Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -13,22 +13,22 @@ anyio==4.8.0 ; python_full_version >= '3.9'
 ase==3.23.0 ; python_full_version < '3.9'
 ase==3.24.0 ; python_full_version >= '3.9'
 async-timeout==5.0.1 ; python_full_version < '3.11'
-attrs==24.3.0
+attrs==25.1.0
 axe-selenium-python==2.1.6
-babel==2.16.0
+babel==2.17.0
 backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
 backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
 black==24.8.0 ; python_full_version < '3.9'
-black==24.10.0 ; python_full_version >= '3.9'
+black==25.1.0 ; python_full_version >= '3.9'
 boto3==1.36.3
 botocore==1.36.3
 build==1.2.2.post1
 cachecontrol==0.14.2
-certifi==2024.12.14
+certifi==2025.1.31
 cffi==1.17.1
 charset-normalizer==3.4.1
 click==8.1.8
-codespell==2.4.0
+codespell==2.4.1
 colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
 contourpy==1.1.1 ; python_full_version < '3.9'
 contourpy==1.3.0 ; python_full_version == '3.9.*'
@@ -42,15 +42,15 @@ darker==2.1.1
 darkgraylib==1.2.1
 decorator==5.1.1 ; python_full_version >= '3.9'
 defusedxml==0.7.1
-deprecated==1.2.17
+deprecated==1.2.18
 docutils==0.20.1 ; python_full_version < '3.9'
 docutils==0.21.2 ; python_full_version >= '3.9'
-dogpile-cache==1.3.3 ; python_full_version >= '3.9'
+dogpile-cache==1.3.4 ; python_full_version >= '3.9'
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
 filelock==3.16.1 ; python_full_version < '3.9'
 filelock==3.17.0 ; python_full_version >= '3.9'
 fluent-logger==0.11.1
-fonttools==4.55.6
+fonttools==4.55.8
 frozenlist==1.5.0
 galaxy-release-util==0.2.0
 graylint==1.1.1
@@ -68,7 +68,8 @@ importlib-resources==6.5.2 ; python_full_version == '3.9.*'
 iniconfig==2.0.0
 isodate==0.6.1 ; python_full_version < '3.9'
 isodate==0.7.2 ; python_full_version >= '3.9' and python_full_version < '3.11'
-isort==5.13.2
+isort==5.13.2 ; python_full_version < '3.9'
+isort==6.0.0 ; python_full_version >= '3.9'
 jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-context==6.0.1 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-functools==4.1.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
@@ -118,18 +119,19 @@ pkce==1.0.3
 pkgutil-resolve-name==1.3.10 ; python_version < '0'
 platformdirs==4.3.6
 playwright==1.48.0 ; python_full_version < '3.9'
-playwright==1.49.1 ; python_full_version >= '3.9'
+playwright==1.50.0 ; python_full_version >= '3.9'
 pluggy==1.5.0
 port-for==0.7.3 ; python_full_version < '3.9'
 port-for==0.7.4 ; python_full_version >= '3.9'
 prettytable==3.11.0 ; python_full_version < '3.9'
-prettytable==3.13.0 ; python_full_version >= '3.9'
+prettytable==3.14.0 ; python_full_version >= '3.9'
 propcache==0.2.0 ; python_full_version < '3.9'
 propcache==0.2.1 ; python_full_version >= '3.9'
 psutil==6.1.1 ; sys_platform != 'cygwin'
 psycopg==3.2.4
 pycparser==2.22
-pyee==12.0.0
+pyee==12.0.0 ; python_full_version < '3.9'
+pyee==12.1.1 ; python_full_version >= '3.9'
 pygithub==2.5.0
 pygments==2.19.1
 pyjwt==2.9.0 ; python_full_version < '3.9'
@@ -150,13 +152,13 @@ pytest-json-report==1.5.0
 pytest-metadata==3.1.1
 pytest-mock==3.14.0
 pytest-playwright==0.5.2 ; python_full_version < '3.9'
-pytest-playwright==0.6.2 ; python_full_version >= '3.9'
+pytest-playwright==0.7.0 ; python_full_version >= '3.9'
 pytest-postgresql==6.1.1
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
 python-irodsclient==3.0.0
 python-slugify==8.0.4
-pytz==2024.2 ; python_full_version < '3.9'
+pytz==2025.1 ; python_full_version < '3.9'
 pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
 pyyaml==6.0.2
 rdflib==6.3.2 ; python_full_version < '3.8.1'
@@ -165,7 +167,7 @@ rdflib==7.1.3 ; python_full_version >= '3.9'
 readme-renderer==43.0 ; python_full_version < '3.9'
 readme-renderer==44.0 ; python_full_version >= '3.9'
 referencing==0.35.1 ; python_version < '0'
-referencing==0.36.1 ; python_full_version >= '3.9'
+referencing==0.36.2 ; python_full_version >= '3.9'
 requests==2.32.3
 requests-toolbelt==1.0.0
 responses==0.25.6
@@ -176,7 +178,7 @@ rpds-py==0.22.3 ; python_full_version >= '3.9'
 ruamel-yaml==0.18.10
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.9' and platform_python_implementation == 'CPython'
 ruamel-yaml-clib==0.2.12 ; python_full_version >= '3.9' and python_full_version < '3.13' and platform_python_implementation == 'CPython'
-rucio-clients==36.1.0 ; python_full_version >= '3.9'
+rucio-clients==36.2.0 ; python_full_version >= '3.9'
 s3transfer==0.11.2
 schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
 schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'

