Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,6 +1,6 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=dev
-aiohappyeyeballs==2.4.3
+aiohappyeyeballs==2.4.4
 aiohttp==3.10.11
 aiosignal==1.3.1
 alabaster==0.7.13
@@ -10,7 +10,7 @@ async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==24.2.0
 axe-selenium-python==2.1.6
 babel==2.16.0
-backports-tarfile==1.2.0 ; python_full_version < '3.12'
+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
 boto3==1.35.36
@@ -22,12 +22,12 @@ cffi==1.17.1
 charset-normalizer==3.4.0
 click==8.1.7
 codespell==2.3.0
-colorama==0.4.6 ; (platform_system != 'Windows' and sys_platform == 'win32') or platform_system == 'Windows' or os_name == 'nt'
+colorama==0.4.6 ; os_name == 'nt' or (platform_system == 'Windows' and sys_platform != 'win32') or sys_platform == 'win32'
 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
@@ -39,59 +39,59 @@ 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==4.55.0
+fonttools==4.55.3
 frozenlist==1.5.0
-galaxy-release-util==0.1.11
+galaxy-release-util==0.2.0
 graylint==1.1.1
 greenlet==3.1.1
 h11==0.14.0
 httpcore==1.0.7
-httpx==0.27.2
+httpx==0.28.1
 idna==3.10
 imagesize==1.4.1
-importlib-metadata==8.5.0
+importlib-metadata==8.5.0 ; (python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')
 importlib-resources==6.4.5 ; python_full_version < '3.10'
 iniconfig==2.0.0
 isodate==0.6.1
 isort==5.13.2
-jaraco-classes==3.4.0
-jaraco-context==6.0.1
-jaraco-functools==4.1.0
-jeepney==0.8.0 ; sys_platform == 'linux'
+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'
+jeepney==0.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 jinja2==3.1.4
 jmespath==1.0.1
 jsonschema==4.23.0 ; python_full_version >= '3.9'
 jsonschema-specifications==2023.12.1 ; python_full_version >= '3.9'
 junit-xml==1.9
-keyring==25.5.0
+keyring==25.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.4.7
 lxml==5.3.0
 markdown-it-py==3.0.0
 markdown-it-reporter==0.0.2
 markupsafe==2.1.5
 matplotlib==3.7.5 ; python_full_version < '3.9'
-matplotlib==3.9.2 ; python_full_version >= '3.9'
+matplotlib==3.9.4 ; python_full_version >= '3.9'
 mdit-py-plugins==0.4.2
 mdurl==0.1.2
 mirakuru==2.5.2
 mistune==3.0.2
-more-itertools==10.5.0
+more-itertools==10.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 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'
+numpy==2.2.0 ; python_full_version >= '3.10'
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 packaging==24.2
 pathspec==0.12.1
 pbr==6.1.0 ; python_full_version >= '3.9'
 pillow==10.4.0
 pkce==1.0.3
-pkginfo==1.10.0
+pkginfo==1.12.0
 pkgutil-resolve-name==1.3.10 ; python_version < '0'
 platformdirs==4.3.6
 playwright==1.48.0
@@ -126,9 +126,10 @@ python-dateutil==2.9.0.post0
 python-irodsclient==2.2.0
 python-slugify==8.0.4
 pytz==2024.2 ; python_full_version < '3.9'
-pywin32-ctypes==0.2.3 ; sys_platform == 'win32'
+pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
 pyyaml==6.0.2
-rdflib==6.3.2
+rdflib==6.3.2 ; python_full_version < '3.8.1'
+rdflib==7.0.0 ; python_full_version >= '3.8.1'
 readme-renderer==43.0
 referencing==0.35.1 ; python_full_version >= '3.9'
 requests==2.32.3
@@ -139,17 +140,17 @@ 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==36.0.0 ; 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
+secretstorage==3.3.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
+selenium==4.27.1
 seletools==1.5.0
 setuptools==75.3.0
-six==1.16.0
+six==1.17.0
 sniffio==1.3.1
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
@@ -163,26 +164,26 @@ 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
+twine==6.0.1
 typing-extensions==4.12.2
 tzdata==2024.2 ; sys_platform == 'win32'
 urllib3==1.26.20
 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
+zipp==3.20.2 ; (python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')

