Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,3 +1,5 @@
+--extra-index-url https://wheels.galaxyproject.org/simple
+
 aiohttp==3.9.5 ; 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"
@@ -10,8 +12,8 @@ babel==2.15.0 ; 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==1.34.106 ; python_version >= "3.8" and python_version < "3.13"
-botocore==1.34.106 ; 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"
 cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
 certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -20,8 +22,9 @@ 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 < "3.13"
-coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13"
+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]==7.5.4 ; 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"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -33,7 +36,7 @@ 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"
 exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11"
-filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13"
+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"
 fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -45,7 +48,7 @@ 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"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.1.0 ; 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"
 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"
@@ -61,7 +64,7 @@ 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==25.2.1 ; 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"
+lxml==5.2.2 ; 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"
@@ -71,28 +74,28 @@ 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==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
+more-itertools==10.3.0 ; 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==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
 onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
-packaging==24.0 ; 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"
 pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-pkginfo==1.11.1 ; 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==1.44.0 ; 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==3.10.0 ; 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"
+psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
 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"
@@ -126,21 +129,22 @@ 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==0.25.2 ; 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==0.18.1 ; 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==34.4.2 ; python_version >= "3.9" and python_version < "3.13"
-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13"
+rucio-clients==34.5.0 ; python_version >= "3.9" and python_version < "3.13"
+s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240503091721 ; 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 < "3.13"
+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"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
-selenium==4.21.0 ; python_version >= "3.8" and python_version < "3.13"
+selenium==4.22.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==70.1.1 ; 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"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -165,14 +169,15 @@ 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==0.25.1 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13"
-twine==5.1.0 ; 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==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
+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"
 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"
 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"

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

@@ -1,7 +1,7 @@
 attrs==23.2.0
-flake8==7.0.0
+flake8==7.1.0
 flake8-bugbear==24.4.26
 mccabe==0.7.0
-pycodestyle==2.11.1
+pycodestyle==2.12.0
 pyflakes==3.2.0
-ruff==0.4.8
+ruff==0.5.0