Merge 'Update gravity requirement to 1.0.4, waiting for required gravity + g…' into branch

extend-exclude = '''

^/(

  | packages

  | lib/tool_shed/test/test_data/repos

)/

'''

repository = "https://github.com/galaxyproject/galaxy/"

documentation = "https://docs.galaxyproject.org/"

[[tool.poetry.source]]

name = "PyPI"

priority = "default"

[[tool.poetry.source]]

name = "galaxyproject"

url = "https://wheels.galaxyproject.org/simple"

priority = "primary"

[tool.poetry.dependencies]

a2wsgi = "*"

dictobj = "*"

dnspython = "*"

docutils = "!=0.17, !=0.17.1"

dparse = "*"

edam-ontology = "*"

fastapi = ">=0.71.0, !=0.89.0, <0.99"  # https://github.com/tiangolo/fastapi/issues/4041 https://github.com/tiangolo/fastapi/issues/5861

fastapi-utils = "*"

fs = "*"

future = "*"

galaxy_sequence_utils = "*"

gravity = ">=1.0"

graphene-sqlalchemy = "3.0.0b3"  # need a beta release to be compat. with starlette plugin

gravity = ">=1.0.4"

gunicorn = "*"

gxformat2 = "*"

h5grove = ">=1.2.1"

h5py = "*"

importlib-metadata = "<5"  # Work around https://github.com/celery/kombu/issues/1600

importlib-resources = "*"

isa-rwval = "*"

isa-rwval = ">=0.10.10"

kombu = "*"

lagom = "*"

Mako = "*"

PyJWT = "*"

pykwalify = "*"

pylibmagic = "*"

pyparsing = "*"

pyparsing = "<3.1"  # Needed by matplotlib on Python >=3.8 https://github.com/matplotlib/matplotlib/issues/26152

pysam = ">=0.21"  # for Python 3.11 support on macOS

python = ">=3.7,<3.12"  # Keep maximum version strict to appease numpy and scipy

python-dateutil = "*"

python-multipart = "*"  # required to support form parsing in FastAPI/Starlette

PyYAML = "*"

refgenconf = ">=0.12.0"

requests = ">=2.25.0,<=2.28.2"

regex = "*"

requests = "*"

rocrate = "*"

Routes = "*"

schema-salad = "!=8.3.20220721194857"  # https://github.com/common-workflow-language/schema_salad/issues/575

fs-sshfs = "*"

starlette = "*"

starlette-context = "*"

starlette-graphene3 = "*"

svgwrite = "*"

tifffile = "*"

tuswsgi = "*"

markdown-it-reporter = "*"

myst-parser = "*"

pkce = "*"

playwright = "*"

pytest = "*"

pytest-asyncio = "*"

pytest-celery = "*"

python-irodsclient = "!=1.1.2"  # https://github.com/irods/python-irodsclient/issues/356

pytest-json-report = "*"

pytest-mock = "*"

pytest-playwright = "*"

pytest-postgresql = "!=3.0.0"  # https://github.com/ClearcodeHQ/pytest-postgresql/issues/426

pytest-shard = "*"

responses = "*"

selenium = "*"

seletools = "*"

Sphinx = ">=4.0"  # support docutils 0.17

sphinx_rtd_theme = ">=1.0.0"

sphinx-rtd-theme = ">=1.0.0,<2"  # https://github.com/python-poetry/poetry/issues/8194

statsd = "*"

testfixtures = "*"

tuspy = "*"

twill = "*"

watchdog = "*"

[tool.poetry.group.typecheck.dependencies]

mypy = "*"

pydantic = "<2"  # for pydantic.mypy plugin

types-bleach = "*"

types-boto = "*"

types-contextvars = "*"

types-dataclasses = "*"

types-docutils = "*"

types-Markdown = "*"

types-paramiko = "*"

types-pkg-resources = "*"

types-python-dateutil = "*"

types-PyYAML = "*"

types-requests = "*"

types-six = "*"

[tool.ruff]

select = ["E", "F", "B", "UP"]

# Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),

# flake8-logging-format (G) and pyupgrade (UP)

select = ["E", "F", "B", "G", "UP"]

target-version = "py37"

# Exceptions:

# B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)

# B9 flake8-bugbear opinionated warnings

# E402 module level import not at top of file # TODO, we would like to improve this.

# E501 is line length (delegated to black)

ignore = ["B008", "B9", "E402", "E501"]

# G* are TODOs

ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"]

exclude = [

  "lib/tool_shed/test/test_data/repos"

]

# Don't check some pyupgrade rules on generated files

"lib/galaxy/schema/bco/*" = ["UP006", "UP007"]

"lib/galaxy/schema/drs/*" = ["UP006", "UP007"]

"lib/tool_shed_client/schema/trs.py" = ["UP006", "UP007"]

"lib/tool_shed_client/schema/trs_service_info.py" = ["UP006", "UP007"]