Update Python dependencies

by running `make update-dependencies`.

Author: galaxybot

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,7 +1,7 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=dev
 aiohappyeyeballs==2.6.1
-aiohttp==3.13.1
+aiohttp==3.13.2
 aiosignal==1.4.0
 alabaster==0.7.16 ; python_full_version < '3.10'
 alabaster==1.0.0 ; python_full_version >= '3.10'
@@ -14,8 +14,8 @@ babel==2.17.0
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
 backports-tarfile==1.2.0 ; python_full_version < '3.12' and platform_machine != 'ppc64le' and platform_machine != 's390x'
 black==25.9.0
-boto3==1.40.49
-botocore==1.40.49
+boto3==1.40.61
+botocore==1.40.61
 build==1.3.0
 cachecontrol==0.14.3
 cachetools==6.2.1
@@ -32,12 +32,12 @@ contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version == '3.10.*'
 contourpy==1.3.3 ; python_full_version >= '3.11'
 coverage==7.10.7 ; python_full_version < '3.10'
-coverage==7.11.0 ; python_full_version >= '3.10'
+coverage==7.11.2 ; python_full_version >= '3.10'
 cryptography==46.0.3
 cwltest==2.6.20250818005349
 cycler==0.12.1
 darker==3.0.0
-darkgraylib==2.4.0
+darkgraylib==2.4.1
 decorator==5.2.1
 defusedxml==0.7.1
 docutils==0.21.2
@@ -91,16 +91,17 @@ matplotlib==3.10.7 ; python_full_version >= '3.10'
 mdit-py-plugins==0.4.2 ; python_full_version < '3.10'
 mdit-py-plugins==0.5.0 ; python_full_version >= '3.10'
 mdurl==0.1.2
-mirakuru==2.6.1
-mistune==3.0.2
+mirakuru==2.6.1 ; python_full_version < '3.10'
+mirakuru==3.0.1 ; python_full_version >= '3.10'
+mistune==3.1.4
 more-itertools==10.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.2
 multidict==6.7.0
 mypy==1.18.2
 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'
-nh3==0.3.1
+nh3==0.3.2
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
 numpy==2.3.4 ; python_full_version >= '3.11'
@@ -124,7 +125,7 @@ port-for==1.0.0 ; python_full_version >= '3.10'
 prettytable==3.16.0
 prompt-toolkit==3.0.52
 propcache==0.4.1
-psutil==7.1.2 ; sys_platform != 'cygwin'
+psutil==7.1.3 ; sys_platform != 'cygwin'
 psycopg==3.2.12
 pycparser==2.23 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
 pyee==13.0.0
@@ -152,10 +153,10 @@ pytest-shard==0.1.2
 python-dateutil==2.9.0.post0
 python-irodsclient==3.2.0
 python-slugify==8.0.4
-pytokens==0.2.0
+pytokens==0.3.0
 pywin32-ctypes==0.2.3 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'win32'
 pyyaml==6.0.3
-rdflib==7.2.1
+rdflib==7.4.0
 readme-renderer==44.0
 referencing==0.36.2 ; python_full_version < '3.10'
 referencing==0.37.0 ; python_full_version >= '3.10'
@@ -174,12 +175,12 @@ rpds-py==0.27.1 ; python_full_version < '3.10'
 rpds-py==0.28.0 ; python_full_version >= '3.10'
 ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==38.4.0
+rucio-clients==38.5.0
 s3transfer==0.14.0
-schema-salad==8.9.20250723145140
+schema-salad==8.9.20251102115403
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
-scipy==1.16.2 ; python_full_version >= '3.11'
+scipy==1.16.3 ; python_full_version >= '3.11'
 secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 secretstorage==3.4.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
 selenium==4.32.0 ; python_full_version < '3.10'
@@ -204,13 +205,14 @@ statsd==4.0.1
 stevedore==5.5.0
 tabulate==0.9.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
-testfixtures==9.2.0 ; python_full_version >= '3.11'
+testfixtures==10.0.0 ; python_full_version >= '3.11'
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
 tomli==2.3.0 ; python_full_version <= '3.11'
 total-perspective-vortex==3.1.2
-trio==0.31.0
+trio==0.31.0 ; python_full_version < '3.10'
+trio==0.32.0 ; python_full_version >= '3.10'
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1

