Merge pull request #18125 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -6,7 +6,7 @@ ase==3.22.1 ; python_version >= "3.8" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
 attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
 axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13"
-babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
+babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 black==24.4.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -21,7 +21,7 @@ codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
 cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -53,19 +53,19 @@ jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-functools==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
 jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
+jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13"
 jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==25.2.0 ; python_version >= "3.8" and python_version < "3.13"
+keyring==25.2.1 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
 matplotlib==3.8.4 ; python_version >= "3.9" and python_version < "3.13"
-mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
+mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -90,7 +90,7 @@ pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
 prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
-psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13"
+psycopg==3.1.19 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -108,7 +108,7 @@ pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13"
 pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
 pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
+pytest-playwright==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -126,16 +126,16 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
 responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
-rpds-py==0.18.0 ; python_version >= "3.9" and python_version < "3.13"
+rpds-py==0.18.1 ; python_version >= "3.9" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
-rucio-clients==34.2.0 ; python_version >= "3.9" and python_version < "3.13"
+rucio-clients==34.3.0 ; python_version >= "3.9" and python_version < "3.13"
 schema-salad==8.5.20240410123758 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 selenium==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
-seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
+seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -169,7 +169,7 @@ urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
 urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
 watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
-werkzeug==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
+werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
 yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -4,4 +4,4 @@ flake8-bugbear==24.4.26
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.4.3
+ruff==0.4.4

lib/galaxy/dependencies/pinned-requirements.txt

@@ -20,7 +20,7 @@ argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
 async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11"
 attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13"
 attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13"
-babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
+babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9"
 bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -29,7 +29,7 @@ bcrypt==4.1.3 ; python_version >= "3.8" and python_version < "3.13"
 bdbag==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
 beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13"
 billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
-bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
+bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
 boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -51,7 +51,7 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows"
 coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13"
 conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
 cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13"
 cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13"
 cwltool==3.1.20240404144621 ; python_version >= "3.8" and python_version < "3.13"
@@ -92,20 +92,20 @@ importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9"
 isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
 isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
-jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
+jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
 jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
 jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
 jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13"
 jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13"
 kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13"
 lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
-mako==1.3.3 ; python_version >= "3.8" and python_version < "3.13"
+mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mercurial==6.7.2 ; python_version >= "3.8" and python_version < "3.13"
+mercurial==6.7.3 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
 mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -159,7 +159,7 @@ pyzmq==26.0.3 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 referencing==0.35.1 ; python_version >= "3.8" and python_version < "3.13"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
-regex==2024.4.28 ; python_version >= "3.8" and python_version < "3.13"
+regex==2024.5.10 ; python_version >= "3.8" and python_version < "3.13"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
 requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -168,7 +168,7 @@ requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13"
 rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
 routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
-rpds-py==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
+rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
 ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8"
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 s3fs==2024.3.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -181,15 +181,15 @@ sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==2.0.29 ; python_version >= "3.8" and python_version < "3.13"
+sqlalchemy==2.0.30 ; python_version >= "3.8" and python_version < "3.13"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13"
 starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13"
 starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13"
 supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13"
 svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13"
-tenacity==8.2.3 ; python_version >= "3.8" and python_version < "3.13"
+tenacity==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
 tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13"
 tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

@@ -1,6 +1,6 @@
 annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
-cryptography==42.0.6 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -20,6 +20,6 @@ types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13"
 types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13"
 types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
-types-six==1.16.21.20240425 ; python_version >= "3.8" and python_version < "3.13"
+types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13"
 types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"

lib/tool_shed/test/functional/conftest.py

@@ -1,16 +1,11 @@
 import os
 from typing import (
-    Any,
     Callable,
-    Dict,
     Generator,
 )
 
 import pytest
-from playwright.sync_api import (
-    Browser,
-    BrowserContext,
-)
+from playwright.sync_api import Browser
 
 from ..base.browser import ShedBrowser
 from ..base.playwrightbrowser import PlaywrightShedBrowser
@@ -23,8 +18,8 @@ def twill_browser() -> Generator[ShedBrowser, None, None]:
     yield TwillShedBrowser()
 
 
-def playwright_browser(class_context: BrowserContext) -> Generator[ShedBrowser, None, None]:
-    page = class_context.new_page()
+def playwright_browser(browser: Browser) -> Generator[ShedBrowser, None, None]:
+    page = browser.new_page()
     yield PlaywrightShedBrowser(page)
 
 
@@ -35,15 +30,3 @@ def playwright_browser(class_context: BrowserContext) -> Generator[ShedBrowser,
     shed_browser = pytest.fixture(scope="class")(playwright_browser)
 else:
     raise ValueError(f"Unrecognized value for TOOL_SHED_TEST_BROWSER: {test_browser}")
-
-
-@pytest.fixture(scope="class")
-def class_context(
-    browser: Browser,
-    browser_context_args: Dict,
-    pytestconfig: Any,
-    request: pytest.FixtureRequest,
-) -> Generator[BrowserContext, None, None]:
-    from pytest_playwright.pytest_playwright import context
-
-    yield from context.__pytest_wrapped__.obj(browser, browser_context_args, pytestconfig, request)