From c9b849d934a6e04eacf9770bfaf0f6d76d81b792 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 18 Apr 2026 04:00:25 +0000 Subject: [PATCH 1/2] Update Python dependencies by running `make update-dependencies`. Downgrade gxformat2 to 0.24.0 to fix workflow API tests --- lib/galaxy/dependencies/dev-requirements.txt | 18 +++--- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 57 ++++++++++--------- .../dependencies/pinned-test-requirements.txt | 16 ++++-- .../pinned-typecheck-requirements.txt | 8 +-- 5 files changed, 55 insertions(+), 46 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 312146774ac..f1f6c8c2b45 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -4,6 +4,7 @@ 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 @@ -40,7 +41,7 @@ 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 @@ -85,7 +86,7 @@ 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 @@ -98,7 +99,7 @@ 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' @@ -128,8 +129,10 @@ 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 @@ -173,7 +176,7 @@ 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' @@ -211,7 +214,8 @@ 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 @@ -221,4 +225,4 @@ 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' diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index fb15e07de1a..5fa73c7532a 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/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 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index b9c52d95b98..e3fcaa22cb0 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/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 @@ -53,7 +53,7 @@ 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 @@ -61,7 +61,7 @@ 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 diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt index 5d2f1c188ea..33d1f196171 100644 --- a/lib/galaxy/dependencies/pinned-test-requirements.txt +++ b/lib/galaxy/dependencies/pinned-test-requirements.txt @@ -3,6 +3,7 @@ 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 @@ -30,7 +31,7 @@ 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 @@ -66,7 +67,7 @@ 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 @@ -76,7 +77,7 @@ 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' @@ -103,6 +104,8 @@ 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 @@ -138,7 +141,7 @@ 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 @@ -162,7 +165,8 @@ 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 @@ -172,4 +176,4 @@ 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' diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index a0b7244a362..f0cb63fba34 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,19 +1,19 @@ # 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==1.42.88 +boto3-stubs==1.42.91 botocore-stubs==1.42.41 cffi==2.0.0 ; platform_python_implementation != 'PyPy' cryptography==46.0.7 librt==0.9.0 ; platform_python_implementation != 'PyPy' lxml-stubs==0.5.1 -mypy==1.20.0 +mypy==1.20.1 mypy-boto3-s3==1.42.85 mypy-extensions==1.1.0 pathspec==1.0.4 pycparser==3.0 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy' -pydantic==2.12.5 -pydantic-core==2.41.5 +pydantic==2.13.2 +pydantic-core==2.46.2 tomli==2.4.1 ; python_full_version < '3.11' types-awscrt==0.31.3 types-bleach==6.3.0.20260408 From d545df98799d72fdf513886118bdda5db1af5108 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Sun, 19 Apr 2026 00:22:24 +0100 Subject: [PATCH 2/2] Rebuild client schema for pydantic 2.13.2 --- client/src/api/schema/schema.ts | 33 ++++----------------------------- 1 file changed, 4 insertions(+), 29 deletions(-) diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts index ff358803742..943dabe0561 100644 --- a/client/src/api/schema/schema.ts +++ b/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"]