Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -26,8 +26,8 @@ colorama==0.4.6 ; (platform_system != 'Windows' and sys_platform == 'win32') or
 contourpy==1.1.1 ; python_full_version < '3.9'
 contourpy==1.3.0 ; python_full_version >= '3.9'
 coverage==7.6.1
-cryptography==43.0.3
-cwltest==2.5.20240906231108
+cryptography==44.0.0
+cwltest==2.5.20241122133319
 cycler==0.12.1
 darker==2.1.1
 darkgraylib==1.2.1
@@ -46,7 +46,7 @@ graylint==1.1.1
 greenlet==3.1.1
 h11==0.14.0
 httpcore==1.0.7
-httpx==0.27.2
+httpx==0.28.0
 idna==3.10
 imagesize==1.4.1
 importlib-metadata==8.5.0
@@ -80,7 +80,7 @@ msgpack==1.1.0
 multidict==6.1.0
 mypy-extensions==1.0.0
 myst-parser==3.0.1
-nh3==0.2.18
+nh3==0.2.19
 numpy==1.24.4 ; python_full_version < '3.9'
 numpy==2.0.2 ; python_full_version == '3.9.*'
 numpy==2.1.3 ; python_full_version >= '3.10'
@@ -139,14 +139,14 @@ rich==13.9.4
 rpds-py==0.20.1 ; python_full_version >= '3.9'
 ruamel-yaml==0.18.6
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
-rucio-clients==35.5.0 ; python_full_version >= '3.9'
-s3transfer==0.10.3
+rucio-clients==35.6.0 ; python_full_version >= '3.9'
+s3transfer==0.10.4
 schema-salad==8.7.20241010092723
 scipy==1.10.1 ; python_full_version < '3.9'
 scipy==1.13.1 ; python_full_version == '3.9.*'
 scipy==1.14.1 ; python_full_version >= '3.10'
 secretstorage==3.3.3 ; sys_platform == 'linux'
-selenium==4.26.1
+selenium==4.27.1
 seletools==1.5.0
 setuptools==75.3.0
 six==1.16.0
@@ -163,16 +163,16 @@ sphinxcontrib-jsmath==1.0.1
 sphinxcontrib-qthelp==1.0.3
 sphinxcontrib-serializinghtml==1.1.5
 statsd==4.0.1
-stevedore==5.3.0 ; python_full_version >= '3.9'
+stevedore==5.4.0 ; python_full_version >= '3.9'
 tabulate==0.9.0 ; python_full_version >= '3.9'
 testfixtures==8.3.0
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
-tomli==2.1.0 ; python_full_version <= '3.11'
+tomli==2.2.1 ; python_full_version <= '3.11'
 trio==0.27.0
 trio-websocket==0.11.1
-tuspy==1.0.3
+tuspy==1.1.0
 twill==3.3
 twine==5.1.1
 typing-extensions==4.12.2
@@ -182,7 +182,7 @@ watchdog==4.0.2
 wcwidth==0.2.13
 websocket-client==1.8.0
 werkzeug==3.0.6
-wrapt==1.16.0
+wrapt==1.17.0
 wsproto==1.2.0
 yarl==1.15.2
 zipp==3.20.2

