Merge pull request #20601 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: nsoranzo

lib/galaxy/dependencies/dev-requirements.txt

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-annotate --no-hashes --only-group=dev
 aiohappyeyeballs==2.6.1
 aiohttp==3.12.13
-aiosignal==1.3.2
+aiosignal==1.4.0
 alabaster==0.7.16 ; python_full_version < '3.10'
 alabaster==1.0.0 ; python_full_version >= '3.10'
 anyio==4.9.0
@@ -28,8 +28,8 @@ colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
 colorlog==6.9.0
 contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version >= '3.10'
-coverage==7.9.1
-cryptography==45.0.4
+coverage==7.9.2
+cryptography==45.0.5
 cwltest==2.6.20250314152537
 cycler==0.12.1
 darker==2.1.1
@@ -43,7 +43,7 @@ enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.18.0
 fluent-logger==0.11.1
-fonttools==4.58.4
+fonttools==4.58.5
 frozenlist==1.7.0
 galaxy-release-util==0.3.0
 graylint==1.1.1
@@ -82,11 +82,11 @@ matplotlib==3.9.4 ; python_full_version < '3.10'
 matplotlib==3.10.3 ; python_full_version >= '3.10'
 mdit-py-plugins==0.4.2
 mdurl==0.1.2
-mirakuru==2.6.0
+mirakuru==2.6.1
 mistune==3.0.2
 more-itertools==10.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.1
-multidict==6.6.0
+multidict==6.6.3
 mypy-extensions==1.1.0
 myst-parser==3.0.1 ; python_full_version < '3.10'
 myst-parser==4.0.1 ; python_full_version >= '3.10'
@@ -156,7 +156,7 @@ roc-validator==0.4.2 ; python_full_version < '3.9.20'
 roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
 roc-validator==0.7.3 ; python_full_version >= '3.10'
 roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
-rpds-py==0.25.1
+rpds-py==0.26.0
 ruamel-yaml==0.18.14
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 rucio-clients==37.6.0
@@ -187,7 +187,8 @@ sphinxcontrib-serializinghtml==2.0.0
 statsd==4.0.1
 stevedore==5.4.1
 tabulate==0.9.0
-testfixtures==8.3.0
+testfixtures==8.3.0 ; python_full_version < '3.11'
+testfixtures==9.0.1 ; python_full_version >= '3.11'
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
@@ -197,7 +198,7 @@ trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3
 twine==6.1.0
-typing-extensions==4.14.0
+typing-extensions==4.14.1
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==1.26.20 ; python_full_version < '3.10'

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.12.1
+ruff==0.12.2

lib/galaxy/dependencies/pinned-requirements.txt

@@ -7,7 +7,7 @@ aiofiles==24.1.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.12.13
 aioitertools==0.12.0
-aiosignal==1.3.2
+aiosignal==1.4.0
 alembic==1.16.2
 amqp==5.3.1
 annotated-types==0.7.0
@@ -47,8 +47,8 @@ cloudauthz==0.6.0
 cloudbridge==3.2.0
 colorama==0.4.6 ; sys_platform == 'win32'
 coloredlogs==15.0.1
-conda-package-streaming==0.11.0
-cryptography==45.0.4
+conda-package-streaming==0.12.0
+cryptography==45.0.5
 ct3==3.4.0
 cwl-upgrader==1.2.12
 cwl-utils==0.38
@@ -109,7 +109,7 @@ mistune==3.0.2
 mrcfile==1.5.4
 msal==1.32.3
 msgpack==1.1.1
-multidict==6.6.0
+multidict==6.6.3
 mypy-extensions==1.1.0
 networkx==3.2.1 ; python_full_version < '3.10'
 networkx==3.4.2 ; python_full_version == '3.10.*'
@@ -173,7 +173,7 @@ rich==13.9.4
 rich-argparse==1.7.1
 rocrate==0.14.0
 routes==2.5.1
-rpds-py==0.25.1
+rpds-py==0.26.0
 ruamel-yaml==0.18.14
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 s3fs==2025.5.1
@@ -204,14 +204,14 @@ tornado==6.5.1
 tqdm==4.67.1
 tuspy==1.1.0
 tuswsgi==0.5.5
-typing-extensions==4.14.0
+typing-extensions==4.14.1
 typing-inspection==0.4.1
 tzdata==2025.2
 tzlocal==5.3.1
 ubiquerg==0.8.1
 urllib3==1.26.20 ; python_full_version < '3.10'
 urllib3==2.5.0 ; python_full_version >= '3.10'
-uvicorn==0.34.3
+uvicorn==0.35.0
 uvloop==0.21.0
 vine==5.1.0
 wcwidth==0.2.13

