Update Python dependencies

by running `make update-dependencies`.

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,31 +1,39 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-hashes --only-group=dev
 aiohappyeyeballs==2.4.4
-aiohttp==3.10.11
-aiosignal==1.3.1
-alabaster==0.7.13
-anyio==4.5.2
+aiohttp==3.10.11 ; python_full_version < '3.9'
+aiohttp==3.11.11 ; python_full_version >= '3.9'
+aiosignal==1.3.1 ; python_full_version < '3.9'
+aiosignal==1.3.2 ; python_full_version >= '3.9'
+alabaster==0.7.13 ; python_full_version < '3.9'
+alabaster==0.7.16 ; python_full_version == '3.9.*'
+alabaster==1.0.0 ; python_full_version >= '3.10'
+anyio==4.5.2 ; python_full_version < '3.9'
+anyio==4.7.0 ; python_full_version >= '3.9'
 ase==3.23.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==24.3.0
 axe-selenium-python==2.1.6
 babel==2.16.0
 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
-boto3==1.35.36
-botocore==1.35.36
+black==24.8.0 ; python_full_version < '3.9'
+black==24.10.0 ; python_full_version >= '3.9'
+boto3==1.35.81
+botocore==1.35.81
 build==1.2.2.post1
 cachecontrol==0.14.1
 certifi==2024.12.14
 cffi==1.17.1
 charset-normalizer==3.4.0
 click==8.1.7
 codespell==2.3.0
-colorama==0.4.6 ; os_name == 'nt' or (platform_system == 'Windows' and sys_platform != 'win32') or sys_platform == 'win32'
+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'
-coverage==7.6.1
+contourpy==1.3.0 ; python_full_version == '3.9.*'
+contourpy==1.3.1 ; python_full_version >= '3.10'
+coverage==7.6.1 ; python_full_version < '3.9'
+coverage==7.6.9 ; python_full_version >= '3.9'
 cryptography==44.0.0
 cwltest==2.5.20241122133319
 cycler==0.12.1
@@ -34,7 +42,8 @@ darkgraylib==1.2.1
 decorator==5.1.1 ; python_full_version >= '3.9'
 defusedxml==0.7.1
 deprecated==1.2.15
-docutils==0.20.1
+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'
 exceptiongroup==1.2.2 ; python_full_version < '3.11'
 filelock==3.16.1
@@ -52,7 +61,8 @@ imagesize==1.4.1
 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
+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
 jaraco-classes==3.4.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 jaraco-context==6.0.1 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
@@ -61,26 +71,31 @@ jeepney==0.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' a
 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'
+jsonschema-specifications==2023.12.1 ; python_version < '0'
+jsonschema-specifications==2024.10.1 ; python_full_version >= '3.9'
 junit-xml==1.9
 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
+markupsafe==2.1.5 ; python_full_version < '3.9'
+markupsafe==3.0.2 ; python_full_version >= '3.9'
 matplotlib==3.7.5 ; python_full_version < '3.9'
-matplotlib==3.9.4 ; python_full_version >= '3.9'
+matplotlib==3.9.4 ; python_full_version == '3.9.*'
+matplotlib==3.10.0 ; python_full_version >= '3.10'
 mdit-py-plugins==0.4.2
 mdurl==0.1.2
-mirakuru==2.5.2
+mirakuru==2.5.2 ; python_full_version < '3.9'
+mirakuru==2.5.3 ; python_full_version >= '3.9'
 mistune==3.0.2
 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==0.2.19
+myst-parser==3.0.1 ; python_full_version < '3.10'
+myst-parser==4.0.0 ; python_full_version >= '3.10'
+nh3==0.2.20
 numpy==1.24.4 ; python_full_version < '3.9'
 numpy==2.0.2 ; python_full_version == '3.9.*'
 numpy==2.2.0 ; python_full_version >= '3.10'
@@ -89,80 +104,102 @@ 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
+pillow==10.4.0 ; python_full_version < '3.9'
+pillow==11.0.0 ; python_full_version >= '3.9'
 pkce==1.0.3
 pkginfo==1.12.0
 pkgutil-resolve-name==1.3.10 ; python_version < '0'
 platformdirs==4.3.6
-playwright==1.48.0
+playwright==1.48.0 ; python_full_version < '3.9'
+playwright==1.49.1 ; python_full_version >= '3.9'
 pluggy==1.5.0
-port-for==0.7.3
-prettytable==3.11.0
-propcache==0.2.0
-psutil==6.1.0 ; sys_platform != 'cygwin'
+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==3.12.0 ; 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==3.2.3
 pycparser==2.22
 pyee==12.0.0
 pygithub==2.5.0
 pygments==2.18.0
-pyjwt==2.9.0
+pyjwt==2.9.0 ; python_full_version < '3.9'
+pyjwt==2.10.1 ; python_full_version >= '3.9'
 pynacl==1.5.0
-pyparsing==3.1.4
+pyparsing==3.1.4 ; python_full_version < '3.9'