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==0.7.4
+ruff==0.8.1

lib/galaxy/dependencies/pinned-requirements.txt

@@ -24,7 +24,7 @@ babel==2.16.0
 backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
 bagit==1.8.1
 bagit-profile==1.3.1
-bcrypt==4.2.0
+bcrypt==4.2.1
 bdbag==1.7.3
 beaker==1.13.0
 billiard==4.2.1
@@ -49,7 +49,7 @@ cloudbridge==3.2.0
 colorama==0.4.6 ; platform_system == 'Windows'
 coloredlogs==15.0.1
 conda-package-streaming==0.11.0
-cryptography==43.0.3
+cryptography==44.0.0
 ct3==3.3.3.post1
 cwl-upgrader==1.2.11
 cwl-utils==0.35
@@ -97,18 +97,18 @@ jsonref==1.1.0
 jsonschema==4.23.0
 jsonschema-specifications==2023.12.1
 kombu==5.4.2
-lagom==2.6.0
+lagom==2.7.1
 legacy-cgi==2.6.1 ; python_full_version >= '3.13'
 lxml==5.3.0
 mako==1.3.6
 markdown==3.7
 markdown-it-py==3.0.0
 markupsafe==2.1.5
 mdurl==0.1.2
-mercurial==6.8.2
+mercurial==6.9
 mistune==3.0.2
 mrcfile==1.5.3
-msal==1.31.0
+msal==1.31.1
 msgpack==1.1.0
 multidict==6.1.0
 mypy-extensions==1.0.0
@@ -118,14 +118,14 @@ numpy==1.24.4 ; python_full_version < '3.9'
 numpy==2.0.2 ; python_full_version == '3.9.*'
 numpy==2.1.3 ; python_full_version >= '3.10'
 oauthlib==3.2.2
-orjson==3.10.11
+orjson==3.10.12
 oyaml==1.0
 packaging==24.2
 paramiko==3.5.0
 parsley==1.3
 paste==3.10.1
 pastedeploy==3.1.0
-pebble==5.0.7
+pebble==5.1.0
 pillow==10.4.0
 pkgutil-resolve-name==1.3.10 ; python_full_version < '3.9'
 promise==2.3
@@ -136,8 +136,8 @@ psutil==6.1.0
 pulsar-galaxy-lib==0.15.6
 pycparser==2.22
 pycryptodome==3.21.0
-pydantic==2.9.2
-pydantic-core==2.23.4
+pydantic==2.10.2
+pydantic-core==2.27.1
 pydantic-tes==0.1.5
 pydot==2.0.0
 pyeventsystem==0.1.0
@@ -152,7 +152,7 @@ pyreadline3==3.5.4 ; sys_platform == 'win32'
 pysam==0.22.1
 python-dateutil==2.9.0.post0
 python-magic==0.4.27
-python-multipart==0.0.17
+python-multipart==0.0.18
 python-slugify==8.0.4
 python3-openid==3.2.0
 pytz==2024.2
@@ -185,7 +185,7 @@ spython==0.3.14
 sqlalchemy==2.0.35
 sqlitedict==2.1.0
 sqlparse==0.5.2
-starlette==0.41.2
+starlette==0.41.3
 starlette-context==0.3.6
 starlette-graphene3==0.6.0
 supervisor==4.2.5
@@ -194,24 +194,24 @@ tenacity==9.0.0
 text-unidecode==1.3
 tifffile==2023.7.10
 tinydb==4.8.2
-tomli==2.1.0 ; python_full_version < '3.11'
+tomli==2.2.1 ; python_full_version < '3.11'
 tornado==6.4.2
-tqdm==4.67.0
-tuspy==1.0.3
+tqdm==4.67.1
+tuspy==1.1.0
 tuswsgi==0.5.5
 typing-extensions==4.12.2
 tzdata==2024.2
 tzlocal==5.2
 ubiquerg==0.8.0
 urllib3==1.26.20
-uvicorn==0.32.0
+uvicorn==0.32.1
 uvloop==0.21.0
 vine==5.1.0
 wcwidth==0.2.13
 webencodings==0.5.1
 webob==1.8.9
 whoosh==2.7.4
-wrapt==1.16.0
+wrapt==1.17.0
 yacman==0.9.3
 yarl==1.15.2
 zipp==3.20.2

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

@@ -1,33 +1,33 @@
 # 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==1.35.63
-botocore-stubs==1.35.63
+boto3-stubs==1.35.71
+botocore-stubs==1.35.71
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
-cryptography==43.0.3
+cryptography==44.0.0
 lxml-stubs==0.5.1
 mypy==1.13.0
-mypy-boto3-s3==1.35.61
+mypy-boto3-s3==1.35.69
 mypy-extensions==1.0.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
-pydantic==2.9.2
-pydantic-core==2.23.4
-tomli==2.1.0 ; python_full_version < '3.11'
-types-awscrt==0.23.0
-types-bleach==6.1.0.20240331
+pydantic==2.10.2
+pydantic-core==2.27.1
+tomli==2.2.1 ; python_full_version < '3.11'
+types-awscrt==0.23.1
+types-bleach==6.2.0.20241123
 types-boto==2.49.18.20241019
 types-contextvars==2.4.7.3
 types-dataclasses==0.6.6
-types-docutils==0.21.0.20241005
+types-docutils==0.21.0.20241128
 types-html5lib==1.1.11.20241018
 types-markdown==3.7.0.20240822
 types-paramiko==3.5.0.20240928
 types-python-dateutil==2.9.0.20241003
 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==75.5.0.20241116
+types-s3transfer==0.10.4
+types-setuptools==75.6.0.20241126
 types-six==1.16.21.20241105
 types-urllib3==1.26.25.14
 typing-extensions==4.12.2