Babel/pyproject.toml at master · NCATSTranslator/Babel · GitHub

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[project]
name = "babel"
version = "1.14"
description = "Babel creates cliques of equivalent identifiers across many biomedical vocabularies. "
readme = "README.md"
license = "MIT"
requires-python = ">=3.11,<3.14"
dependencies = [
    "apybiomart",
    "beautifulsoup4>=4.14.2",
    "biopython>=1.85",
    "bmt>=1.4.6",
    "curies>=0.12.1",
    "deprecated~=1.2.18",
    "duckdb>=1.4.1",
    "humanfriendly>=10.0",
    "jsonlines>=4.0.0",
    "more-itertools>=10.8.0",
    "oaklib>=0.5.1",
    "pandas>=2.3.3",
    "psutil>=7.1.1",
    "psycopg2-binary>=2.9.11",
    "py-spy>=0.4.1",
    "pyoxigraph~=0.4.11",
    "pytest>=8.4.2",
    "pytest-cov>=7.0.0",
    "pytest-timeout>=2.3",
    "pytest-xdist>=3",
    "python-levenshtein>=0.27.1",
    "pyyaml>=6.0.3",
    "requests>=2.32.5",
    "snakemake>=9.13.3",
    "snakemake-executor-plugin-slurm>=1.9.2",
    "sparqlwrapper>=2.0.0",
    "tqdm>=4.67.1",
    "wheel>=0.45.1",
    "xmltodict>=1.0.2",
]

[project.urls]
Homepage = "https://github.com/NCATSTranslator/Babel"
Repository = "https://github.com/NCATSTranslator/Babel"
Issues = "https://github.com/NCATSTranslator/Babel/issues"

[dependency-groups]
dev = [
    "ipykernel>=7.1.0",
    "ruff>=0.14.14",
    "rumdl>=0.1.26",
    "snakefmt>=0.11.2",
]

# Linting/formatting configuration
[tool.ruff]
line-length = 120

[tool.ruff.lint]
# Enable all rules that ruff format would normally apply
select = [
    "E",   # pycodestyle errors
    "F",   # pyflakes
    "I",   # isort (import sorting)
    "UP",  # pyupgrade
]

# Optional but common
ignore = [
    "E501",  # let Ruff handle wrapping consistently
]

fixable = ["ALL"]
unfixable = []

[tool.snakefmt]
line_length = 120
include = '\.snakefile$|^Snakefile'

[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = ""
timeout = 30          # global fallback (seconds); overridden per mark in conftest.py
# Canonical marker definitions — conftest.py intentionally does NOT re-register these.
markers = [
    "unit: fast offline tests with no external dependencies",
    "network: requires live internet access (use --network to run)",
    "slow: correct but takes >30s even offline",
    "pipeline: invokes Snakemake rules; requires babel_downloads/ (use --pipeline to run)",
]

[tool.coverage.run]
source = ["src"]
omit = ["tests/*"]

[tool.coverage.report]
show_missing = true
precision = 1

[tool.coverage.html]
directory = "htmlcov"

[tool.rumdl]
flavor = "gfm"
disable = [
    "MD014",    # Allow '$ shell command' without displaying the output -- we have some long outputs!
]

[tool.rumdl.MD013]
line-length = 100
code-blocks = false
tables = false
reflow = true  # Enable automatic line wrapping (required for --fix)