Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,12 +1,12 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=dev
 aiohappyeyeballs==2.4.3
-aiohttp==3.10.10
+aiohttp==3.10.11
 aiosignal==1.3.1
 alabaster==0.7.13
 anyio==4.5.2
 ase==3.23.0
-async-timeout==4.0.3 ; python_full_version < '3.11'
+async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==24.2.0
 axe-selenium-python==2.1.6
 babel==2.16.0
@@ -33,19 +33,19 @@ darker==2.1.1
 darkgraylib==1.2.1
 decorator==5.1.1 ; python_full_version >= '3.9'
 defusedxml==0.7.1
-deprecated==1.2.14
+deprecated==1.2.15
 docutils==0.20.1
 dogpile-cache==1.3.3 ; python_full_version >= '3.9'
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
 filelock==3.16.1
 fluent-logger==0.11.1
-fonttools==4.54.1
+fonttools==4.55.0
 frozenlist==1.5.0
 galaxy-release-util==0.1.11
 graylint==1.1.1
 greenlet==3.1.1
 h11==0.14.0
-httpcore==1.0.6
+httpcore==1.0.7
 httpx==0.27.2
 idna==3.10
 imagesize==1.4.1
@@ -154,7 +154,7 @@ sniffio==1.3.1
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
 sphinx==7.1.2
-sphinx-rtd-theme==3.0.1
+sphinx-rtd-theme==3.0.2
 sphinxcontrib-applehelp==1.0.4
 sphinxcontrib-devhelp==1.0.2
 sphinxcontrib-htmlhelp==2.0.1
@@ -169,7 +169,7 @@ testfixtures==8.3.0
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
-tomli==2.0.2 ; python_full_version <= '3.11'
+tomli==2.1.0 ; python_full_version <= '3.11'
 trio==0.27.0
 trio-websocket==0.11.1
 tuspy==1.0.3

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.10.31
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.7.3
+ruff==0.7.4

lib/galaxy/dependencies/pinned-requirements.txt

@@ -6,18 +6,18 @@ aiobotocore==2.15.2
 aiodataloader==0.4.0
 aiofiles==24.1.0
 aiohappyeyeballs==2.4.3
-aiohttp==3.10.10
+aiohttp==3.10.11
 aioitertools==0.12.0
 aiosignal==1.3.1
 alembic==1.14.0
-amqp==5.2.0
+amqp==5.3.1
 annotated-types==0.7.0
 anyio==4.5.2
 apispec==6.6.1
 appdirs==1.4.4
 arcp==0.2.1
 argcomplete==3.5.1
-async-timeout==4.0.3 ; python_full_version < '3.11'
+async-timeout==5.0.1 ; python_full_version < '3.11'
 attmap==0.13.2
 attrs==24.2.0
 babel==2.16.0
@@ -64,7 +64,7 @@ dparse==0.6.4
 edam-ontology==1.25.2
 email-validator==2.2.0
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
-fastapi-slim==0.115.4
+fastapi-slim==0.115.5
 filelock==3.16.1
 fissix==24.4.24 ; python_full_version >= '3.13'
 frozenlist==1.5.0
@@ -184,7 +184,7 @@ sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.35
 sqlitedict==2.1.0
-sqlparse==0.5.1
+sqlparse==0.5.2
 starlette==0.41.2
 starlette-context==0.3.6
 starlette-graphene3==0.6.0
@@ -194,7 +194,7 @@ tenacity==9.0.0
 text-unidecode==1.3
 tifffile==2023.7.10
 tinydb==4.8.2
-tomli==2.0.2 ; python_full_version < '3.11'
+tomli==2.1.0 ; python_full_version < '3.11'
 tornado==6.4.1
 tqdm==4.67.0
 tuspy==1.0.3

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

@@ -1,18 +1,18 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.35.57
-botocore-stubs==1.35.57
+boto3-stubs==1.35.63
+botocore-stubs==1.35.63
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==43.0.3
 lxml-stubs==0.5.1
 mypy==1.13.0
-mypy-boto3-s3==1.35.46
+mypy-boto3-s3==1.35.61
 mypy-extensions==1.0.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.9.2
 pydantic-core==2.23.4
-tomli==2.0.2 ; python_full_version < '3.11'
+tomli==2.1.0 ; python_full_version < '3.11'
 types-awscrt==0.23.0
 types-bleach==6.1.0.20240331
 types-boto==2.49.18.20241019
@@ -27,7 +27,7 @@ types-python-slugify==8.0.2.20240310
 types-pyyaml==6.0.12.20240917
 types-requests==2.31.0.6
 types-s3transfer==0.10.3
-types-setuptools==75.3.0.20241107
+types-setuptools==75.5.0.20241116
 types-six==1.16.21.20241105
 types-urllib3==1.26.25.14
 typing-extensions==4.12.2