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

@@ -1,7 +1,7 @@
 attrs==24.2.0
 flake8==7.1.1
-flake8-bugbear==24.10.31
+flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.8.2
+ruff==0.8.3

lib/galaxy/dependencies/pinned-requirements.txt

@@ -5,7 +5,7 @@ adal==1.2.7
 aiobotocore==2.15.2
 aiodataloader==0.4.0
 aiofiles==24.1.0
-aiohappyeyeballs==2.4.3
+aiohappyeyeballs==2.4.4
 aiohttp==3.10.11
 aioitertools==0.12.0
 aiosignal==1.3.1
@@ -16,15 +16,15 @@ anyio==4.5.2
 apispec==6.6.1
 appdirs==1.4.4
 arcp==0.2.1
-argcomplete==3.5.1
+argcomplete==3.5.2
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attmap==0.13.2
 attrs==24.2.0
 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
@@ -49,8 +49,8 @@ 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
-ct3==3.3.3.post1
+cryptography==44.0.0
+ct3==3.4.0
 cwl-upgrader==1.2.11
 cwl-utils==0.35
 cwltool==3.1.20241007082533
@@ -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==0.115.5
+fastapi-slim==0.115.6
 filelock==3.16.1
 fissix==24.4.24 ; python_full_version >= '3.13'
 frozenlist==1.5.0
@@ -73,7 +73,7 @@ fsspec==2024.10.0
 future==1.0.0
 galaxy2cwl==0.1.4
 graphene==3.4.3
-graphene-sqlalchemy==3.0.0rc1
+graphene-sqlalchemy==3.0.0rc2
 graphql-core==3.2.5
 graphql-relay==3.2.0
 gravity==1.0.6
@@ -97,35 +97,35 @@ jsonref==1.1.0
 jsonschema==4.23.0
 jsonschema-specifications==2023.12.1
 kombu==5.4.2
-lagom==2.6.0
+lagom==2.7.5
 legacy-cgi==2.6.1 ; python_full_version >= '3.13'
 lxml==5.3.0
-mako==1.3.6
+mako==1.3.8
 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
 networkx==3.1
 nodeenv==1.9.1
 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'
+numpy==2.2.0 ; 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==2.10.3
+pydantic-core==2.27.1
 pydantic-tes==0.1.5
 pydot==2.0.0
 pyeventsystem==0.1.0
@@ -152,13 +152,14 @@ pyreadline3==3.5.4 ; sys_platform == 'win32'
 pysam==0.22.1
 python-dateutil==2.9.0.post0
 python-magic==0.4.27
-python-multipart==0.0.18
+python-multipart==0.0.19
 python-slugify==8.0.4
 python3-openid==3.2.0
 pytz==2024.2
 pyyaml==6.0.2
 pyzmq==26.2.0
-rdflib==6.3.2
+rdflib==6.3.2 ; python_full_version < '3.8.1'
+rdflib==7.0.0 ; python_full_version >= '3.8.1'
 referencing==0.35.1
 refgenconf==0.12.2
 regex==2024.11.6
@@ -177,15 +178,15 @@ s3fs==2024.10.0
 schema-salad==8.7.20241010092723
 setuptools==75.3.0
 setuptools-scm==5.0.2
-six==1.16.0
+six==1.17.0
 sniffio==1.3.1
 social-auth-core==4.5.4
 sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.35
 sqlitedict==2.1.0
-sqlparse==0.5.2
-starlette==0.41.2
+sqlparse==0.5.3
+starlette==0.41.3
 starlette-context==0.3.6
 starlette-graphene3==0.6.0
 supervisor==4.2.5
@@ -194,24 +195,24 @@ 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