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

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-annotate --no-hashes --only-group=test
 aiohappyeyeballs==2.6.1
 aiohttp==3.12.13
-aiosignal==1.3.2
+aiosignal==1.4.0
 anyio==4.9.0
 ase==3.25.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
@@ -21,7 +21,7 @@ colorama==0.4.6 ; sys_platform == 'win32'
 colorlog==6.9.0
 contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version >= '3.10'
-coverage==7.9.1
+coverage==7.9.2
 cwltest==2.6.20250314152537
 cycler==0.12.1
 decorator==5.2.1
@@ -31,7 +31,7 @@ enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
 filelock==3.18.0
 fluent-logger==0.11.1
-fonttools==4.58.4
+fonttools==4.58.5
 frozenlist==1.7.0
 greenlet==3.2.3
 h11==0.16.0
@@ -58,10 +58,10 @@ markupsafe==3.0.2
 matplotlib==3.9.4 ; python_full_version < '3.10'
 matplotlib==3.10.3 ; python_full_version >= '3.10'
 mdurl==0.1.2
-mirakuru==2.6.0
+mirakuru==2.6.1
 mistune==3.0.2
 msgpack==1.1.1
-multidict==6.6.0
+multidict==6.6.3
 mypy-extensions==1.1.0
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
@@ -118,7 +118,7 @@ rich-click==1.8.9
 roc-validator==0.4.2 ; python_full_version < '3.9.20'
 roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
 roc-validator==0.7.3 ; python_full_version >= '3.10'
-rpds-py==0.25.1
+rpds-py==0.26.0
 ruamel-yaml==0.18.14
 ruamel-yaml-clib==0.2.12 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 rucio-clients==37.6.0
@@ -136,7 +136,8 @@ sortedcontainers==2.4.0
 statsd==4.0.1
 stevedore==5.4.1
 tabulate==0.9.0
-testfixtures==8.3.0
+testfixtures==8.3.0 ; python_full_version < '3.11'
+testfixtures==9.0.1 ; python_full_version >= '3.11'
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
@@ -145,7 +146,7 @@ trio==0.30.0
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3
-typing-extensions==4.14.0
+typing-extensions==4.14.1
 tzdata==2025.2 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==1.26.20 ; python_full_version < '3.10'

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

@@ -1,20 +1,20 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.38.46
-botocore-stubs==1.38.30
+boto3-stubs==1.39.3
+botocore-stubs==1.38.46
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
-cryptography==45.0.4
+cryptography==45.0.5
 lxml-stubs==0.5.1
 mypy==1.16.1
-mypy-boto3-s3==1.38.44
+mypy-boto3-s3==1.39.2
 mypy-extensions==1.1.0
 pathspec==0.12.1
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.11.7
 pydantic-core==2.33.2
 tomli==2.2.1 ; python_full_version < '3.11'
-types-awscrt==0.27.2
+types-awscrt==0.27.4
 types-bleach==6.2.0.20250514
 types-boto==2.49.18.20241019
 types-contextvars==2.4.7.3
@@ -32,6 +32,6 @@ types-s3transfer==0.13.0
 types-setuptools==80.9.0.20250529
 types-six==1.17.0.20250515
 types-urllib3==1.26.25.14 ; python_full_version < '3.10'
-typing-extensions==4.14.0
+typing-extensions==4.14.1
 typing-inspection==0.4.1
 urllib3==2.5.0 ; python_full_version >= '3.10'