+pyparsing==3.2.0 ; python_full_version >= '3.9'
 pyproject-hooks==1.2.0
 pysocks==1.7.1
 pytest==7.4.4
 pytest-asyncio==0.23.8
 pytest-base-url==2.1.0
-pytest-cov==5.0.0
+pytest-cov==5.0.0 ; python_full_version < '3.9'
+pytest-cov==6.0.0 ; python_full_version >= '3.9'
 pytest-html==4.1.1
 pytest-httpserver==1.1.0
 pytest-json-report==1.5.0
 pytest-metadata==3.1.1
 pytest-mock==3.14.0
-pytest-playwright==0.5.2
+pytest-playwright==0.5.2 ; python_full_version < '3.9'
+pytest-playwright==0.6.2 ; python_full_version >= '3.9'
 pytest-postgresql==6.1.1
 pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
-python-irodsclient==2.2.0
+python-irodsclient==3.0.0
 python-slugify==8.0.4
 pytz==2024.2 ; 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'
-rdflib==7.0.0 ; python_full_version >= '3.8.1'
-readme-renderer==43.0
+rdflib==7.0.0 ; python_full_version >= '3.8.1' and python_full_version < '3.9'
+rdflib==7.1.1 ; 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_full_version >= '3.9'
 requests==2.32.3
 requests-toolbelt==1.0.0
 responses==0.25.3
 rfc3986==2.0.0
 rich==13.9.4
-rpds-py==0.20.1 ; python_full_version >= '3.9'
+rpds-py==0.20.1 ; python_version < '0'
+rpds-py==0.22.3 ; 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==36.0.0.post1 ; python_full_version >= '3.9'
+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==36.0.0.post2 ; python_full_version >= '3.9'
 s3transfer==0.10.4
-schema-salad==8.7.20241010092723
+schema-salad==8.7.20241010092723 ; python_full_version < '3.9'
+schema-salad==8.8.20241206093842 ; python_full_version >= '3.9'
 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 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 selenium==4.27.1
 seletools==1.5.0
-setuptools==75.3.0
+setuptools==75.3.0 ; python_full_version < '3.9'
+setuptools==75.6.0 ; python_full_version >= '3.9'
 six==1.17.0
 sniffio==1.3.1
 snowballstemmer==2.2.0
 sortedcontainers==2.4.0
-sphinx==7.1.2
+sphinx==7.1.2 ; python_full_version < '3.9'
+sphinx==7.4.7 ; python_full_version == '3.9.*'
+sphinx==8.1.3 ; python_full_version >= '3.10'
 sphinx-rtd-theme==3.0.2
-sphinxcontrib-applehelp==1.0.4
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==2.0.1
+sphinxcontrib-applehelp==1.0.4 ; python_full_version < '3.9'
+sphinxcontrib-applehelp==2.0.0 ; python_full_version >= '3.9'
+sphinxcontrib-devhelp==1.0.2 ; python_full_version < '3.9'
+sphinxcontrib-devhelp==2.0.0 ; python_full_version >= '3.9'
+sphinxcontrib-htmlhelp==2.0.1 ; python_full_version < '3.9'
+sphinxcontrib-htmlhelp==2.1.0 ; python_full_version >= '3.9'
 sphinxcontrib-jquery==4.1
 sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.5
+sphinxcontrib-qthelp==1.0.3 ; python_full_version < '3.9'
+sphinxcontrib-qthelp==2.0.0 ; python_full_version >= '3.9'
+sphinxcontrib-serializinghtml==1.1.5 ; python_full_version < '3.9'
+sphinxcontrib-serializinghtml==2.0.0 ; python_full_version >= '3.9'
 statsd==4.0.1
 stevedore==5.4.0 ; python_full_version >= '3.9'
 tabulate==0.9.0 ; python_full_version >= '3.9'
@@ -178,12 +215,17 @@ twill==3.3
 twine==6.0.1
 typing-extensions==4.12.2
 tzdata==2024.2 ; sys_platform == 'win32'
-urllib3==1.26.20
-watchdog==4.0.2
+urllib3==1.26.20 ; python_full_version < '3.10'
+urllib3==2.2.3 ; python_full_version >= '3.10'
+watchdog==4.0.2 ; python_full_version < '3.9'
+watchdog==6.0.0 ; python_full_version >= '3.9'
 wcwidth==0.2.13
 websocket-client==1.8.0
-werkzeug==3.0.6
+werkzeug==3.0.6 ; python_full_version < '3.9'
+werkzeug==3.1.3 ; python_full_version >= '3.9'
 wrapt==1.17.0
 wsproto==1.2.0
-yarl==1.15.2
-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')
+yarl==1.15.2 ; python_full_version < '3.9'
+yarl==1.18.3 ; python_full_version >= '3.9'
+zipp==3.20.2 ; python_full_version < '3.9'
+zipp==3.21.0 ; (python_full_version >= '3.9' and python_full_version < '3.10.2' and platform_machine == 'ppc64le') or (python_full_version >= '3.9' and python_full_version < '3.10.2' and platform_machine == 's390x') or (python_full_version >= '3.9' and python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x')

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

@@ -4,4 +4,4 @@ flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.12.1
 pyflakes==3.2.0
-ruff==0.8.3
+ruff==0.8.4