Merge pull request #21043 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

Author: mvdbeek

client/src/api/schema/schema.ts

@@ -372,7 +372,7 @@ if ("name" in props.initialElements) {
 
 initialize();
 
-type ColumnDefinition = components["schemas"]["SampleSheetColumnDefinition"];
+type ColumnDefinition = components["schemas"]["SampleSheetColumnDefinition-Input"];
 
 function uriFromRow(row: AgRowData): string {
     return row["url"] as string as string;

client/src/components/Collections/sheet/SampleSheetGrid.vue

@@ -27,6 +27,7 @@ const SAMPLE_RUN_COUNT = 100;
 const TEST_HISTORY_ID = "test-history-id";
 const TEST_HISTORY = {
     id: TEST_HISTORY_ID,
+    genome_build: "?",
     name: "fake-history-name",
 };
 

client/src/components/Workflow/WorkflowAnnotation.test.ts

@@ -1,5 +1,6 @@
 import datetime
 from abc import abstractmethod
+from typing import cast
 
 from celery import Task
 from sqlalchemy import (
@@ -10,6 +11,7 @@
     update,
 )
 from sqlalchemy.dialects.postgresql import insert as ps_insert
+from sqlalchemy.engine import CursorResult
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.orm import scoped_session
 
@@ -143,7 +145,9 @@ def calculate_task_start_time(
             except IntegrityError:
                 #  Row was inserted by another thread since we tried the update above.
                 sched_time = now + datetime.timedelta(seconds=task_interval_secs)
-                result = sa_session.execute(self._update_stmt, {"userid": user_id, "sched_time": sched_time})
+                result = cast(
+                    CursorResult, sa_session.execute(self._update_stmt, {"userid": user_id, "sched_time": sched_time})
+                )
                 if result.rowcount == 0:
                     raise Exception(f"Failed to update a celery_user_rate_limit row for user id {user_id}")
                 sa_session.commit()

