mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
247 lines
7.1 KiB
TOML
247 lines
7.1 KiB
TOML
[project]
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name = "galaxy"
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version = "0.1.0" # Not the real version, which is instead defined in lib/galaxy/version.py
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description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
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authors = [
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{name = "Galaxy Contributors"},
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]
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maintainers = [
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{name = "Galaxy Committers", email = "galaxy-committers@lists.galaxyproject.org"}
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]
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license = {file = "LICENSE.txt"}
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readme = "README.rst"
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requires-python = ">=3.8"
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dependencies = [
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"a2wsgi",
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"aiofiles",
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"alembic",
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"apispec",
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"Babel",
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"bdbag>=1.6.3",
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"Beaker",
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"bioblend",
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"bleach",
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"boltons",
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"boto",
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"bx-python",
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"celery",
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"cloudauthz==0.6.0",
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"cloudbridge",
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"circus",
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"conda-package-streaming",
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"CT3>=3.3.3", # Python 3.13 support
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"cwltool>=3.1.20230624081518", # save time, minimum needed by cwl-1.0 branch
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"dictobj",
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"dnspython",
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"docutils!=0.17,!=0.17.1",
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"dparse",
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"edam-ontology",
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"fastapi-slim>=0.111.0",
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"fissix ; python_version>='3.13'",
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"fs",
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"future>=1.0.0", # Python 3.12 support
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"graphene",
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"graphene-sqlalchemy>=3.0.0rc1", # need a beta release to be compat. with starlette plugin
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"graphql-core",
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"gravity>=1.0.4",
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"gunicorn",
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"gxformat2",
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"h5grove>=1.2.1",
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"h5py", # Python 3.8 support
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"h5py>=3.12 ; python_version>='3.9'", # Python 3.13 support
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"importlib-resources ; python_version<'3.9'", # for importlib.{abc.Traversable,resources.{files, Package}}
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"isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master", # https://github.com/ISA-tools/isa-rwval/pull/17
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"isal>=1.7.0", # Python 3.13 support
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"jinja2",
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"kombu>=5.3", # for importlib-metadata fix
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"lagom",
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"Mako",
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"Markdown",
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"MarkupSafe",
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"mercurial>=6.8.2", # Python 3.13 support
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"mrcfile",
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"msal",
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"nodeenv",
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"numpy",
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"numpy>=1.26.0 ; python_version=='3.9'", # Python 3.12 support
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"numpy>=2.1.0 ; python_version>='3.10'", # Python 3.13 support
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"packaging",
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"paramiko!=2.9.0,!=2.9.1", # https://github.com/paramiko/paramiko/issues/1961
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"Parsley",
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"Paste",
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"pebble",
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"pillow",
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"psutil",
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"pulsar-galaxy-lib>=0.15.0.dev0",
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"pycryptodome",
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"pydantic[email]>=2.7.4", # https://github.com/pydantic/pydantic/pull/9639
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"PyJWT",
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"pykwalify",
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"pylibmagic",
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"pyparsing",
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"pysam>=0.21", # for Python 3.11 support on macOS
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"python-dateutil",
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"python-magic",
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"python-multipart", # required to support form parsing in FastAPI/Starlette
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"python-slugify",
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"PyYAML",
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"refgenconf>=0.12.0",
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"regex",
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"requests",
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"rocrate",
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"Routes",
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"s3fs>=2023.1.0",
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"schema-salad>=8.7.20240905150001", # Python 3.13 support
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"social-auth-core>=4.5.0", # to drop dependency on abandoned python-jose
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"sortedcontainers",
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"SQLAlchemy>=2.0,<2.1,!=2.0.36", # https://github.com/sqlalchemy/sqlalchemy/issues/12019,
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"sqlitedict",
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"sqlparse",
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"starlette",
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"starlette-context",
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"starlette-graphene3",
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"svgwrite",
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"tifffile",
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"tuswsgi",
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"typing-extensions",
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"uvicorn!=0.28.0", # https://github.com/galaxyproject/galaxy/issues/17669
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"uvloop>=0.21.0", # Python 3.13 support
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"WebOb>=1.8.9", # Python 3.13 support
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"Whoosh",
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"zipstream-new",
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]
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[project.urls]
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Homepage = "https://galaxyproject.org/"
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Documentation = "https://docs.galaxyproject.org/"
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Repository = "https://github.com/galaxyproject/galaxy"
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"Bug Tracker" = "https://github.com/galaxyproject/galaxy/issues"
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[dependency-groups]
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dev = [
