pyproject.toml

# See https://setuptools.readthedocs.io/en/latest/build_meta.html
[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[tool.black]
line-length = 100
target-version = ["py39", "py310", "py311", "py312"]

[tool.isort]
profile = "black"
multi_line_output = 3
include_trailing_comma = true
reverse_relative = true

# Pytest, see https://docs.pytest.org/en/stable/reference/customize.html#pyproject-toml
[tool.pytest.ini_options]
markers = [
    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
]

[project]
name = "bioregistry"
version = "0.11.30-dev"
description = "Integrated registry of biological databases and nomenclatures"
readme = "README.md"
authors = [
    { name = "Charles Tapley Hoyt", email = "cthoyt@gmail.com" }
]
maintainers = [
    { name = "Charles Tapley Hoyt", email = "cthoyt@gmail.com" }
]

# See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#classifiers
# Search tags using the controlled vocabulary at https://pypi.org/classifiers
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Framework :: Pytest",
    "Framework :: tox",
    "Framework :: Sphinx",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3 :: Only",
]
keywords = [
    "snekpack", # please keep this keyword to credit the cookiecutter-snekpack template
    "cookiecutter",
    "databases",
    "biological databases",
    "biomedical databases",
    "persistent identifiers",
]

# License Information. This can be any valid SPDX identifiers that can be resolved
# with URLs like https://spdx.org/licenses/MIT
# See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
license = { file = "LICENSE" }

requires-python = ">=3.9"
dependencies = [
    "requests",
    "tqdm",
    "pystow>=0.1.13",
    "click",
    "more_click>=0.1.2",
    "pydantic",
    "curies>=0.7.0"
]

[project.optional-dependencies]
tests = [
    "pytest",
    "coverage",
    "more_itertools",
    "httpx",
    "indra",
    "scikit-learn"
]
docs = [
    "sphinx>=8",
    "sphinx-rtd-theme>=3.0",
    "sphinx-click",
    "sphinx_automodapi",
    "autodoc_pydantic",
]
gha = [
    "more_itertools",
]
align = [
    "pyyaml",
    "beautifulsoup4",
    "tabulate",
    "defusedxml",
    "class-resolver",
    "fairsharing-client>=0.1.0",
    "pandas",
]
export = [
    "pyyaml",
    "rdflib",
    "rdflib-jsonld",
    "ndex2",
]
charts = [
    "matplotlib",
    "matplotlib_venn",
    "seaborn",
    "pandas",
    "jinja2",
]
health = [
    "click_default_group",
    "pandas",
    "tabulate",
    "pyyaml",
    "jinja2",
]
web = [
    "pyyaml",
    "rdflib",
    "rdflib-jsonld",
    "rdflib-endpoint",
    "flask<2.2.4",
    "werkzeug<2.3.0",
    "fastapi",
    "uvicorn",
    "bootstrap-flask<=2.0.0",
    "markdown",
    "curies[fastapi]",
    "a2wsgi",
]


# See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#urls
[project.urls]
"Bug Tracker" = "https://github.com/biopragmatics/bioregistry/issues"
Homepage = "https://github.com/biopragmatics/bioregistry"
Repository = "https://github.com/biopragmatics/bioregistry.git"
Documentation = "https://bioregistry.readthedocs.io"

[tool.setuptools]
package-dir = { "" = "src" }

[tool.setuptools.packages.find]
# this implicitly sets `packages = ":find"`
where = ["src"]  # list of folders that contain the packages (["."] by default)

# See https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[tool.setuptools.package-data]
"*" = ["*.*"]

[project.scripts]
bioregistry = "bioregistry.cli:main"

[tool.cruft]
skip = [
    "**/__init__.py",
    "tests/*"
]

# MyPy, see https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
plugins = [
    "pydantic.mypy",
]

# Doc8, see https://doc8.readthedocs.io/en/stable/readme.html#ini-file-usage
[tool.doc8]
max-line-length = 120

# Coverage, see https://coverage.readthedocs.io/en/latest/config.html
[tool.coverage.run]
branch = true
source = [
    "bioregistry",
]
omit = [
    "tests/*",
    "docs/*",
    "src/bioregistry/cli.py",
    "src/bioregistry/__main__.py",
]

[tool.coverage.paths]
source = [
    "src/bioregistry",
    ".tox/*/lib/python*/site-packages/bioregistry",
]

[tool.coverage.report]
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "raise NotImplementedError",
    "if __name__ == \"__main__\":",
    "if TYPE_CHECKING:",
    "def __str__",
    "def __repr__",
]

[tool.ruff]
line-length = 100
extend-include = ["*.ipynb"]

[tool.ruff.lint]
# See https://docs.astral.sh/ruff/rules
extend-select = [
    "F", # pyflakes
    "E", # pycodestyle errors
    "W", # pycodestyle warnings
    "C90", # mccabe
    "I", # isort
    "UP", # pyupgrade
    "D", # pydocstyle
    "DOC", # pydoclint
    "B", # bugbear
    "S", # bandit
    "T20", # print
    "N", # pep8 naming
    "ERA", # eradicate commented out code
    "NPY", # numpy checks
    "RUF", # ruff rules
    "C4", # comprehensions
]
ignore = [
    "D105", # Missing docstring in magic method
    "E203", # Black conflicts with the following
]

# See https://docs.astral.sh/ruff/settings/#per-file-ignores
[tool.ruff.lint.per-file-ignores]
# Ignore security issues in the version.py, which are inconsistent
"src/bioregistry/version.py" = ["S603", "S607"]
# Ignore commented out code in Sphinx configuration file
"docs/source/conf.py" = ["ERA001"]
# Prints are okay in notebooks
"notebooks/**/*.ipynb" = ["T201"]

[tool.ruff.lint.pydocstyle]
convention = "pep257"

[tool.ruff.lint.isort]
relative-imports-order = "closest-to-furthest"
known-third-party = [
    "tqdm",
]
known-first-party = [
    "bioregistry",
    "tests",
]

[tool.ruff.format]
# see https://docs.astral.sh/ruff/settings/#format_docstring-code-format
docstring-code-format = true

[tool.bumpversion]
current_version = "0.11.30-dev"
parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
serialize = [
    "{major}.{minor}.{patch}-{release}+{build}",
    "{major}.{minor}.{patch}+{build}",
    "{major}.{minor}.{patch}-{release}",
    "{major}.{minor}.{patch}",
]
commit = true
tag = false

[tool.bumpversion.parts.release]
optional_value = "production"
first_value = "dev"
values = [
    "dev",
    "production",
]

[[tool.bumpversion.files]]
filename = "pyproject.toml"
search = "version = \"{current_version}\""
replace = "version = \"{new_version}\""

[[tool.bumpversion.files]]
filename = "docs/source/conf.py"
search = "release = \"{current_version}\""
replace = "release = \"{new_version}\""

[[tool.bumpversion.files]]
filename = "src/bioregistry/version.py"
search = "VERSION = \"{current_version}\""
replace = "VERSION = \"{new_version}\""