From 87276502d75ee267239c1a69dba7378d82186e72 Mon Sep 17 00:00:00 2001
From: galaxybot <galaxybot@users.noreply.github.com>
Date: Sat, 7 Feb 2026 03:49:05 +0000
Subject: [PATCH] Update Python dependencies

by running `make update-dependencies`.
---
 lib/galaxy/dependencies/dev-requirements.txt  | 36 +++++-----
 .../dependencies/pinned-lint-requirements.txt |  2 +-
 .../dependencies/pinned-requirements.txt      | 65 ++++++++++---------
 .../dependencies/pinned-test-requirements.txt | 32 ++++-----
 .../pinned-typecheck-requirements.txt         |  4 +-
 5 files changed, 70 insertions(+), 69 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 5163000cb7a..157aed53111 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -10,15 +10,15 @@ async-generator==1.10
 async-timeout==5.0.1 ; python_full_version < '3.11'
 attrs==25.4.0
 axe-selenium-python==2.1.6
-babel==2.17.0
+babel==2.18.0
 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==26.1.0
-boto3==1.42.30
-botocore==1.42.30
+boto3==1.42.42
+botocore==1.42.42
 build==1.4.0
 cachecontrol==0.14.4
-cachetools==6.2.6
+cachetools==7.0.0
 cattrs==25.3.0
 certifi==2026.1.4
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
@@ -29,7 +29,7 @@ colorama==0.4.6 ; os_name == 'nt' or sys_platform == 'win32'
 colorlog==6.10.1
 contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.13.2
+coverage==7.13.3
 cryptography==46.0.4
 cwltest==2.6.20251216093331
 cycler==0.12.1
@@ -46,27 +46,27 @@ filelock==3.20.3
 fluent-logger==0.11.1
 fonttools==4.61.1
 frozenlist==1.8.0
-fsspec==2026.1.0
+fsspec==2026.2.0
 galaxy-release-util==0.3.2
-gcsfs==2026.1.0
+gcsfs==2026.2.0
 google-api-core==2.29.0
 google-auth==2.48.0
 google-auth-oauthlib==1.2.4
 google-cloud-core==2.5.0
-google-cloud-storage==3.8.0
+google-cloud-storage==3.9.0
 google-cloud-storage-control==1.9.0
 google-crc32c==1.8.0
 google-resumable-media==2.8.0
 googleapis-common-protos==1.72.0
 greenlet==3.3.1
 grpc-google-iam-v1==0.14.3
-grpcio==1.76.0
-grpcio-status==1.76.0
+grpcio==1.78.0
+grpcio-status==1.78.0
 h11==0.16.0
 html5rdf==1.2.1
 httpcore==1.0.9
 httpx==0.28.1
-id==1.5.0
+id==1.6.1
 idna==3.11
 imagesize==1.4.1
 importlib-metadata==8.7.1
@@ -107,7 +107,7 @@ myst-parser==4.0.1 ; python_full_version < '3.11'
 myst-parser==5.0.0 ; python_full_version >= '3.11'
 nh3==0.3.2
 numpy==2.2.6 ; python_full_version < '3.11'
-numpy==2.4.1 ; python_full_version >= '3.11'
+numpy==2.4.2 ; python_full_version >= '3.11'
 oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
@@ -124,7 +124,7 @@ port-for==1.0.0
 prettytable==3.17.0
 prompt-toolkit==3.0.52
 propcache==0.4.1
-proto-plus==1.27.0
+proto-plus==1.27.1
 protobuf==6.33.5
 psutil==7.2.2 ; sys_platform != 'cygwin'
 psycopg==3.3.2
@@ -162,20 +162,20 @@ rdflib==7.5.0
 readme-renderer==44.0
 referencing==0.36.2
 requests==2.32.5
-requests-cache==1.2.1
+requests-cache==1.3.0
 requests-oauthlib==2.0.0
 requests-toolbelt==1.0.0
 responses==0.25.8
 rfc3986==2.0.0
 rich==13.9.4
-rich-click==1.9.6
+rich-click==1.9.7
 roc-validator==0.8.0
 roman-numerals==4.1.0 ; python_full_version >= '3.11'
 rpds-py==0.30.0
