pytest.ini_options]
addopts = "--cov=src --cov-report term-missing"
testpaths = ["tests"]
asyncio_mode = "auto"
[tool.coverage.run]
branch = true
[tool.ruff]
src = ["src"]
[tool.ruff.lint]
select = [
"F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
"E", "W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
"I", # https://docs.astral.sh/ruff/rules/#isort-i
"N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n
"D", # https://docs.astral.sh/ruff/rules/#pydocstyle-d
"UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
"ANN", # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
"ASYNC", # https://docs.astral.sh/ruff/rules/#flake8-async-async
"S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
"B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
"A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
"C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
"DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
"T10", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
"EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
"LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log
"G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
"INP", # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
"PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
"T20", # https://docs.astral.sh/ruff/rules/#flake8-print-t20
"PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
"Q", # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
"RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
"RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret
"SLF", # https://docs.astral.sh/ruff/rules/#flake8-self-slf
"SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
"ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
"PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
"PGH", # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
"PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf
"FURB", # https://docs.astral.sh/ruff/rules/#refurb-furb
"RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
]
fixable = [
"I",
"F401",
"D",
"UP",
"ANN",
"B",
"C4",
"LOG",
"G",
"PIE",
"PT",
"RSE",
"SIM",
"PERF",
"FURB",
"RUF"
]
# ANN003 - missing-type-kwargs
# ANN101 - missing-type-self
# ANN102 - missing-type-cls
# D203 - one-blank-line-before-class
# D205 - blank-line-after-summary
# D206 - indent-with-spaces*
# D213 - multi-line-summary-second-line
# D300 - triple-single-quotes*
# D400 - ends-in-period
# D415 - ends-in-punctuation
# E111 - indentation-with-invalid-multiple*
# E114 - indentation-with-invalid-multiple-comment*
# E117 - over-indented*
# E501 - line-too-long*
# W191 - tab-indentation*
# S321 - suspicious-ftp-lib-usage
# *ignored for compatibility with formatter
ignore = [
"ANN003", "ANN101", "ANN102",
"D203", "D205", "D206", "D213", "D300", "D400", "D415",
"E111", "E114", "E117", "E501",
"W191",
"S321",
"PGH003",
]
[tool.ruff.lint.per-file-ignores]
# ANN001 - missing-type-function-argument
# ANN2 - missing-return-type
# ANN102 - missing-type-cls
# S101 - assert
# B011 - assert-false
# INP001 - implicit-namespace-package
"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "D103", "INP001"]
"scripts/*" = ["INP001"]
[tool.ruff.format]
docstring-code-format = true