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==0.14.2
+ruff==0.14.4

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,14 +2,14 @@
 #    uv export --frozen --no-annotate --no-hashes --no-dev
 a2wsgi==1.10.10
 adal==1.2.7
-aiobotocore==2.25.0
+aiobotocore==2.25.1
 aiofiles==25.1.0
 aiohappyeyeballs==2.6.1
-aiohttp==3.13.1
-aioitertools==0.12.0
+aiohttp==3.13.2
+aioitertools==0.13.0
 aiosignal==1.4.0
 alembic==1.16.5 ; python_full_version < '3.10'
-alembic==1.17.0 ; python_full_version >= '3.10'
+alembic==1.17.1 ; python_full_version >= '3.10'
 amqp==5.3.1
 annotated-types==0.7.0
 anyio==4.11.0
@@ -27,11 +27,12 @@ bcrypt==5.0.0
 bdbag==1.8.0
 beaker==1.13.0
 billiard==4.2.2
-bioblend==1.6.0
-bleach==6.2.0
+bioblend==1.7.0
+bleach==6.2.0 ; python_full_version < '3.10'
+bleach==6.3.0 ; python_full_version >= '3.10'
 boltons==25.0.0
 boto==2.49.0
-botocore==1.40.49
+botocore==1.40.61
 bx-python==0.14.0
 cachecontrol==0.14.3
 cachetools==6.2.1
@@ -54,17 +55,17 @@ cryptography==46.0.3
 ct3==3.4.0
 cwl-upgrader==1.2.12
 cwl-utils==0.40
-cwltool==3.1.20250925164626
+cwltool==3.1.20251031082601
 defusedxml==0.7.1
-deprecated==1.2.18
+deprecated==1.3.1
 deprecation==2.1.0
 dictobj==0.4
 dnspython==2.7.0 ; python_full_version < '3.10'
 dnspython==2.8.0 ; python_full_version >= '3.10'
 docopt==0.6.2
 docutils==0.21.2
 dparse==0.6.4
-edam-ontology==1.25.2
+edam-ontology==1.25.3
 email-validator==2.3.0
 et-xmlfile==2.0.0
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
@@ -74,12 +75,12 @@ filelock==3.20.0 ; python_full_version >= '3.10'
 fissix==24.4.24
 frozenlist==1.8.0
 fs==2.4.16
-fsspec==2025.9.0
+fsspec==2025.10.0
 future==1.0.0
-google-api-core==2.27.0
-google-auth==2.41.1
+google-api-core==2.28.1
+google-auth==2.43.0
 google-cloud-batch==0.18.0
-googleapis-common-protos==1.71.0
+googleapis-common-protos==1.72.0
 gravity==1.1.1
 greenlet==3.2.4 ; platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64'
 grpcio==1.76.0
@@ -113,12 +114,13 @@ limits==4.2 ; python_full_version < '3.10'
 limits==5.6.0 ; python_full_version >= '3.10'
 lxml==6.0.2
 mako==1.3.10
-markdown==3.9
+markdown==3.9 ; python_full_version < '3.10'
+markdown==3.10 ; python_full_version >= '3.10'
 markdown-it-py==3.0.0
 markupsafe==3.0.3
 mdurl==0.1.2
 mercurial==7.1.1
-mistune==3.0.2
+mistune==3.1.4
 more-itertools==10.8.0
 mrcfile==1.5.4
 msal==1.34.0
@@ -151,14 +153,14 @@ propcache==0.4.1
 proto-plus==1.26.1
 protobuf==6.33.0
 prov==1.5.1
-psutil==7.1.2
+psutil==7.1.3
 pulsar-galaxy-lib==0.15.11
 pyasn1==0.6.1
 pyasn1-modules==0.4.2
 pycparser==2.23 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
 pycryptodome==3.23.0
-pydantic==2.12.3
-pydantic-core==2.41.4
+pydantic==2.12.4
+pydantic-core==2.41.5
 pydantic-tes==0.2.0
 pydot==4.0.1
 pyeventsystem==0.1.0
@@ -180,27 +182,27 @@ python3-openid==3.2.0
 pytz==2025.2
 pyyaml==6.0.3
 pyzmq==27.1.0
-rdflib==7.2.1
+rdflib==7.4.0
 referencing==0.36.2 ; python_full_version < '3.10'
 referencing==0.37.0 ; python_full_version >= '3.10'
 refgenconf==0.12.2
-regex==2025.10.23
+regex==2025.11.3
 repoze-lru==0.7
 requests==2.32.5
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
 requests-unixsocket==0.4.1
 rich==13.9.4
-rich-argparse==1.7.1
+rich-argparse==1.7.2
 rocrate==0.14.2
 routes==2.5.1
 rpds-py==0.27.1 ; python_full_version < '3.10'
 rpds-py==0.28.0 ; python_full_version >= '3.10'
 rsa==4.9.1
 ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-s3fs==2025.9.0
-schema-salad==8.9.20250723145140
+s3fs==2025.10.0
+schema-salad==8.9.20251102115403
 setuptools==80.9.0
 six==1.17.0
 slowapi==0.1.9
@@ -225,7 +227,7 @@ tomli==2.3.0 ; python_full_version < '3.11'
 tornado==6.5.2
 tqdm==4.67.1
 tuspy==1.1.0
-tuspyserver==4.2.0
+tuspyserver==4.2.3
 typing-extensions==4.15.0
 typing-inspection==0.4.2
 tzdata==2025.2
@@ -241,7 +243,7 @@ webencodings==0.5.1
 webob==1.8.9
 whoosh==2.7.4
 wrapt==1.17.3
-yacman==0.9.3
+yacman==0.9.4
 yarl==1.22.0
 zipp==3.23.0 ; python_full_version < '3.10'
 zipstream-new==1.1.8