lib/galaxy/celery/base_task.py

@@ -1,26 +1,26 @@
 # 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==3.12.15
+aiohttp==3.13.0
 aiosignal==1.4.0
 alabaster==0.7.16 ; python_full_version < '3.10'
 alabaster==1.0.0 ; python_full_version >= '3.10'
 anyio==4.11.0
 ase==3.26.0
 async-timeout==5.0.1 ; python_full_version < '3.11'
-attrs==25.3.0
+attrs==25.4.0
 axe-selenium-python==2.1.6
 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==1.40.18
-botocore==1.40.18
+boto3==1.40.49
+botocore==1.40.49
 build==1.3.0
 cachecontrol==0.14.3
 cachetools==6.2.0
-cattrs==25.2.0
-certifi==2025.8.3
+cattrs==25.3.0
+certifi==2025.10.5
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.3
 click==8.1.8 ; python_full_version < '3.10'
@@ -43,10 +43,11 @@ docutils==0.21.2
 dogpile-cache==1.4.1
 enum-tools==0.12.0 ; python_full_version >= '3.10'
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
-filelock==3.19.1
+filelock==3.19.1 ; python_full_version < '3.10'
+filelock==3.20.0 ; python_full_version >= '3.10'
 fluent-logger==0.11.1
 fonttools==4.60.1
-frozenlist==1.7.0
+frozenlist==1.8.0
 galaxy-release-util==0.3.1
 greenlet==3.2.4
 h11==0.16.0
@@ -82,20 +83,20 @@ markdown-it-py==3.0.0
 markdown-it-reporter==0.0.2
 markupsafe==3.0.3
 matplotlib==3.9.4 ; python_full_version < '3.10'
-matplotlib==3.10.6 ; python_full_version >= '3.10'
+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
 more-itertools==10.8.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x'
-msgpack==1.1.1
-multidict==6.6.4
+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==0.3.0
+nh3==0.3.1
 numpy==2.0.2 ; python_full_version < '3.10'
 numpy==2.2.6 ; python_full_version == '3.10.*'
 numpy==2.3.3 ; python_full_version >= '3.11'
@@ -109,14 +110,15 @@ pathspec==0.12.1
 pfzy==0.3.4
 pillow==11.3.0
 pkce==1.0.3
-platformdirs==4.4.0
+platformdirs==4.4.0 ; python_full_version < '3.10'
+platformdirs==4.5.0 ; python_full_version >= '3.10'
 playwright==1.55.0
 pluggy==1.6.0
 port-for==0.7.4 ; python_full_version < '3.10'
 port-for==1.0.0 ; python_full_version >= '3.10'
 prettytable==3.16.0
 prompt-toolkit==3.0.52
-propcache==0.3.2
+propcache==0.4.1
 psutil==7.1.0 ; sys_platform != 'cygwin'
 psycopg==3.2.10
 pycparser==2.23 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy')
@@ -157,7 +159,7 @@ requests-toolbelt==1.0.0
 responses==0.25.8
 rfc3986==2.0.0
 rich==13.9.4
-rich-click==1.9.1
+rich-click==1.9.3
 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'
@@ -166,7 +168,7 @@ rpds-py==0.27.1
 ruamel-yaml==0.18.15
 ruamel-yaml-clib==0.2.14 ; python_full_version < '3.14' and platform_python_implementation == 'CPython'
 rucio-clients==38.3.0
-s3transfer==0.13.1
+s3transfer==0.14.0
 schema-salad==8.9.20250723145140
 scipy==1.13.1 ; python_full_version < '3.10'
 scipy==1.15.3 ; python_full_version == '3.10.*'
@@ -199,7 +201,7 @@ testfixtures==9.1.0 ; python_full_version >= '3.11'
 text-unidecode==1.3
 tinydb==4.8.2
 toml==0.10.2
-tomli==2.2.1 ; python_full_version <= '3.11'
+tomli==2.3.0 ; python_full_version <= '3.11'
 total-perspective-vortex==3.1.1
 trio==0.31.0
 trio-websocket==0.12.2
@@ -218,8 +220,8 @@ urllib3==2.5.0 ; python_full_version >= '3.10'
 watchdog==6.0.0
 wcwidth==0.2.14
 webencodings==0.5.1 ; python_full_version < '3.10'
-websocket-client==1.8.0
+websocket-client==1.9.0
 werkzeug==3.1.3
 wsproto==1.2.0
-yarl==1.20.1
+yarl==1.22.0
 zipp==3.23.0 ; python_full_version < '3.12'

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,7 +1,7 @@
-attrs==25.3.0
+attrs==25.4.0
 flake8==7.3.0
 flake8-bugbear==24.12.12
 mccabe==0.7.0
 pycodestyle==2.14.0
 pyflakes==3.4.0
-ruff==0.13.3
+ruff==0.14.0

