Merge pull request #18943 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,5 +1,7 @@
-aiohappyeyeballs==2.4.2 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.10.8 ; python_version >= "3.8" and python_version < "3.13"
+--extra-index-url https://wheels.galaxyproject.org/simple
+
+aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.10.9 ; 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==4.5.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -43,7 +45,7 @@ galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13
 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"
+httpcore==1.0.6 ; python_version >= "3.8" and python_version < "3.13"
 httpx==0.27.2 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.10 ; python_version >= "3.8" and python_version < "3.13"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -131,7 +133,7 @@ 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==13.8.1 ; python_version >= "3.8" and python_version < "3.13"
+rich==13.9.2 ; 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"
@@ -165,7 +167,7 @@ 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"
+tomli==2.0.2 ; 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==0.26.2 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; 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==0.6.8
+ruff==0.6.9

lib/galaxy/dependencies/pinned-requirements.txt

@@ -5,8 +5,8 @@ adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
 aiobotocore==2.15.1 ; python_version >= "3.8" and python_version < "3.13"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
 aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13"
-aiohappyeyeballs==2.4.2 ; python_version >= "3.8" and python_version < "3.13"
-aiohttp==3.10.8 ; python_version >= "3.8" and python_version < "3.13"
+aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.10.9 ; python_version >= "3.8" and python_version < "3.13"
 aioitertools==0.12.0 ; python_version >= "3.8" and python_version < "3.13"
 aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 alembic==1.13.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -134,7 +134,7 @@ prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13"
 psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
-pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
+pycryptodome==3.21.0 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -167,7 +167,7 @@ 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"
 requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13"
-rich==13.8.1 ; python_version >= "3.8" and python_version < "3.13"
+rich==13.9.2 ; python_version >= "3.8" and python_version < "3.13"
 rocrate==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
 routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13"
 rpds-py==0.20.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -194,7 +194,7 @@ svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13"
 tenacity==9.0.0 ; 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"
+tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11"
 tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13"
 tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -1,26 +1,28 @@
+--extra-index-url https://wheels.galaxyproject.org/simple
+
 annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
-boto3-stubs[s3]==1.35.29 ; python_version >= "3.8" and python_version < "3.13"
-botocore-stubs==1.35.29 ; python_version >= "3.8" and python_version < "3.13"
+boto3-stubs[s3]==1.35.34 ; python_version >= "3.8" and python_version < "3.13"
+botocore-stubs==1.35.34 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13"
 lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13"
-mypy-boto3-s3==1.35.22 ; python_version >= "3.8" and python_version < "3.13"
+mypy-boto3-s3==1.35.32 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.11.2 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 pydantic-core==2.23.4 ; python_version >= "3.8" and python_version < "3.13"
 pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13"
-tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
-types-awscrt==0.21.5 ; python_version >= "3.8" and python_version < "3.13"
+tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11"
+types-awscrt==0.22.0 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
 types-boto==2.49.18.20240806 ; python_version >= "3.8" and python_version < "3.13"
 types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13"
 types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13"
-types-docutils==0.21.0.20240907 ; python_version >= "3.8" and python_version < "3.13"
+types-docutils==0.21.0.20241005 ; python_version >= "3.8" and python_version < "3.13"
 types-html5lib==1.1.11.20240806 ; python_version >= "3.8" and python_version < "3.13"
 types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13"
 types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3.13"
-types-python-dateutil==2.9.0.20240906 ; python_version >= "3.8" and python_version < "3.13"
+types-python-dateutil==2.9.0.20241003 ; python_version >= "3.8" and python_version < "3.13"
 types-pyyaml==6.0.12.20240917 ; 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-s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13"