Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -53,7 +53,8 @@ fonttools==4.60.1 ; python_full_version < '3.10'
 fonttools==4.61.0 ; python_full_version >= '3.10'
 frozenlist==1.8.0
 galaxy-release-util==0.3.1
-greenlet==3.2.4
+greenlet==3.2.4 ; python_full_version < '3.10'
+greenlet==3.3.0 ; python_full_version >= '3.10'
 h11==0.16.0
 html5lib==1.1 ; python_full_version < '3.10'
 html5rdf==1.2.1 ; python_full_version >= '3.10'
@@ -84,7 +85,7 @@ junit-xml==1.9
 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.4.7 ; python_full_version < '3.10'
 kiwisolver==1.4.9 ; python_full_version >= '3.10'
-librt==0.6.3
+librt==0.7.0
 lxml==6.0.2
 markdown-it-py==3.0.0
 markdown-it-reporter==0.0.2
@@ -120,7 +121,7 @@ pillow==11.3.0 ; python_full_version < '3.10'
 pillow==12.0.0 ; python_full_version >= '3.10'
 pkce==1.0.3
 platformdirs==4.4.0 ; python_full_version < '3.10'
-platformdirs==4.5.0 ; python_full_version >= '3.10'
+platformdirs==4.5.1 ; python_full_version >= '3.10'
 playwright==1.56.0
 pluggy==1.6.0
 port-for==0.7.4 ; python_full_version < '3.10'
@@ -130,7 +131,8 @@ prettytable==3.17.0 ; python_full_version >= '3.10'
 prompt-toolkit==3.0.52
 propcache==0.4.1
 psutil==7.1.3 ; sys_platform != 'cygwin'
-psycopg==3.2.13
+psycopg==3.2.13 ; python_full_version < '3.10'
+psycopg==3.3.1 ; python_full_version >= '3.10'
 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
 pygithub==2.8.1
@@ -178,7 +180,7 @@ roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version <
 roc-validator==0.7.3 ; python_full_version >= '3.10'
 roman-numerals-py==3.1.0 ; python_full_version >= '3.11'
 rpds-py==0.27.1 ; python_full_version < '3.10'
-rpds-py==0.29.0 ; python_full_version >= '3.10'
+rpds-py==0.30.0 ; python_full_version >= '3.10'
 ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 rucio-clients==38.5.1
@@ -217,7 +219,7 @@ 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
+total-perspective-vortex==3.1.3
 trio==0.31.0 ; python_full_version < '3.10'
 trio==0.32.0 ; python_full_version >= '3.10'
 trio-websocket==0.12.2

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==0.14.7
+ruff==0.14.8

lib/galaxy/dependencies/pinned-requirements.txt

@@ -11,9 +11,11 @@ aiosignal==1.4.0
 alembic==1.16.5 ; python_full_version < '3.10'
 alembic==1.17.2 ; python_full_version >= '3.10'
 amqp==5.3.1
+annotated-doc==0.0.4
 annotated-types==0.7.0
 anyio==4.12.0
-apispec==6.8.4
+apispec==6.8.4 ; python_full_version < '3.10'
+apispec==6.9.0 ; python_full_version >= '3.10'
 appdirs==1.4.4
 arcp==0.2.1
 argcomplete==3.6.3
@@ -70,20 +72,22 @@ edam-ontology==1.25.3
 email-validator==2.3.0
 et-xmlfile==2.0.0
 exceptiongroup==1.3.1
-fastapi==0.118.3
+fastapi==0.123.10
 filelock==3.19.1 ; python_full_version < '3.10'
 filelock==3.20.0 ; python_full_version >= '3.10'
 fissix==24.4.24
 frozenlist==1.8.0
 fs==2.4.16
-fsspec==2025.10.0
+fsspec==2025.10.0 ; python_full_version < '3.10'
+fsspec==2025.12.0 ; python_full_version >= '3.10'
 future==1.0.0
 google-api-core==2.28.1
 google-auth==2.43.0
-google-cloud-batch==0.18.0
+google-cloud-batch==0.19.0
 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'
+greenlet==3.2.4 ; (python_full_version < '3.10' and platform_machine == 'AMD64') or (python_full_version < '3.10' and platform_machine == 'WIN32') or (python_full_version < '3.10' and platform_machine == 'aarch64') or (python_full_version < '3.10' and platform_machine == 'amd64') or (python_full_version < '3.10' and platform_machine == 'ppc64le') or (python_full_version < '3.10' and platform_machine == 'win32') or (python_full_version < '3.10' and platform_machine == 'x86_64')
+greenlet==3.3.0 ; (python_full_version >= '3.10' and platform_machine == 'AMD64') or (python_full_version >= '3.10' and platform_machine == 'WIN32') or (python_full_version >= '3.10' and platform_machine == 'aarch64') or (python_full_version >= '3.10' and platform_machine == 'amd64') or (python_full_version >= '3.10' and platform_machine == 'ppc64le') or (python_full_version >= '3.10' and platform_machine == 'win32') or (python_full_version >= '3.10' and platform_machine == 'x86_64')
 grpcio==1.76.0
 grpcio-status==1.76.0
 gunicorn==23.0.0
@@ -152,7 +156,7 @@ pillow==12.0.0 ; python_full_version >= '3.10'
 prompt-toolkit==3.0.52
 propcache==0.4.1
 proto-plus==1.26.1
-protobuf==6.33.1
+protobuf==6.33.2
 prov==1.5.1
 psutil==7.1.3
 pulsar-galaxy-lib==0.15.12
@@ -198,11 +202,12 @@ 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==0.29.0 ; python_full_version >= '3.10'
+rpds-py==0.30.0 ; python_full_version >= '3.10'
 rsa==4.9.1
 ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
-s3fs==2025.10.0
+s3fs==2025.10.0 ; python_full_version < '3.10'
+s3fs==2025.12.0 ; python_full_version >= '3.10'
 schema-salad==8.9.20251102115403
 setuptools==80.9.0
 six==1.17.0
@@ -213,7 +218,8 @@ sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.44
 sqlparse==0.5.4
-starlette==0.48.0
+starlette==0.49.3 ; python_full_version < '3.10'
+starlette==0.50.0 ; python_full_version >= '3.10'
 starlette-context==0.4.0
 supervisor==4.3.0
 svgwrite==1.4.3
@@ -232,7 +238,7 @@ typing-extensions==4.15.0
 typing-inspection==0.4.2
 tzdata==2025.2
 tzlocal==5.3.1
-ubiquerg==0.8.1
+ubiquerg==0.8.2
 urllib3==1.26.20 ; python_full_version < '3.10'
 urllib3==2.6.0 ; python_full_version >= '3.10'
 uvicorn==0.38.0

