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d159d26764ba3044fcd62f762d3ab4f0689b6fe0
galaxy/pyproject.toml
T
Nicola Soranzo d159d26764 Pin twill to >=3.2.1 
twill 3.2 replaced `requests` with `httpx`, and `httpx` has a default
timeout of 5 s on a request, while `requests` didn't enforce a timeout by
default.

Fix errors like the following in ToolShed tests, where resetting
repository metadata takes longer than 5 s:

```
self = <tool_shed.test.functional.test_0000_basic_repository_features.TestBasicRepositoryFeatures object at 0x7f28f99197c0>

    def test_0090_verify_repository_metadata(self):
        """Verify that resetting the metadata does not change it."""
        repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
>       self.verify_unchanged_repository_metadata(repository)

lib/tool_shed/test/functional/test_0000_basic_repository_features.py:264:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
lib/tool_shed/test/base/twilltestcase.py:2073: in verify_unchanged_repository_metadata
    self.reset_repository_metadata(repository)
lib/tool_shed/test/base/twilltestcase.py:1774: in reset_repository_metadata
    self.visit_url("/repository/reset_all_metadata", params=params)
lib/tool_shed/test/base/twilltestcase.py:845: in visit_url
    return self._browser.visit_url(url, allowed_codes=allowed_codes)
lib/tool_shed/test/base/twillbrowser.py:35: in visit_url
    return visit_url(url, allowed_codes=allowed_codes)
lib/tool_shed/test/base/twillbrowser.py:20: in visit_url
    new_url = tc.go(url)
.venv/lib/python3.8/site-packages/twill/commands.py:120: in go
    browser.go(url)
.venv/lib/python3.8/site-packages/twill/browser.py:192: in go
    self._journey("open", try_url)
.venv/lib/python3.8/site-packages/twill/browser.py:677: in _journey
    result = self._client.get(url)
.venv/lib/python3.8/site-packages/httpx/_client.py:1041: in get
    return self.request(
.venv/lib/python3.8/site-packages/httpx/_client.py:814: in request
    return self.send(request, auth=auth, follow_redirects=follow_redirects)
.venv/lib/python3.8/site-packages/httpx/_client.py:901: in send
    response = self._send_handling_auth(
.venv/lib/python3.8/site-packages/httpx/_client.py:929: in _send_handling_auth
    response = self._send_handling_redirects(
.venv/lib/python3.8/site-packages/httpx/_client.py:966: in _send_handling_redirects
    response = self._send_single_request(request)
.venv/lib/python3.8/site-packages/httpx/_client.py:1002: in _send_single_request
    response = transport.handle_request(request)
.venv/lib/python3.8/site-packages/httpx/_transports/default.py:228: in handle_request
    resp = self._pool.handle_request(req)
/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/contextlib.py:131: in __exit__
    self.gen.throw(type, value, traceback)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

    @contextlib.contextmanager
    def map_httpcore_exceptions() -> typing.Iterator[None]:
        try:
            yield
        except Exception as exc:
            mapped_exc = None

            for from_exc, to_exc in HTTPCORE_EXC_MAP.items():
                if not isinstance(exc, from_exc):
                    continue
                # We want to map to the most specific exception we can find.
                # Eg if `exc` is an `httpcore.ReadTimeout`, we want to map to
                # `httpx.ReadTimeout`, not just `httpx.TimeoutException`.
                if mapped_exc is None or issubclass(to_exc, mapped_exc):
                    mapped_exc = to_exc

            if mapped_exc is None:  # pragma: no cover
                raise

            message = str(exc)
>           raise mapped_exc(message) from exc
E           httpx.ReadTimeout: timed out

.venv/lib/python3.8/site-packages/httpx/_transports/default.py:83: ReadTimeout
```
2023-11-27 00:01:50 +00:00

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[tool.black]
line-length = 120
target-version = ['py38']
include = '\.pyi?$'
extend-exclude = '''
^/(
| packages
| lib/tool_shed/test/test_data/repos
)/
'''
[tool.darker]
isort = true
[tool.poetry]
name = "galaxy"
version = "22.01.dev0"
description = "Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research."
