mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
Nicola Soranzo
741ecf6f44
This reverts commit 353c08cbb9 .
pysam 0.20.0 doesn't build for Python 3.11 on macOS, so we need to
temporarily add the unnecessary Cython runtime dependency that
pysam 0.21 brings in.
181 lines
4.6 KiB
TOML
181 lines
4.6 KiB
TOML
[tool.black]
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line-length = 120
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target-version = ['py37']
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include = '\.pyi?$'
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extend-exclude = '''
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^/(
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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.poetry]
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name = "galaxy"
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version = "22.01.dev0"
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description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
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authors = ["Galaxy Contributors"]
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license = "AFL-3.0"
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readme = "README.rst"
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homepage = "https://galaxyproject.org/"
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repository = "https://github.com/galaxyproject/galaxy/"
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documentation = "https://docs.galaxyproject.org/"
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[[tool.poetry.source]]
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name = "galaxyproject"
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url = "https://wheels.galaxyproject.org/simple"
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[tool.poetry.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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Cheetah3 = "!=3.2.6.post2" # yanked release, https://github.com/python-poetry/poetry/issues/2453
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cloudauthz = "==0.6.0"
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cloudbridge = "*"
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circus = "*"
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cwltool = "==3.1.20221109155812"
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conda-package-streaming = "*"
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dictobj = "*"
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dnspython = "*"
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docutils = "!=0.17, !=0.17.1"
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edam-ontology = "*"
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fastapi = ">=0.71.0, !=0.89.0, <0.99" # https://github.com/tiangolo/fastapi/issues/4041 https://github.com/tiangolo/fastapi/issues/5861
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fastapi-utils = "*"
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fs = "*"
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future = "*"
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galaxy_sequence_utils = "*"
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gravity = ">=1.0"
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gunicorn = "*"
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gxformat2 = "*"
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h5grove = ">=1.2.1"
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h5py = "*"
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importlib-metadata = "<5" # Work around https://github.com/celery/kombu/issues/1600
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importlib-resources = "*"
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isa-rwval = "*"
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kombu = "*"
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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 = "*"
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mrcfile = "*"
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msal = "*"
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nodeenv = "*"
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numpy = "*"
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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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psutil = "*"
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pulsar-galaxy-lib = ">=0.15.0.dev0"
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pycryptodome = "*"
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pydantic = {version = "<2", extras = ["email"]}
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PyJWT = "*"
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pykwalify = "*"
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pylibmagic = "*"
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pyparsing = "<3.1" # Needed by matplotlib on Python >=3.8 https://github.com/matplotlib/matplotlib/issues/26152
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pysam = ">=0.21" # for Python 3.11 support on macOS
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python = ">=3.7,<3.12" # Keep maximum version strict to appease numpy and scipy
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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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PyYAML = "*"
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refgenconf = ">=0.12.0"
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requests = "*"
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rocrate = "*"
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Routes = "*"
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schema-salad = "!=8.3.20220721194857" # https://github.com/common-workflow-language/schema_salad/issues/575
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social-auth-core = {version = "==4.0.3", extras = ["openidconnect"]}
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sortedcontainers = "*"
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SQLAlchemy = ">=1.4.25,<2"
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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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svgwrite = "*"
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tifffile = "*"
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tuswsgi = "*"
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typing-extensions = "*"
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uvicorn = "*"
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uvloop = "*"
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WebOb = "*"
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Whoosh = "*"
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zipstream-new = "*"
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s3fs = "^2023.1.0"
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[tool.poetry.group.dev.dependencies]
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ase = ">=3.18.1"
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axe-selenium-python = "*"
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black = "*"
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codespell = "*"
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cwltest = "*"
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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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pkce = "*"
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pytest = "*"
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pytest-asyncio = "*"
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pytest-celery = "*"
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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-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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selenium = "*"
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seletools = "*"
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Sphinx = ">=4.0" # support docutils 0.17
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sphinx_rtd_theme = ">=1.0.0"
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statsd = "*"
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testfixtures = "*"
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tuspy = "*"
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twill = "*"
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watchdog = "*"
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[tool.ruff]
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select = ["E", "F", "B", "UP"]
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target-version = "py37"
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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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ignore = ["B008", "B9", "E402", "E501"]
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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.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.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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