 rsa==4.9.1
 ruamel-yaml==0.18.17
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
-rucio-clients==39.1.0
+rucio-clients==39.2.0
 s3transfer==0.16.0
 schema-salad==8.9.20251102115403
 scipy==1.15.3 ; python_full_version < '3.11'
@@ -219,12 +219,12 @@ types-certifi==2021.10.8.3
 types-requests==2.32.4.20260107
 types-urllib3==1.26.25.14
 typing-extensions==4.15.0
-typos==1.42.3
+typos==1.43.3
 tzdata==2025.3 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==2.6.3
 watchdog==6.0.0
-wcwidth==0.5.2
+wcwidth==0.6.0
 websocket-client==1.9.0
 werkzeug==3.1.5
 wsproto==1.3.2
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index e2a62374340..e3226f49fc5 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/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==0.14.14
+ruff==0.15.0
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 9d40240ce22..4ee6d024cf1 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -3,7 +3,7 @@
 a2wsgi==1.10.10
 adal==1.2.7
 ag-ui-protocol==0.1.10
-aiobotocore==3.1.1
+aiobotocore==3.1.2
 aiofiles==25.1.0
 aiohappyeyeballs==2.6.1
 aiohttp==3.13.3
@@ -13,7 +13,7 @@ alembic==1.18.3
 amqp==5.3.1
 annotated-doc==0.0.4
 annotated-types==0.7.0
-anthropic==0.77.0
+anthropic==0.78.0
 anyio==4.12.1
 apispec==6.9.0
 appdirs==1.4.4
@@ -22,8 +22,8 @@ argcomplete==3.6.3
 async-timeout==5.0.1 ; python_full_version < '3.11.3'
 attmap==0.13.2
 attrs==25.4.0
-authlib==1.6.6
-babel==2.17.0
+authlib==1.6.7
+babel==2.18.0
 backports-tarfile==1.2.0 ; python_full_version < '3.12'
 bagit==1.9.0
 bagit-profile==1.3.1
@@ -36,11 +36,11 @@ bioblend==1.7.0
 bleach==6.3.0
 boltons==25.0.0
 boto==2.49.0
-boto3==1.42.30
-botocore==1.42.30
+boto3==1.42.42
+botocore==1.42.42
 bx-python==0.14.0
 cachecontrol==0.14.4
-cachetools==6.2.6
+cachetools==7.0.0
 celery==5.6.2
 certifi==2026.1.4
 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy'
@@ -53,10 +53,11 @@ click-repl==0.3.0
 cloudauthz==0.6.0
 cloudbridge==3.2.0
 cloudpickle==3.1.2
-cohere==5.20.2 ; sys_platform != 'emscripten'
+cohere==5.20.4 ; sys_platform != 'emscripten'
 colorama==0.4.6
 coloredlogs==15.0.1
 conda-package-streaming==0.12.0
+croniter==6.0.0
 cryptography==46.0.4
 ct3==3.4.0.post5
 cwl-upgrader==1.2.14
@@ -82,28 +83,28 @@ eval-type-backport==0.3.1
 exceptiongroup==1.3.1
 executing==2.2.1
 fakeredis==2.33.0
-fastapi==0.128.0
+fastapi==0.128.3
 fastavro==1.12.1 ; sys_platform != 'emscripten'
-fastmcp==2.14.4
+fastmcp==2.14.5
 filelock==3.20.3
 fissix==24.4.24
 frozenlist==1.8.0
 fs==2.4.16
-fsspec==2026.1.0
+fsspec==2026.2.0
 future==1.0.0
 genai-prices==0.0.52
 google-api-core==2.29.0
 google-auth==2.48.0
 google-cloud-batch==0.20.0
-google-genai==1.61.0
+google-genai==1.62.0
 googleapis-common-protos==1.72.0
 gravity==1.2.0
 greenlet==3.3.1 ; 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'
 griffe==1.15.0
 groq==1.0.0
-grpcio==1.76.0
-grpcio-status==1.76.0
-gunicorn==24.1.1
+grpcio==1.78.0
+grpcio-status==1.78.0
+gunicorn==25.0.2
 gxformat2==0.21.0
 h11==0.16.0
 h5grove==2.3.0
@@ -112,7 +113,7 @@ hf-xet==1.2.0 ; platform_machine == 'aarch64' or platform_machine == 'amd64' or