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

@@ -41,7 +41,8 @@ fluent-logger==0.11.1
 fonttools==4.60.1 ; python_full_version < '3.10'
 fonttools==4.61.0 ; python_full_version >= '3.10'
 frozenlist==1.8.0
-greenlet==3.2.4
+greenlet==3.2.4 ; python_full_version < '3.10'
+greenlet==3.3.0 ; python_full_version >= '3.10'
 h11==0.16.0
 html5lib==1.1 ; python_full_version < '3.10'
 html5rdf==1.2.1 ; python_full_version >= '3.10'
@@ -63,7 +64,7 @@ jsonschema-specifications==2025.9.1
 junit-xml==1.9
 kiwisolver==1.4.7 ; python_full_version < '3.10'
 kiwisolver==1.4.9 ; python_full_version >= '3.10'
-librt==0.6.3
+librt==0.7.0
 lxml==6.0.2
 markdown-it-py==3.0.0
 markupsafe==3.0.3
@@ -92,7 +93,7 @@ pillow==11.3.0 ; python_full_version < '3.10'
 pillow==12.0.0 ; python_full_version >= '3.10'
 pkce==1.0.3
 platformdirs==4.4.0 ; python_full_version < '3.10'
-platformdirs==4.5.0 ; python_full_version >= '3.10'
+platformdirs==4.5.1 ; python_full_version >= '3.10'
 playwright==1.56.0
 pluggy==1.6.0
 port-for==0.7.4 ; python_full_version < '3.10'
@@ -102,7 +103,8 @@ prettytable==3.17.0 ; python_full_version >= '3.10'
 prompt-toolkit==3.0.52
 propcache==0.4.1
 psutil==7.1.3 ; sys_platform != 'cygwin'
-psycopg==3.2.13
+psycopg==3.2.13 ; python_full_version < '3.10'
+psycopg==3.3.1 ; python_full_version >= '3.10'
 pycparser==2.23 ; implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt'
 pyee==13.0.0
 pygments==2.19.2
@@ -140,7 +142,7 @@ roc-validator==0.4.2 ; python_full_version < '3.9.20'
 roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < '3.10'
 roc-validator==0.7.3 ; python_full_version >= '3.10'
 rpds-py==0.27.1 ; python_full_version < '3.10'
-rpds-py==0.29.0 ; python_full_version >= '3.10'
+rpds-py==0.30.0 ; python_full_version >= '3.10'
 ruamel-yaml==0.18.16
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 rucio-clients==38.5.1
@@ -165,7 +167,7 @@ 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
+total-perspective-vortex==3.1.3
 trio==0.31.0 ; python_full_version < '3.10'
 trio==0.32.0 ; python_full_version >= '3.10'
 trio-websocket==0.12.2

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

@@ -1,21 +1,21 @@
 # This file was autogenerated by uv via the following command:
 #    uv export --frozen --no-annotate --no-hashes --only-group=typecheck
 annotated-types==0.7.0
-boto3-stubs==1.41.5
-botocore-stubs==1.41.5
+boto3-stubs==1.42.4
+botocore-stubs==1.42.4
 cffi==2.0.0 ; platform_python_implementation != 'PyPy'
 cryptography==46.0.3
-librt==0.6.3
+librt==0.7.0
 lxml-stubs==0.5.1
 mypy==1.19.0
-mypy-boto3-s3==1.41.1
+mypy-boto3-s3==1.42.3
 mypy-extensions==1.1.0
 pathspec==0.12.1
 pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy'
 pydantic==2.12.5
 pydantic-core==2.41.5
 tomli==2.3.0 ; python_full_version < '3.11'
-types-awscrt==0.29.1
+types-awscrt==0.29.2
 types-bleach==6.3.0.20251115
 types-boto==2.49.18.20241019
 types-contextvars==2.4.7.3