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

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[project]
name = "babel-pipeline"
version = "1.17"
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",
    "duckdb>=1.4.1",
    "humanfriendly>=10.0",
    "jsonlines>=4.0.0",
    "more-itertools>=10.8.0",
    "psutil>=7.1.1",
    "psycopg2-binary>=2.9.12",
    "pyoxigraph>=0.5.8",
    "pytest>=8.4.2",
    "pytest-cov>=7.0.0",
    "pytest-timeout>=2.3",
    "pytest-xdist>=3",
    "pyyaml>=6.0.3",
    "requests>=2.32.5",
    "snakemake>=9.21.1",
    "snakemake-executor-plugin-slurm>=2.7.1",
    "sparqlwrapper>=2.0.0",
    "tqdm>=4.67.1",
    "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",
    "py-spy>=0.4.2",
    "ruff>=0.14.14",
    "rumdl>=0.2.4",
    "snakefmt>=2.0.3",
]

[project.scripts]
babel-slurm-errors = "src.tools.slurm.errors:main"
babel-slurm-resources = "src.tools.slurm.resources:main"
babel-clique-diff = "src.tools.clique_diff.cli:main"
source-impact-report = "src.tools.source_impact_report.cli:main"
babel-overused-xrefs = "src.tools.overused_xrefs.cli:main"

[tool.uv]
package = true

[build-system]
requires = ["setuptools>=83.0.0"]
build-backend = "setuptools.build_meta"

[tool.setuptools.packages.find]
where = ["."]
include = ["src", "src.*"]


# Linting/formatting configuration
[tool.ruff]
line-length = 120
# Ruff 0.16 began formatting Python inside Markdown code blocks. Our snippets are illustrative
# fragments, not runnable modules, and Ruff mangles them (it wraps a trailing-comma list element in
# tests/pipeline/README.md into a single-element tuple). rumdl owns the Markdown files instead.
extend-exclude = ["*.md"]

[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.ruff.format]
# Ruff 0.16.0 began formatting Python code fences inside Markdown, which overlaps with the
# dedicated rumdl Markdown check and broke CI when astral-sh/ruff-action@v3 floated to 0.16.0
# (pyproject pins only a floor, >=0.14.14). Keep ruff's formatter scoped to Python source and
# leave Markdown to rumdl so formatting CI stays deterministic across ruff releases.
exclude = ["*.md"]

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

[tool.pytest.ini_options]
testpaths = ["tests"]
pythonpath = ["."]
addopts = "--dist=loadgroup"  # required for xdist_group marks to route pipeline tests to one worker
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: genuinely long-running (a full-file scan, a multi-GB load); raises the timeout to an hour",
    "pipeline: invokes Snakemake rules; requires babel_downloads/ (use --pipeline to run)",
    "min_memory_gb(n): test needs at least n GiB of system RAM; auto-skipped on smaller machines",
]

[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!
]
# Captured verbatim tool output, not authored prose -- regenerated by re-running the tool, so it
# must not be reflowed or held to line-length/heading rules. `releases/*/reports/` is the same case
# one step further: those files are copied byte-for-byte out of a build (see releases/ARTIFACTS.md),
# and reflowing one would make the archive disagree with the build it claims to be a subset of.
exclude = ["docs/tools/examples/", "releases/*/reports/"]

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