Merge pull request galaxyproject#22517 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: mvdbeek

client/src/api/schema/schema.ts

@@ -15518,32 +15518,7 @@ export interface components {
             type: "in_range";
         };
         /** IncomingToolOutputCollection */
-        "IncomingToolOutputCollection-Input": {
-            /**
-             * hidden
-             * @description If true, the output will not be shown in the history.
-             */
-            hidden?: boolean | null;
-            /**
-             * label
-             * @description Output label. Will be used as dataset name in history.
-             */
-            label?: string | null;
-            /**
-             * name
-             * @description Parameter name. Used when referencing parameter in workflows.
-             */
-            name?: string | null;
-            /** structure */
-            structure: components["schemas"]["ToolOutputCollectionStructure"];
-            /**
-             * @description discriminator enum property added by openapi-typescript
-             * @enum {string}
-             */
-            type: "collection";
-        };
-        /** IncomingToolOutputCollection */
-        "IncomingToolOutputCollection-Output": {
+        IncomingToolOutputCollection: {
             /**
              * hidden
              * @description If true, the output will not be shown in the history.
@@ -24795,7 +24770,7 @@ export interface components {
              */
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
-                | components["schemas"]["IncomingToolOutputCollection-Input"]
+                | components["schemas"]["IncomingToolOutputCollection"]
                 | components["schemas"]["ToolOutputText"]
                 | components["schemas"]["ToolOutputInteger"]
                 | components["schemas"]["ToolOutputFloat"]
@@ -24894,7 +24869,7 @@ export interface components {
              */
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
-                | components["schemas"]["IncomingToolOutputCollection-Output"]
+                | components["schemas"]["IncomingToolOutputCollection"]
                 | components["schemas"]["ToolOutputText"]
                 | components["schemas"]["ToolOutputInteger"]
                 | components["schemas"]["ToolOutputFloat"]
@@ -26591,7 +26566,7 @@ export interface components {
              */
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
-                | components["schemas"]["IncomingToolOutputCollection-Input"]
+                | components["schemas"]["IncomingToolOutputCollection"]
                 | components["schemas"]["ToolOutputText"]
                 | components["schemas"]["ToolOutputInteger"]
                 | components["schemas"]["ToolOutputFloat"]

lib/galaxy/dependencies/dev-requirements.txt

@@ -5,6 +5,7 @@ aiohappyeyeballs==2.6.1
 aiohttp==3.13.5
 aiosignal==1.4.0
 alabaster==1.0.0
+annotated-types==0.7.0
 ase==3.28.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==26.1.0
@@ -41,7 +42,7 @@ docutils==0.22.4 ; python_full_version >= '3.11'
 dogpile-cache==1.5.0
 enum-tools==0.12.0
 exceptiongroup==1.3.1 ; python_full_version < '3.11'
-filelock==3.25.2
+filelock==3.28.0
 fluent-logger==0.11.1
 fonttools==4.62.1
 frozenlist==1.8.0
@@ -86,7 +87,7 @@ junit-xml==1.9
 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 kiwisolver==1.5.0
 librt==0.9.0 ; platform_python_implementation != 'PyPy'
-lxml==6.0.3
+lxml==6.0.4
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.0.0 ; python_full_version >= '3.11'
 markdown-it-reporter==0.0.2
@@ -99,7 +100,7 @@ mistune==3.2.0
 more-itertools==11.0.2 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
 msgpack==1.1.2
 multidict==6.7.1
-mypy==1.20.0
+mypy==1.20.1
 mypy-extensions==1.1.0
 myst-parser==4.0.1 ; python_full_version < '3.11'
 myst-parser==5.0.0 ; python_full_version >= '3.11'
@@ -129,8 +130,10 @@ psycopg==3.3.3
 pyasn1==0.6.3
 pyasn1-modules==0.4.2
 pycparser==3.0 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
+pydantic==2.13.2
+pydantic-core==2.46.2
 pyee==13.0.1
-pygithub==2.9.0
+pygithub==2.9.1
 pygments==2.20.0
 pyjwt==2.12.1
 pynacl==1.6.2
@@ -174,7 +177,7 @@ rpds-py==0.30.0
 ruamel-yaml==0.19.1
 rucio-clients==39.4.1
 s3transfer==0.16.0
-schema-salad==8.9.20260327095315
+schema-salad==8.9.20260417192335
 scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.1 ; python_full_version >= '3.11'
 secretstorage==3.5.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux'
@@ -212,7 +215,8 @@ twine==6.2.0
 types-cachetools==6.2.0.20260408
 types-requests==2.33.0.20260408
 typing-extensions==4.15.0
-typos==1.45.0
+typing-inspection==0.4.2
+typos==1.45.1
 tzdata==2026.1 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==2.6.3
@@ -222,4 +226,4 @@ websocket-client==1.9.0
 werkzeug==3.1.8
 wsproto==1.3.2
 yarl==1.23.0
-zipp==3.23.0 ; python_full_version < '3.12'
+zipp==3.23.1 ; python_full_version < '3.12'