authors = ["Galaxy Contributors"]
license = "AFL-3.0"
readme = "README.rst"
homepage = "https://galaxyproject.org/"
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 = "*"
aiofiles = "*"
alembic = "*"
apispec = "*"
Babel = "*"
bdbag = ">=1.6.3"
Beaker = "*"
bioblend = "*"
bleach = "*"
boltons = "*"
boto = "*"
bx-python = "*"
celery = "*"
Cheetah3 = "!=3.2.6.post2" # yanked release, https://github.com/python-poetry/poetry/issues/2453
cloudauthz = "==0.6.0"
cloudbridge = "*"
circus = "*"
cwltool = ">=3.1.20230624081518" # save time, minimum needed by cwl-1.0 branch
conda-package-streaming = "*"
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 = "*"
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 = ">=0.10.10"
kombu = "*"
lagom = "*"
Mako = "*"
Markdown = "*"
MarkupSafe = "*"
Mercurial = "*"
mrcfile = "*"
msal = "*"
nodeenv = "*"
numpy = "*"
packaging = "*"
paramiko = "!=2.9.0, !=2.9.1" # https://github.com/paramiko/paramiko/issues/1961
Parsley = "*"
Paste = "*"
pebble = "*"
psutil = "*"
pulsar-galaxy-lib = ">=0.15.0.dev0"
pycryptodome = "*"
pydantic = {version = "<2", extras = ["email"]}
PyJWT = "*"
pykwalify = "*"
pylibmagic = "*"
pyparsing = "*"
pysam = ">=0.21" # for Python 3.11 support on macOS
python = ">=3.8,<3.12" # Keep maximum version strict to appease numpy and scipy
python-dateutil = "*"
python-magic = "*"
python-multipart = "*" # required to support form parsing in FastAPI/Starlette
PyYAML = "*"
refgenconf = ">=0.12.0"
regex = "*"
requests = "*"
rocrate = "*"
Routes = "*"
schema-salad = "!=8.3.20220721194857" # https://github.com/common-workflow-language/schema_salad/issues/575
social-auth-core = {version = "==4.0.3", extras = ["openidconnect"]}
sortedcontainers = "*"
SQLAlchemy = ">=1.4.25,<2"
sqlitedict = "*"
sqlparse = "*"
starlette = "*"
starlette-context = "*"
starlette-graphene3 = "*"
svgwrite = "*"
tifffile = "*"
tuswsgi = "*"
typing-extensions = "*"
uvicorn = "*"
uvloop = "*"
WebOb = "*"
Whoosh = "*"
zipstream-new = "*"
s3fs = "^2023.1.0"
[tool.poetry.group.dev.dependencies]
ase = ">=3.18.1"
axe-selenium-python = "*"
black = "*"
codespell = "*"
cwltest = "*"
darker = "*"
fluent-logger = "*"
galaxy-release-util = "*"
httpx = "*"
isort = "*"
lxml = "!=4.2.2"
markdown-it-reporter = "*"
myst-parser = "*"
pkce = "*"
playwright = "*"
pytest = "*"
pytest-asyncio = "*"
pytest-celery = "*"
pytest-cov = "*"
pytest-html = "*"
pytest-httpserver = "*"
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 = "*"
urllib3 = "<2" # Necessary for poetry for resolve deps for Python 3.8+
seletools = "*"
Sphinx = ">=4.0" # support docutils 0.17
sphinx-rtd-theme = ">=1.0.0,<2" # https://github.com/python-poetry/poetry/issues/8194
statsd = "*"
testfixtures = "*"
tuspy = "*"
twill = ">=3.2.1" # https://github.com/twill-tools/twill/issues/18
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]
# Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B),
# flake8-logging-format (G) and pyupgrade (UP)
select = ["E", "F", "B", "G", "UP"]
target-version = "py38"
# 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)
# G* are TODOs
ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"]
exclude = [
"lib/tool_shed/test/test_data/repos"
]
[tool.ruff.isort]
# We are not selecting "I" rules in ruff yet because support for all the isort
# options we need is not complete, but these are the one currently implemented.
combine-as-imports = true
relative-imports-order = "closest-to-furthest"
[tool.ruff.per-file-ignores]
# Don't check pyupgrade rules on tool scripts, which may use different Python versions
"test/functional/tools/*" = ["UP"]
"tools/*" = ["UP"]
# 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"]
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