 httpcore==1.0.9
 httpx==0.28.1
 httpx-sse==0.4.3
-huggingface-hub==0.36.0
+huggingface-hub==0.36.2
 humanfriendly==10.0
 idna==3.11
 ijson==3.4.0.post0
@@ -127,7 +128,7 @@ jaraco-context==6.1.0
 jaraco-functools==4.4.0
 jeepney==0.9.0 ; sys_platform == 'linux'
 jinja2==3.1.6
-jiter==0.12.0
+jiter==0.13.0
 jmespath==1.1.0
 jsonref==1.1.0
 jsonschema==4.26.0
@@ -137,9 +138,9 @@ keyring==25.7.0
 kombu==5.6.2
 lagom==2.7.7
 legacy-cgi==2.6.4 ; python_full_version >= '3.13'
-limits==5.6.0
-logfire==4.21.0
-logfire-api==4.21.0
+limits==5.8.0
+logfire==4.22.0
+logfire-api==4.22.0
 lupa==2.6
 lxml==6.0.2
 mako==1.3.10
@@ -164,22 +165,21 @@ nexus-rpc==1.2.0
 nodejs-wheel==22.20.0
 nodejs-wheel-binaries==22.20.0
 numpy==2.2.6 ; python_full_version < '3.11'
-numpy==2.4.1 ; python_full_version >= '3.11'
+numpy==2.4.2 ; python_full_version >= '3.11'
 oauthlib==3.3.1
-openai==2.16.0
+openai==2.17.0
 openapi-pydantic==0.5.1
 openpyxl==3.1.5
 opentelemetry-api==1.39.1
 opentelemetry-exporter-otlp-proto-common==1.39.1
 opentelemetry-exporter-otlp-proto-http==1.39.1
-opentelemetry-exporter-prometheus==0.60b1
 opentelemetry-instrumentation==0.60b1
 opentelemetry-instrumentation-httpx==0.60b1
 opentelemetry-proto==1.39.1
 opentelemetry-sdk==1.39.1
 opentelemetry-semantic-conventions==0.60b1
 opentelemetry-util-http==0.60b1
-orjson==3.11.6
+orjson==3.11.7
 oyaml==1.0
 packaging==26.0
 paramiko==4.0.0
@@ -194,7 +194,7 @@ platformdirs==4.5.1
 prometheus-client==0.24.1
 prompt-toolkit==3.0.52
 propcache==0.4.1
-proto-plus==1.27.0
+proto-plus==1.27.1
 protobuf==6.33.5
 prov==1.5.1
 psutil==7.2.2
@@ -214,7 +214,7 @@ pydantic-graph==1.44.0
 pydantic-settings==2.12.0
 pydantic-tes==0.2.0
 pydicom==3.0.1
-pydocket==0.16.6
+pydocket==0.17.5
 pydot==4.0.1
 pyeventsystem==0.1.0
 pyfaidx==0.9.0.3
@@ -259,11 +259,11 @@ rpds-py==0.30.0
 rsa==4.9.1
 ruamel-yaml==0.18.17
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
-s3fs==2026.1.0
+s3fs==2026.2.0
 s3transfer==0.16.0
 schema-salad==8.9.20251102115403
 secretstorage==3.5.0 ; sys_platform == 'linux'
-setuptools==80.10.2
+setuptools==81.0.0
 shellingham==1.5.4
 six==1.17.0
 slowapi==0.1.9
@@ -274,12 +274,13 @@ spython==0.3.14
 sqlalchemy==2.0.46
 sqlparse==0.5.5
 sse-starlette==3.2.0
-starlette==0.50.0
+starlette==0.52.1
 starlette-context==0.4.0
 supervisor==4.3.0
 svgwrite==1.4.3
+taskgroup==0.2.2 ; python_full_version < '3.11'
 temporalio==1.20.0
-tenacity==9.1.2
+tenacity==9.1.3
 text-unidecode==1.3
 tifffile==2025.5.10 ; python_full_version < '3.11'
 tifffile==2026.1.28 ; python_full_version >= '3.11'
@@ -288,7 +289,7 @@ tinydb==4.8.2
 tokenizers==0.22.2 ; sys_platform != 'emscripten'
 tomli==2.4.0 ; python_full_version < '3.11'
 tornado==6.5.4
-tqdm==4.67.2
+tqdm==4.67.3
 tuspy==1.1.0
 tuspyserver==4.2.3
 typer==0.21.1
@@ -303,7 +304,7 @@ urllib3==2.6.3
 uvicorn==0.40.0
 uvloop==0.22.1
 vine==5.1.0
-wcwidth==0.5.2
+wcwidth==0.6.0
 webencodings==0.5.1
 webob==1.8.9
 websockets==15.0.1
diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt
index cd2c9e345bb..9dc95c4aacb 100644