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"ase>=3.18.1",
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"axe-selenium-python",
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"black",
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"boto3",
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"codespell",
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"cwltest>=2.5.20240906231108", # Python 3.13 support
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"darker",
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"fluent-logger",
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"galaxy-release-util",
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"httpx",
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"isort",
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"lxml!=4.2.2",
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"markdown-it-reporter",
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"myst-parser",
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"onedatafilerestclient==21.2.5.2",
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"pkce",
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"playwright>=1.48.0", # Python 3.13 support
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"pytest<8", # https://github.com/galaxyproject/galaxy/issues/17561
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"pytest-asyncio",
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"pytest-cov",
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"pytest-html",
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"pytest-httpserver",
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"python-irodsclient!=1.1.2", # https://github.com/irods/python-irodsclient/issues/356
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"pytest-json-report",
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"pytest-mock",
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"pytest-playwright",
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"pytest-postgresql!=3.0.0", # https://github.com/ClearcodeHQ/pytest-postgresql/issues/426
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"pytest-shard",
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"responses",
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"rucio-clients>=33.6.0 ; python_version>='3.9'", # https://github.com/galaxyproject/galaxy/pull/17156
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"selenium",
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"seletools",
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"Sphinx>=4.0", # support docutils 0.17
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"sphinx-rtd-theme",
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"statsd",
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"testfixtures",
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"tuspy",
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"twill>=3.2.5", # Python 3.13 support
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"watchdog",
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"Werkzeug",
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]
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typecheck = [
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"boto3-stubs[s3]",
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"lxml-stubs",
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"mypy",
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"pydantic>=2.7.4", # for pydantic.mypy plugin
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"types-bleach",
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"types-boto",
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"types-contextvars",
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"types-dataclasses",
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"types-docutils",
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"types-Markdown",
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"types-paramiko",
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"types-python-dateutil",
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"types-python-slugify",
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"types-PyYAML",
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"types-requests",
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"types-setuptools",
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"types-six",
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]
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[tool.black]
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line-length = 120
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target-version = ['py38']
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include = '\.pyi?$'
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extend-exclude = '''
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^/(
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| packages
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| lib/tool_shed/test/test_data/repos
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)/
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'''
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[tool.darker]
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isort = true
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[tool.ruff]
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target-version = "py38"
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exclude = [
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"lib/tool_shed/test/test_data/repos"
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]
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[tool.ruff.lint]
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# Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
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# flake8-comprehensions (C4), flake8-logging-format (G),
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# flake8-implicit-str-concat (ISC) and pyupgrade (UP)
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select = ["E", "F", "B", "C4", "G", "ISC", "NPY", "UP"]
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# Exceptions:
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# B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
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# B9 flake8-bugbear opinionated warnings
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# E402 module level import not at top of file # TODO, we would like to improve this.
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# E501 is line length (delegated to black)
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# G* are TODOs
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ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"]
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[tool.ruff.lint.flake8-comprehensions]
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allow-dict-calls-with-keyword-arguments = true
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[tool.ruff.lint.isort]
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# We are not selecting "I" rules in ruff yet because support for all the isort
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# options we need is not complete, but these are the one currently implemented.
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combine-as-imports = true
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relative-imports-order = "closest-to-furthest"
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[tool.ruff.lint.pyupgrade]
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# Preserve types, even if a file imports `from __future__ import annotations`.
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keep-runtime-typing = true
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[tool.ruff.lint.per-file-ignores]
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# Don't check pyupgrade rules on tool scripts, which may use different Python versions
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"test/functional/tools/*" = ["UP"]
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"tools/*" = ["UP"]
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# Don't check some pyupgrade rules on generated files
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"lib/galaxy/schema/bco/*" = ["UP006", "UP007"]
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"lib/galaxy/schema/drs/*" = ["UP006", "UP007"]
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"lib/tool_shed_client/schema/trs.py" = ["UP006", "UP007"]
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"lib/tool_shed_client/schema/trs_service_info.py" = ["UP006", "UP007"]
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[tool.uv]
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constraint-dependencies = [
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"scipy>=1.14.1; python_version>='3.10'", # Python 3.13 support
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]
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default-groups = []
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extra-index-url = ["https://wheels.galaxyproject.org/simple"]
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index-strategy = "unsafe-best-match"
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package = false
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