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

@@ -1,16 +1,16 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=test
 aiohappyeyeballs==2.6.1
-aiohttp==3.13.1
+aiohttp==3.13.2
 aiosignal==1.4.0
 anyio==4.11.0
 ase==3.26.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.4.0
 axe-selenium-python==2.1.6
 backports-asyncio-runner==1.2.0 ; python_full_version < '3.11'
-boto3==1.40.49
-botocore==1.40.49
+boto3==1.40.61
+botocore==1.40.61
 cachecontrol==0.14.3
 cachetools==6.2.1
 cattrs==25.3.0
@@ -25,7 +25,7 @@ contourpy==1.3.0 ; python_full_version < '3.10'
 contourpy==1.3.2 ; python_full_version == '3.10.*'
 contourpy==1.3.3 ; python_full_version >= '3.11'
 coverage==7.10.7 ; python_full_version < '3.10'
-coverage==7.11.0 ; python_full_version >= '3.10'
+coverage==7.11.2 ; python_full_version >= '3.10'
 cwltest==2.6.20250818005349
 cycler==0.12.1
 decorator==5.2.1
@@ -67,8 +67,9 @@ markupsafe==3.0.3
 matplotlib==3.9.4 ; python_full_version < '3.10'
 matplotlib==3.10.7 ; python_full_version >= '3.10'
 mdurl==0.1.2
-mirakuru==2.6.1
-mistune==3.0.2
+mirakuru==2.6.1 ; python_full_version < '3.10'
+mirakuru==3.0.1 ; python_full_version >= '3.10'
+mistune==3.1.4
 msgpack==1.1.2
 multidict==6.7.0
 mypy==1.18.2
@@ -96,7 +97,7 @@ port-for==1.0.0 ; python_full_version >= '3.10'
 prettytable==3.16.0
 prompt-toolkit==3.0.52
 propcache==0.4.1
-psutil==7.1.2 ; sys_platform != 'cygwin'
+psutil==7.1.3 ; sys_platform != 'cygwin'
 psycopg==3.2.12
 pycparser==2.23 ; implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt'
 pyee==13.0.0
@@ -121,7 +122,7 @@ python-dateutil==2.9.0.post0
 python-irodsclient==3.2.0
 python-slugify==8.0.4
 pyyaml==6.0.3
-rdflib==7.2.1
+rdflib==7.4.0
 referencing==0.36.2 ; python_full_version < '3.10'
 referencing==0.37.0 ; python_full_version >= '3.10'
 requests==2.32.5
@@ -136,12 +137,12 @@ rpds-py==0.27.1 ; python_full_version < '3.10'
 rpds-py==0.28.0 ; python_full_version >= '3.10'
 ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-rucio-clients==38.4.0
+rucio-clients==38.5.0
 s3transfer==0.14.0
-schema-salad==8.9.20250723145140
+schema-salad==8.9.20251102115403
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
-scipy==1.16.2 ; python_full_version >= '3.11'
+scipy==1.16.3 ; python_full_version >= '3.11'
 selenium==4.32.0 ; python_full_version < '3.10'
 selenium==4.38.0 ; python_full_version >= '3.10'
 seletools==1.5.0
@@ -152,13 +153,14 @@ statsd==4.0.1
 stevedore==5.5.0
 tabulate==0.9.0
 testfixtures==8.3.0 ; python_full_version < '3.11'
-testfixtures==9.2.0 ; python_full_version >= '3.11'
+testfixtures==10.0.0 ; python_full_version >= '3.11'
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
 tomli==2.3.0 ; python_full_version <= '3.11'
 total-perspective-vortex==3.1.2
-trio==0.31.0
+trio==0.31.0 ; python_full_version < '3.10'
+trio==0.32.0 ; python_full_version >= '3.10'
 trio-websocket==0.12.2
 tuspy==1.1.0
 twill==3.3.1