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

@@ -1,7 +1,7 @@
-attrs==24.3.0
+attrs==25.1.0
 flake8==7.1.1
 flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.9.3
+ruff==0.9.4

lib/galaxy/dependencies/pinned-requirements.txt

@@ -23,8 +23,8 @@ arcp==0.2.1
 argcomplete==3.5.3
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attmap==0.13.2
-attrs==24.3.0
-babel==2.16.0
+attrs==25.1.0
+babel==2.17.0
 backports-zoneinfo==0.2.1 ; python_full_version < '3.9'
 bagit==1.8.1
 bagit-profile==1.3.1
@@ -35,13 +35,13 @@ billiard==4.2.1
 bioblend==1.4.0
 bleach==6.1.0 ; python_full_version < '3.9'
 bleach==6.2.0 ; python_full_version >= '3.9'
-boltons==24.1.0
+boltons==25.0.0
 boto==2.49.0
 botocore==1.36.3
 bx-python==0.13.0
 cachecontrol==0.14.2
 celery==5.4.0
-certifi==2024.12.14
+certifi==2025.1.31
 cffi==1.17.1
 charset-normalizer==3.4.1
 circus==0.18.0
@@ -74,19 +74,19 @@ 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==0.115.7
+fastapi-slim==0.115.8
 filelock==3.16.1 ; python_full_version < '3.9'
 filelock==3.17.0 ; python_full_version >= '3.9'
 fissix==24.4.24 ; python_full_version >= '3.13'
 frozenlist==1.5.0
 fs==2.4.16
 fsspec==2024.10.0 ; python_full_version < '3.9'
-fsspec==2024.12.0 ; python_full_version >= '3.9'
+fsspec==2025.2.0 ; python_full_version >= '3.9'
 future==1.0.0
 galaxy2cwl==0.1.4 ; python_full_version < '3.9'
 graphene==3.4.3
 graphene-sqlalchemy==3.0.0rc2
-graphql-core==3.2.5
+graphql-core==3.2.6
 graphql-relay==3.2.0
 gravity==1.0.7
 greenlet==3.1.1 ; (python_full_version < '3.14' and platform_machine == 'AMD64') or (python_full_version < '3.14' and platform_machine == 'WIN32') or (python_full_version < '3.14' and platform_machine == 'aarch64') or (python_full_version < '3.14' and platform_machine == 'amd64') or (python_full_version < '3.14' and platform_machine == 'ppc64le') or (python_full_version < '3.14' and platform_machine == 'win32') or (python_full_version < '3.14' and platform_machine == 'x86_64')
@@ -178,14 +178,14 @@ python-magic==0.4.27
 python-multipart==0.0.20
 python-slugify==8.0.4
 python3-openid==3.2.0
-pytz==2024.2
+pytz==2025.1
 pyyaml==6.0.2
-pyzmq==26.2.0
+pyzmq==26.2.1
 rdflib==6.3.2 ; python_full_version < '3.8.1'
 rdflib==7.0.0 ; python_full_version >= '3.8.1' and python_full_version < '3.9'
 rdflib==7.1.3 ; python_full_version >= '3.9'
 referencing==0.35.1 ; python_full_version < '3.9'
-referencing==0.36.1 ; python_full_version >= '3.9'
+referencing==0.36.2 ; python_full_version >= '3.9'
 refgenconf==0.12.2
 regex==2024.11.6
 repoze-lru==0.7
@@ -204,7 +204,7 @@ ruamel-yaml==0.18.10
 ruamel-yaml-clib==0.2.8 ; python_full_version < '3.9' and platform_python_implementation == 'CPython'
 ruamel-yaml-clib==0.2.12 ; python_full_version >= '3.9' and python_full_version < '3.13' and platform_python_implementation == 'CPython'
 s3fs==2024.10.0 ; python_full_version < '3.9'
-s3fs==2024.12.0 ; python_full_version >= '3.9'
+s3fs==2025.2.0 ; python_full_version >= '3.9'
 schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
 schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'
 setuptools==75.3.0 ; python_full_version < '3.9'

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

@@ -1,19 +1,19 @@
 # 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==1.36.6
-botocore-stubs==1.36.6
+boto3-stubs==1.36.12
+botocore-stubs==1.36.12
 cffi==1.17.1 ; platform_python_implementation != 'PyPy'
 cryptography==44.0.0
 lxml-stubs==0.5.1
 mypy==1.14.1
-mypy-boto3-s3==1.36.0
+mypy-boto3-s3==1.36.9
 mypy-extensions==1.0.0
 pycparser==2.22 ; platform_python_implementation != 'PyPy'
 pydantic==2.10.6
 pydantic-core==2.27.2
 tomli==2.2.1 ; python_full_version < '3.11'
-types-awscrt==0.23.7
+types-awscrt==0.23.9
 types-bleach==6.2.0.20241123
 types-boto==2.49.18.20241019
 types-contextvars==2.4.7.3