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

@@ -4,4 +4,4 @@ flake8-bugbear==25.11.29
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.15.10
+ruff==0.15.11

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 #    uv export --frozen --no-annotate --no-hashes --no-dev
 a2wsgi==1.10.10
 adal==1.2.7
-ag-ui-protocol==0.1.15
+ag-ui-protocol==0.1.16
 aiobotocore==3.4.0
 aiofile==3.9.0
 aiofiles==25.1.0
@@ -14,7 +14,7 @@ alembic==1.18.4
 amqp==5.3.1
 annotated-doc==0.0.4
 annotated-types==0.7.0
-anthropic==0.94.0
+anthropic==0.96.0
 anyio==4.13.0
 apispec==6.10.0
 appdirs==1.4.4
@@ -32,7 +32,7 @@ bdbag==1.8.0
 beaker==1.13.0
 beartype==0.22.9
 billiard==4.2.4
-bioblend==1.8.0
+bioblend==1.9.0
 bleach==6.3.0
 boltons==25.0.0
 boto==2.49.0
@@ -53,15 +53,15 @@ click-plugins==1.1.1.2
 click-repl==0.3.0
 cloudauthz==0.6.0
 cloudbridge==3.2.0
-cohere==6.1.0 ; sys_platform != 'emscripten'
+cohere==5.21.1 ; sys_platform != 'emscripten'
 colorama==0.4.6 ; sys_platform == 'win32'
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
 cryptography==46.0.7
 ct3==3.4.0.post5
 cwl-upgrader==1.2.15
 cwl-utils==0.41
-cwltool==3.1.20260315121657
+cwltool==3.2.20260413085819
 cyclopts==4.10.2
 defusedxml==0.7.1
 deprecated==1.3.1
@@ -70,7 +70,7 @@ dictobj==0.4
 distro==1.9.0
 dnspython==2.8.0
 docopt==0.6.2
-docstring-parser==0.17.0
+docstring-parser==0.18.0
 docutils==0.21.2 ; python_full_version < '3.11'
 docutils==0.22.4 ; python_full_version >= '3.11'
 dparse==0.6.4
@@ -80,10 +80,10 @@ et-xmlfile==2.0.0
 eval-type-backport==0.3.1
 exceptiongroup==1.3.1
 executing==2.2.1
-fastapi==0.135.3
+fastapi==0.136.0
 fastavro==1.12.1 ; sys_platform != 'emscripten'
-fastmcp==3.2.3
-filelock==3.25.2
+fastmcp==3.2.4
+filelock==3.28.0
 fissix==24.4.24
 frozenlist==1.8.0
 fs==2.4.16
@@ -93,7 +93,7 @@ genai-prices==0.0.56
 google-api-core==2.30.3
 google-auth==2.49.2
 google-cloud-batch==0.21.0
-google-genai==1.72.0
+google-genai==1.73.1
 googleapis-common-protos==1.74.0
 gravity==1.2.1
 greenlet==3.4.0 ; 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'
@@ -104,18 +104,18 @@ grpcio-status==1.80.0
 gunicorn==25.3.0
 gxformat2==0.24.0
 h11==0.16.0
-h5grove==3.0.0
+h5grove==4.0.0
 h5py==3.16.0
 hf-xet==1.4.3 ; platform_machine == 'AMD64' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'
 httpcore==1.0.9
 httpx==0.28.1
 httpx-sse==0.4.3
-huggingface-hub==1.10.1
+huggingface-hub==1.11.0
 humanfriendly==10.0
 idna==3.11
 ijson==3.5.0
 importlib-metadata==8.7.1
-importlib-resources==6.5.2 ; python_full_version < '3.12'
+importlib-resources==7.1.0 ; python_full_version < '3.12'
 invoke==3.0.3
 isa-rwval==0.10.11
 isal==1.8.0
@@ -137,9 +137,9 @@ kombu==5.6.2
 lagom==2.7.7
 legacy-cgi==2.6.4 ; python_full_version >= '3.13'
 limits==5.8.0
-logfire==4.32.0
-logfire-api==4.32.0
-lxml==6.0.3
+logfire==4.32.1
+logfire-api==4.32.1
+lxml==6.0.4
 mako==1.3.11
 markdown==3.10.2
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
@@ -148,7 +148,7 @@ markupsafe==3.0.3
 mcp==1.27.0
 mdurl==0.1.2
 mercurial==7.2.1
-mistralai==2.3.2
+mistralai==2.4.0
 mistune==3.2.0
 more-itertools==11.0.2
 mrcfile==1.5.4
@@ -164,7 +164,7 @@ nodejs-wheel-binaries==22.20.0
 numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.4 ; python_full_version >= '3.11'
 oauthlib==3.3.1
-openai==2.31.0
+openai==2.32.0
 openapi-pydantic==0.5.1
 openpyxl==3.1.5
 opentelemetry-api==1.39.1
@@ -198,12 +198,12 @@ pyasn1==0.6.3
 pyasn1-modules==0.4.2
 pycparser==3.0 ; (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') or (implementation_name == 'pypy' and platform_python_implementation == 'PyPy')
 pycryptodome==3.23.0
-pydantic==2.12.5
-pydantic-ai==1.80.0
-pydantic-ai-slim==1.80.0
-pydantic-core==2.41.5
-pydantic-evals==1.80.0
-pydantic-graph==1.80.0
+pydantic==2.13.2
+pydantic-ai==1.84.1
+pydantic-ai-slim==1.84.1
+pydantic-core==2.46.2
+pydantic-evals==1.84.1
+pydantic-graph==1.84.1
 pydantic-handlebars==0.1.0
 pydantic-settings==2.13.1
 pydantic-tes==0.4.0
@@ -250,7 +250,7 @@ rpds-py==0.30.0
 ruamel-yaml==0.19.1
 s3fs==2026.3.0
 s3transfer==0.16.0
-schema-salad==8.9.20260327095315
+schema-salad==8.9.20260417192335
 secretstorage==3.5.0 ; sys_platform == 'linux'
 setuptools==81.0.0
 shellingham==1.5.4
@@ -267,11 +267,12 @@ starlette==1.0.0
 starlette-context==0.5.1
 supervisor==4.3.0
 svgwrite==1.4.3
-temporalio==1.25.0
+temporalio==1.26.0
 tenacity==9.1.4
 text-unidecode==1.3
 tifffile==2025.5.10 ; python_full_version < '3.11'
-tifffile==2026.3.3 ; python_full_version >= '3.11'
+tifffile==2026.3.3 ; python_full_version == '3.11.*'
+tifffile==2026.4.11 ; python_full_version >= '3.12'
 tiktoken==0.12.0
 tinydb==4.8.2
 tokenizers==0.22.2 ; sys_platform != 'emscripten'
@@ -303,6 +304,6 @@ wrapt==1.17.3
 xai-sdk==1.11.0
 yacman==1.0.0
 yarl==1.23.0
-zipp==3.23.0
+zipp==3.23.1
 zipstream-new==1.1.8
 zstandard==0.25.0