--- a/lib/galaxy/dependencies/pinned-test-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-test-requirements.txt
@@ -10,10 +10,10 @@ 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==1.42.30
-botocore==1.42.30
+boto3==1.42.42
+botocore==1.42.42
 cachecontrol==0.14.4
-cachetools==6.2.6
+cachetools==7.0.0
 cattrs==25.3.0
 certifi==2026.1.4
 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy'
@@ -23,7 +23,7 @@ colorama==0.4.6 ; sys_platform == 'win32'
 colorlog==6.10.1
 contourpy==1.3.2 ; python_full_version < '3.11'
 contourpy==1.3.3 ; python_full_version >= '3.11'
-coverage==7.13.2
+coverage==7.13.3
 cryptography==46.0.4
 cwltest==2.6.20251216093331
 cycler==0.12.1
@@ -36,21 +36,21 @@ filelock==3.20.3
 fluent-logger==0.11.1
 fonttools==4.61.1
 frozenlist==1.8.0
-fsspec==2026.1.0
-gcsfs==2026.1.0
+fsspec==2026.2.0
+gcsfs==2026.2.0
 google-api-core==2.29.0
 google-auth==2.48.0
 google-auth-oauthlib==1.2.4
 google-cloud-core==2.5.0
-google-cloud-storage==3.8.0
+google-cloud-storage==3.9.0
 google-cloud-storage-control==1.9.0
 google-crc32c==1.8.0
 google-resumable-media==2.8.0
 googleapis-common-protos==1.72.0
 greenlet==3.3.1
 grpc-google-iam-v1==0.14.3
-grpcio==1.76.0
-grpcio-status==1.76.0
+grpcio==1.78.0
+grpcio-status==1.78.0
 h11==0.16.0
 html5rdf==1.2.1
 httpcore==1.0.9
@@ -82,7 +82,7 @@ multidict==6.7.1
 mypy==1.19.1
 mypy-extensions==1.1.0
 numpy==2.2.6 ; python_full_version < '3.11'
-numpy==2.4.1 ; python_full_version >= '3.11'
+numpy==2.4.2 ; python_full_version >= '3.11'
 oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
@@ -99,7 +99,7 @@ port-for==1.0.0
 prettytable==3.17.0
 prompt-toolkit==3.0.52
 propcache==0.4.1
-proto-plus==1.27.0
+proto-plus==1.27.1
 protobuf==6.33.5
 psutil==7.2.2 ; sys_platform != 'cygwin'
 psycopg==3.3.2
@@ -130,17 +130,17 @@ pyyaml==6.0.3
 rdflib==7.5.0
 referencing==0.36.2
 requests==2.32.5
-requests-cache==1.2.1
+requests-cache==1.3.0
 requests-oauthlib==2.0.0
 responses==0.25.8
 rich==13.9.4
-rich-click==1.9.6
+rich-click==1.9.7
 roc-validator==0.8.0
 rpds-py==0.30.0
 rsa==4.9.1
 ruamel-yaml==0.18.17
 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.15' and platform_python_implementation == 'CPython'
-rucio-clients==39.1.0
+rucio-clients==39.2.0
 s3transfer==0.16.0
 schema-salad==8.9.20251102115403
 scipy==1.15.3 ; python_full_version < '3.11'
@@ -170,12 +170,12 @@ types-certifi==2021.10.8.3
 types-requests==2.32.4.20260107
 types-urllib3==1.26.25.14
 typing-extensions==4.15.0
-typos==1.42.3
+typos==1.43.3
 tzdata==2025.3 ; sys_platform == 'win32'
 url-normalize==2.2.1
 urllib3==2.6.3
 watchdog==6.0.0
-wcwidth==0.5.2
+wcwidth==0.6.0
 websocket-client==1.9.0
 werkzeug==3.1.5
 wsproto==1.3.2
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
index f96edaed55f..1cbf430f416 100644
--- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -1,8 +1,8 @@
 # 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==1.42.39
-botocore-stubs==1.42.39
+boto3-stubs==1.42.44
+botocore-stubs==1.42.41
 cffi==2.0.0 ; platform_python_implementation != 'PyPy'
 cryptography==46.0.4
 librt==0.7.8 ; platform_python_implementation != 'PyPy'