Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,40 +1,39 @@
---extra-index-url https://wheels.galaxyproject.org/simple
-
-aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13"
+aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.10.5 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13"
 anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13"
 ase==3.23.0 ; 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"
+attrs==24.2.0 ; 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==2.15.0 ; python_version >= "3.8" and python_version < "3.13"
+babel==2.16.0 ; python_version >= "3.8" and python_version < "3.13"
 backports-tarfile==1.2.0 ; 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"
-boto3==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13"
-build==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
+black==24.8.0 ; python_version >= "3.8" and python_version < "3.13"
+boto3==1.35.7 ; python_version >= "3.8" and python_version < "3.13"
+botocore==1.35.7 ; python_version >= "3.8" and python_version < "3.13"
+build==1.2.2 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2024.7.4 ; python_version >= "3.8" and python_version < "3.13"
-cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13"
+cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
 codespell==2.3.0 ; 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 < "3.9"
-contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13"
-coverage[toml]==7.6.0 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13"
+contourpy==1.3.0 ; python_version >= "3.9" and python_version < "3.13"
+coverage[toml]==7.6.1 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
+cwltest==2.5.20240714110256 ; 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"
 darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13"
 decorator==5.1.1 ; python_version >= "3.9" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
 deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
 docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
-dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13"
+dogpile-cache==1.3.3 ; python_version >= "3.9" and python_version < "3.13"
 exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -45,106 +44,107 @@ graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13"
-httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
-idna==3.7 ; python_version >= "3.8" and python_version < "3.13"
+httpx==0.27.2 ; python_version >= "3.8" and python_version < "3.13"
+idna==3.8 ; python_version >= "3.8" and python_version < "3.13"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10"
+importlib-metadata==8.4.0 ; python_version >= "3.8" and python_version < "3.13"
+importlib-resources==6.4.4 ; python_version >= "3.8" and python_version < "3.10"
 iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
 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"
+jaraco-context==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
+jaraco-functools==4.0.2 ; 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==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
 jmespath==1.0.1 ; 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"
+jsonschema==4.23.0 ; python_version >= "3.9" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==25.2.1 ; python_version >= "3.8" and python_version < "3.13"
-kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
-lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13"
+keyring==25.3.0 ; python_version >= "3.8" and python_version < "3.13"
+kiwisolver==1.4.7 ; python_version >= "3.8" and python_version < "3.13"
+lxml==5.3.0 ; 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==3.9.1 ; python_version >= "3.9" and python_version < "3.13"
+matplotlib==3.9.2 ; python_version >= "3.9" 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"
-more-itertools==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
+more-itertools==10.5.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
 multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.18 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
+numpy==2.0.2 ; python_version >= "3.9" and python_version < "3.10"
+numpy==2.1.1 ; python_version >= "3.10" and python_version < "3.13"
 onedatafilerestclient==21.2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
-pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13"
+pbr==6.1.0 ; python_version >= "3.9" and python_version < "3.13"
 pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13"
-playwright==1.45.0 ; python_version >= "3.8" and python_version < "3.13"
+playwright==1.46.0 ; python_version >= "3.8" and python_version < "3.13"
 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==3.10.2 ; python_version >= "3.8" and python_version < "3.13"
+port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13"
+prettytable==3.11.0 ; python_version >= "3.8" and python_version < "3.13"
 psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
 psycopg==3.2.1 ; 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"
+pygithub==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13"
-pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
+pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13"
 pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13"
+pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13"
 pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-asyncio==0.23.7 ; python_version >= "3.8" and python_version < "3.13"
+pytest-asyncio==0.24.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-cov==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13"
+pytest-httpserver==1.1.0 ; 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==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-playwright==0.5.2 ; python_version >= "3.8" and python_version < "3.13"
+pytest-postgresql==6.1.1 ; 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"
+pytest==8.3.2 ; python_version >= "3.8" and python_version < "3.13"
 python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-python-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13"
+python-irodsclient==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
 pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9"
-pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
+pywin32-ctypes==0.2.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
+pyyaml==6.0.2 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13"
 referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
 responses==0.25.3 ; 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==0.19.0 ; python_version >= "3.9" and python_version < "3.13"
+rich==13.8.0 ; python_version >= "3.8" and python_version < "3.13"
+rpds-py==0.20.0 ; 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==34.5.0 ; python_version >= "3.9" and python_version < "3.13"
+rucio-clients==35.2.1 ; python_version >= "3.9" and python_version < "3.13"
 s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
-schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13"
+schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
 scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10"
-scipy==1.14.0 ; python_version >= "3.10" and python_version < "3.13"
+scipy==1.14.1 ; python_version >= "3.10" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.22.0 ; python_version >= "3.8" and python_version < "3.13"
+selenium==4.24.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==74.1.2 ; 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"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -159,27 +159,27 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13
 sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
-stevedore==5.2.0 ; python_version >= "3.9" and python_version < "3.13"
+stevedore==5.3.0 ; python_version >= "3.9" and python_version < "3.13"
 tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13"
 testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13"
 text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13"
 tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13"
 toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6"
 trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13"
-trio==0.26.0 ; python_version >= "3.8" and python_version < "3.13"
+trio==0.26.2 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
-urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
-urllib3[socks]==1.26.19 ; python_version >= "3.8" and python_version < "3.13"
-watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13"
+urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
+urllib3[socks]==1.26.20 ; python_version >= "3.8" and python_version < "3.13"
+watchdog==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
 websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13"
-werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
+werkzeug==3.0.4 ; 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"
-zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13"
+yarl==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
+zipp==3.20.1 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.8.19
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.6.3
+ruff==0.6.4