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

@@ -4,6 +4,7 @@ aiocop==1.1.4
 aiohappyeyeballs==2.6.1
 aiohttp==3.13.5
 aiosignal==1.4.0
+annotated-types==0.7.0
 ase==3.28.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==26.1.0
@@ -31,7 +32,7 @@ defusedxml==0.7.1
 dogpile-cache==1.5.0
 enum-tools==0.12.0
 exceptiongroup==1.3.1 ; python_full_version < '3.11'
-filelock==3.25.2
+filelock==3.28.0
 fluent-logger==0.11.1
 fonttools==4.62.1
 frozenlist==1.8.0
@@ -67,7 +68,7 @@ jsonschema-specifications==2025.9.1
 junit-xml==1.9
 kiwisolver==1.5.0
 librt==0.9.0 ; platform_python_implementation != 'PyPy'
-lxml==6.0.3
+lxml==6.0.4
 markdown-it-py==3.0.0 ; python_full_version < '3.11'
 markdown-it-py==4.0.0 ; python_full_version >= '3.11'
 markupsafe==3.0.3
@@ -77,7 +78,7 @@ mirakuru==3.0.2
 mistune==3.2.0
 msgpack==1.1.2
 multidict==6.7.1
-mypy==1.20.0
+mypy==1.20.1
 mypy-extensions==1.1.0
 numpy==2.2.6 ; python_full_version < '3.11'
 numpy==2.4.4 ; python_full_version >= '3.11'
@@ -104,6 +105,8 @@ psycopg==3.3.3
 pyasn1==0.6.3
 pyasn1-modules==0.4.2
 pycparser==3.0 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
+pydantic==2.13.2
+pydantic-core==2.46.2
 pyee==13.0.1
 pygments==2.20.0
 pyparsing==3.3.2
@@ -139,7 +142,7 @@ rpds-py==0.30.0
 ruamel-yaml==0.19.1
 rucio-clients==39.4.1
 s3transfer==0.16.0
-schema-salad==8.9.20260327095315
+schema-salad==8.9.20260417192335
 scipy==1.15.3 ; python_full_version < '3.11'
 scipy==1.17.1 ; python_full_version >= '3.11'
 selenium==4.43.0
@@ -163,7 +166,8 @@ tuspy==1.1.0
 types-cachetools==6.2.0.20260408
 types-requests==2.33.0.20260408
 typing-extensions==4.15.0
-typos==1.45.0
+typing-inspection==0.4.2
+typos==1.45.1
 tzdata==2026.1 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==2.6.3
@@ -173,4 +177,4 @@ websocket-client==1.9.0
 werkzeug==3.1.8
 wsproto==1.3.2
 yarl==1.23.0
-zipp==3.23.0 ; python_full_version < '3.12'
+zipp==3.23.1 ; python_full_version < '3.12'