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

@@ -2,10 +2,10 @@
 #    uv export --frozen --no-annotate --no-hashes --no-dev
 a2wsgi==1.10.10
 adal==1.2.7
-aiobotocore==2.24.2
-aiofiles==24.1.0
+aiobotocore==2.25.0
+aiofiles==25.1.0
 aiohappyeyeballs==2.6.1
-aiohttp==3.12.15
+aiohttp==3.13.0
 aioitertools==0.12.0
 aiosignal==1.4.0
 alembic==1.16.5
@@ -18,7 +18,7 @@ arcp==0.2.1
 argcomplete==3.6.2
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attmap==0.13.2
-attrs==25.3.0
+attrs==25.4.0
 babel==2.17.0
 bagit==1.9.0
 bagit-profile==1.3.1
@@ -30,12 +30,12 @@ bioblend==1.6.0
 bleach==6.2.0
 boltons==25.0.0
 boto==2.49.0
-botocore==1.40.18
+botocore==1.40.49
 bx-python==0.14.0
 cachecontrol==0.14.3
 cachetools==6.2.0
 celery==5.5.3
-certifi==2025.8.3
+certifi==2025.10.5
 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
 charset-normalizer==3.4.3
 circus==0.19.0
@@ -67,19 +67,20 @@ edam-ontology==1.25.2
 email-validator==2.3.0
 et-xmlfile==2.0.0
 exceptiongroup==1.3.0 ; python_full_version < '3.11'
-fastapi-slim==0.118.0
-filelock==3.19.1
+fastapi-slim==0.118.3
+filelock==3.19.1 ; python_full_version < '3.10'
+filelock==3.20.0 ; python_full_version >= '3.10'
 fissix==24.4.24
-frozenlist==1.7.0
+frozenlist==1.8.0
 fs==2.4.16
 fsspec==2025.9.0
 future==1.0.0
-google-api-core==2.25.2
+google-api-core==2.26.0
 google-auth==2.41.1
 google-cloud-batch==0.17.37
 googleapis-common-protos==1.70.0
 gravity==1.1.1
-greenlet==3.2.4 ; (python_full_version < '3.14' and platform_machine == 'AMD64') or (python_full_version < '3.14' and platform_machine == 'WIN32') or (python_full_version < '3.14' and platform_machine == 'aarch64') or (python_full_version < '3.14' and platform_machine == 'amd64') or (python_full_version < '3.14' and platform_machine == 'ppc64le') or (python_full_version < '3.14' and platform_machine == 'win32') or (python_full_version < '3.14' and platform_machine == 'x86_64')
+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==1.75.1
 grpcio-status==1.75.1
 gunicorn==23.0.0
@@ -91,10 +92,10 @@ httpcore==1.0.9
 httpx==0.28.1
 humanfriendly==10.0
 idna==3.10
-ijson==3.4.0
+ijson==3.4.0.post0
 importlib-metadata==8.7.0 ; python_full_version < '3.10'
 importlib-resources==6.5.2 ; python_full_version < '3.12'
-invoke==2.2.0
+invoke==2.2.1
 isa-rwval==0.10.11
 isal==1.8.0
 isodate==0.7.2 ; python_full_version < '3.11'
@@ -118,8 +119,8 @@ mercurial==7.1.1
 mistune==3.0.2
 mrcfile==1.5.4
 msal==1.34.0
-msgpack==1.1.1
-multidict==6.6.4
+msgpack==1.1.2
+multidict==6.7.0
 mypy-extensions==1.1.0
 networkx==3.2.1 ; python_full_version < '3.10'
 networkx==3.4.2 ; python_full_version == '3.10.*'
@@ -142,7 +143,7 @@ pastedeploy==3.1.0
 pebble==5.1.3
 pillow==11.3.0
 prompt-toolkit==3.0.52
-propcache==0.3.2
+propcache==0.4.1
 proto-plus==1.26.1
 protobuf==6.32.1
 prov==1.5.1
@@ -152,8 +153,8 @@ 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==2.11.9
-pydantic-core==2.33.2
+pydantic==2.12.2
+pydantic-core==2.41.4
 pydantic-tes==0.2.0
 pydot==4.0.1
 pyeventsystem==0.1.0
@@ -198,10 +199,11 @@ setuptools==80.9.0
 six==1.17.0
 slowapi==0.1.9
 sniffio==1.3.1
-social-auth-core==4.7.0
+social-auth-core==4.7.0 ; python_full_version < '3.10'
+social-auth-core==4.8.1 ; python_full_version >= '3.10'
 sortedcontainers==2.4.0
 spython==0.3.14
-sqlalchemy==2.0.43
+sqlalchemy==2.0.44
 sqlparse==0.5.3
 starlette==0.48.0
 starlette-context==0.4.0
@@ -211,9 +213,9 @@ tenacity==9.1.2
 text-unidecode==1.3
 tifffile==2024.8.30 ; python_full_version < '3.10'
 tifffile==2025.5.10 ; python_full_version == '3.10.*'
-tifffile==2025.9.30 ; python_full_version >= '3.11'
+tifffile==2025.10.4 ; python_full_version >= '3.11'
 tinydb==4.8.2
-tomli==2.2.1 ; python_full_version < '3.11'
+tomli==2.3.0 ; python_full_version < '3.11'
 tornado==6.5.2
 tqdm==4.67.1
 tuspy==1.1.0
@@ -234,7 +236,7 @@ webob==1.8.9
 whoosh==2.7.4
 wrapt==1.17.3
 yacman==0.9.3
-yarl==1.20.1
+yarl==1.22.0
 zipp==3.23.0 ; python_full_version < '3.10'
 zipstream-new==1.1.8
 zstandard==0.25.0