mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-30 16:58:03 +08:00
Nuwan Goonasekera
dac85e51c0
cloudbridge picked the read size itself and it was never a tuning decision: 4 KiB on AWS, inherited from a 2017 boto2 shim. A 10 GB download is 2.6 million reads at that size, each one a threadpool hop on the way to the client. 4.4.0 takes a chunk_size, so pass the same STREAM_CHUNK_SIZE the other backends stream at, and require that version where the dependency is declared.
267 lines
8.2 KiB
TOML
267 lines
8.2 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/__init__.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 = ">=3.10"
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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>=5.4.0", # prefer not downgrading this to upgrading typing-extensions
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"cloudauthz==0.6.0",
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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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"cwl-utils>=0.13",
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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>=0.137.2", # https://github.com/fastapi/fastapi/pull/15785
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"fastmcp>=2.13.0",
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"fissix",
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"fs",
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"future>=1.0.0", # Python 3.12 support
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"gravity>=1.2.3", # Graceful restart on galaxy >= 26.1
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"gunicorn!=25.1.0", # https://github.com/benoitc/gunicorn/discussions/3509
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"gxformat2>=0.27.0",
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"h5grove>=1.2.1",
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"h5py>=3.12", # Python 3.13 support
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"httpx",
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"ijson",
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"importlib-resources ; python_version<'3.12'", # for importlib.{abc.Traversable,resources.{files, Package}}
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"isa-rwval>=0.10.11", # 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>=5.5.0", # prefer not downgrading this to upgrading typing-extensions
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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>=7.2", # Python 3.14 support
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"mrcfile",
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"more-itertools",
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"msal",
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"nodejs-wheel>=22,<23",
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"numpy>=1.26.0", # Python 3.12 support
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"numpy>=2.1.0 ; python_version>='3.10'", # Python 3.13 support
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"openpyxl>=3.1.5", # Minimum version ever tested with
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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!=5.2.1", # https://github.com/noxdafox/pebble/issues/164
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"pillow",
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"psutil",
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"pulsar-galaxy-lib>=0.15.15",
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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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"pydantic-ai>=1.56.0", # https://github.com/pydantic/pydantic-ai/security/advisories/GHSA-2jrp-274c-jhv3
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"pydantic-extra-types",
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"pydicom; python_version >= '3.10'",
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"PyJWT",
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"pykwalify",
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"pylibmagic",
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"pyparsing>=3.0.0",
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"pypng",
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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>=0.13.0", # https://github.com/refgenie/refgenconf/pull/149
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"regex",
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"requests",
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"rocrate<0.15.0", # https://github.com/crs4/rocrate-validator/issues/107
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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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"slowapi",
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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>=2.0.37,<2.1,!=2.0.41", # https://github.com/sqlalchemy/sqlalchemy/issues/12019 , https://github.com/sqlalchemy/sqlalchemy/issues/12600
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"sqlparse",
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"starlette>=1.0.1", # CVE-2026-48710 BadHost
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"starlette-context",
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"svgwrite",
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"tifffile",
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"typing-extensions",
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"tuspyserver",
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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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"fsspec>=2025.7.0",
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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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test = [
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"aiocop",
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"ase>=3.18.1",
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"axe-selenium-python",
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"boto3",
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"cloudbridge>=4.4.0",
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"cwltest>=2.5.20240906231108", # Python 3.13 support
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"fluent-logger",
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"gcsfs",
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"hvac",
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"lxml!=4.2.2",
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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",
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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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"roc-validator!=0.7.2", # https://github.com/crs4/rocrate-validator/pull/97
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"rucio-clients>=40.2.0", # https://github.com/rucio/rucio/pull/7665
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"selenium",
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"seletools",
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"statsd",
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"testfixtures",
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"total-perspective-vortex>=3.1.1,<4", # https://github.com/galaxyproject/total-perspective-vortex/pull/173
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"tuspy",
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"watchdog",
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"Werkzeug",
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]
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dev = [
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{include-group = "test"},
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"black",
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"codespell",
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"darker",
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"galaxy-release-util",
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"isort",
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"markdown-it-reporter",
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"myst-parser",
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"Sphinx>=4.0", # support docutils 0.17
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"sphinx-rtd-theme",
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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>=2.2.0", # support for closed TypedDicts
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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-cachetools",
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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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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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exclude = [
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"lib/tool_shed/test/test_data/repos"
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]
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line-length = 120
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src = ["lib"]
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namespace-packages = ["lib/galaxy"]
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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 the isort option
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# force_grid_wrap=2 is not currently supported:
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# https://github.com/astral-sh/ruff/issues/2601
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case-sensitive = false
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combine-as-imports = true
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no-lines-before = ["local-folder"]
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order-by-type = false
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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 pyupgrade rules on generated files
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"lib/galaxy/schema/bco/*" = ["UP"]
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"lib/galaxy/schema/drs/*" = ["UP"]
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"lib/tool_shed_client/schema/trs.py" = ["UP"]
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"lib/tool_shed_client/schema/trs_service_info.py" = ["UP"]
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[tool.uv]
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constraint-dependencies = [
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"limits>=2.5.0", # prefer not downgrading this to upgrading packaging
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"mirakuru!=3.0.0", # https://github.com/dbfixtures/mirakuru/pull/949
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"setuptools<82", # https://github.com/PyFilesystem/pyfilesystem2/issues/597
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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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