biolink-model/pyproject.toml at master · biolink/biolink-model · GitHub

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[project]
name = "biolink-model"
dynamic = ["version"]
description = "The Biolink Model is a high-level data model designed to standardize types and relationships in biological knowledgebases."
authors = [
    {name = "Chris Mungall", email = "cjm@berkeleybop.org"},
    {name = "Deepak Unni", email = "deepak.unni3@gmail.com"},
    {name = "Sierra Moxon", email = "smoxon@lbl.gov"},
    {name = "Richard Bruskiewich", email = "richard@delphinai.ca"},
]
license = {text = "MIT"}
readme = "README.md"
requires-python = ">=3.10"
classifiers = [
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]
dependencies = [
    "pydantic>=2,<3",
    "linkml-runtime==1.11.1",
]

[project.scripts]
generate_viz_json = "biolink_model.scripts.generate_json:generate_viz_json"

[project.optional-dependencies]
scripts = [
    "linkml==1.11.1",
    "rdflib",
    "curies",
]
docs = [
    # Must cover everything mkdocs.yml declares: `theme: material` and `plugins: [search, mermaid2]`.
    # Bounds mirror the dev group so a standalone `pip install biolink-model[docs]` builds the same
    # site CI builds.
    "mkdocs>=1.4.2,<2",
    "mkdocs-material>=9.5.17,<10",
    "mkdocs-mermaid2-plugin>=1.1.1,<2",
]
all = [
    "biolink-model[scripts,docs]",
]

[dependency-groups]
dev = [
    "linkml==1.11.1",
    "mkdocs>=1.4.2,<2",
    "mkdocs-material>=9.5.17,<10",
    "mkdocs-mermaid2-plugin>=1.1.1,<2",
    "schemasheets>=0.2.1,<0.5",
    "codespell>=2.2.6,<3",
    "pytest>=8.1.1,<10",
    "yamllint>=1.35.1,<2",
]

[build-system]
requires = ["hatchling", "uv-dynamic-versioning"]
build-backend = "hatchling.build"

[tool.uv-dynamic-versioning]
vcs = "git"
style = "pep440"
fallback-version = "0.0.0"

[tool.hatch.version]
source = "uv-dynamic-versioning"

[tool.hatch.build.targets.wheel]
packages = ["src/biolink_model"]

[tool.uv]
# Dependency cooldown: ignore releases newer than 7 days so malware/CVE advisories have time to surface.
# uv records this as `exclude-newer-span = "P7D"` in uv.lock (and may also include a placeholder
# `exclude-newer` timestamp for backwards compatibility), avoiding per-relock absolute timestamps and
# reducing cross-branch merge conflicts (see astral-sh/uv#18708). Requires uv >= 0.9.17.
exclude-newer = "7 days"

[tool.codespell]
skip = '.idea,.git,SEMMEDDB*,semmed*,*.svg,docs,./src/docs/registry.md,./.venv'
ignore-words-list = 'amination,ehr,mor,brite,nin,mirgate'