From 1aec8006faaed69b6f5517ebee99c64098e678a1 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 13 Dec 2025 03:29:11 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 8 ++++---- lib/galaxy/dependencies/pinned-lint-requirements.txt | 2 +- lib/galaxy/dependencies/pinned-requirements.txt | 10 +++++----- lib/galaxy/dependencies/pinned-test-requirements.txt | 8 ++++---- .../dependencies/pinned-typecheck-requirements.txt | 8 ++++---- 5 files changed, 18 insertions(+), 18 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 00cde72cb1d..475b80fa2da 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -20,7 +20,7 @@ botocore==1.41.5 build==1.3.0 cachecontrol==0.14.3 ; python_full_version < '3.10' cachecontrol==0.14.4 ; python_full_version >= '3.10' -cachetools==6.2.2 +cachetools==6.2.3 cattrs==25.3.0 certifi==2025.11.12 cffi==2.0.0 ; (implementation_name != 'pypy' and os_name == 'nt') or platform_python_implementation != 'PyPy' @@ -51,7 +51,7 @@ filelock==3.19.1 ; python_full_version < '3.10' filelock==3.20.0 ; python_full_version >= '3.10' fluent-logger==0.11.1 fonttools==4.60.2 ; python_full_version < '3.10' -fonttools==4.61.0 ; python_full_version >= '3.10' +fonttools==4.61.1 ; python_full_version >= '3.10' frozenlist==1.8.0 galaxy-release-util==0.3.1 greenlet==3.2.4 ; python_full_version < '3.10' @@ -92,7 +92,7 @@ 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==3.10.7 ; python_full_version >= '3.10' +matplotlib==3.10.8 ; 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 @@ -235,7 +235,7 @@ typing-extensions==4.15.0 tzdata==2025.2 ; sys_platform == 'win32' url-normalize==2.2.1 urllib3==1.26.20 ; python_full_version < '3.10' -urllib3==2.6.1 ; python_full_version >= '3.10' +urllib3==2.6.2 ; python_full_version >= '3.10' watchdog==6.0.0 wcwidth==0.2.14 webencodings==0.5.1 ; python_full_version < '3.10' diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 5d07414b13d..2769506fefb 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==0.14.8 +ruff==0.14.9 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 161e31f92ab..bbc8557aa70 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -38,7 +38,7 @@ botocore==1.41.5 bx-python==0.14.0 cachecontrol==0.14.3 ; python_full_version < '3.10' cachecontrol==0.14.4 ; python_full_version >= '3.10' -cachetools==6.2.2 +cachetools==6.2.3 celery==5.6.0 certifi==2025.11.12 cffi==2.0.0 ; implementation_name == 'pypy' or platform_python_implementation != 'PyPy' @@ -72,7 +72,7 @@ edam-ontology==1.25.3 email-validator==2.3.0 et-xmlfile==2.0.0 exceptiongroup==1.3.1 -fastapi==0.124.0 +fastapi==0.124.4 filelock==3.19.1 ; python_full_version < '3.10' filelock==3.20.0 ; python_full_version >= '3.10' fissix==24.4.24 @@ -216,7 +216,7 @@ 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==2.0.44 +sqlalchemy==2.0.45 sqlparse==0.5.4 starlette==0.49.3 ; python_full_version < '3.10' starlette==0.50.0 ; python_full_version >= '3.10' @@ -230,7 +230,7 @@ tifffile==2025.5.10 ; python_full_version == '3.10.*' tifffile==2025.10.16 ; python_full_version >= '3.11' tinydb==4.8.2 tomli==2.3.0 ; python_full_version < '3.11' -tornado==6.5.2 +tornado==6.5.3 tqdm==4.67.1 tuspy==1.1.0 tuspyserver==4.2.3 @@ -240,7 +240,7 @@ tzdata==2025.2 tzlocal==5.3.1 ubiquerg==0.8.2 urllib3==1.26.20 ; python_full_version < '3.10' -urllib3==2.6.1 ; python_full_version >= '3.10' +urllib3==2.6.2 ; python_full_version >= '3.10' uvicorn==0.38.0 uvloop==0.22.1 vine==5.1.0 diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt index f269cd90221..5a93dfa41d4 100644 --- a/lib/galaxy/dependencies/pinned-test-requirements.txt +++ b/lib/galaxy/dependencies/pinned-test-requirements.txt @@ -13,7 +13,7 @@ boto3==1.41.5 botocore==1.41.5 cachecontrol==0.14.3 ; python_full_version < '3.10' cachecontrol==0.14.4 ; python_full_version >= '3.10' -cachetools==6.2.2 +cachetools==6.2.3 cattrs==25.3.0 certifi==2025.11.12 cffi==2.0.0 ; implementation_name != 'pypy' and os_name == 'nt' @@ -39,7 +39,7 @@ filelock==3.19.1 ; python_full_version < '3.10' filelock==3.20.0 ; python_full_version >= '3.10' fluent-logger==0.11.1 fonttools==4.60.2 ; python_full_version < '3.10' -fonttools==4.61.0 ; python_full_version >= '3.10' +fonttools==4.61.1 ; python_full_version >= '3.10' frozenlist==1.8.0 greenlet==3.2.4 ; python_full_version < '3.10' greenlet==3.3.0 ; python_full_version >= '3.10' @@ -69,7 +69,7 @@ lxml==6.0.2 markdown-it-py==3.0.0 markupsafe==3.0.3 matplotlib==3.9.4 ; python_full_version < '3.10' -matplotlib==3.10.7 ; python_full_version >= '3.10' +matplotlib==3.10.8 ; python_full_version >= '3.10' mdurl==0.1.2 mirakuru==2.6.1 ; python_full_version < '3.10' mirakuru==3.0.1 ; python_full_version >= '3.10' @@ -181,7 +181,7 @@ typing-extensions==4.15.0 tzdata==2025.2 ; sys_platform == 'win32' url-normalize==2.2.1 urllib3==1.26.20 ; python_full_version < '3.10' -urllib3==2.6.1 ; python_full_version >= '3.10' +urllib3==2.6.2 ; python_full_version >= '3.10' watchdog==6.0.0 wcwidth==0.2.14 webencodings==0.5.1 ; python_full_version < '3.10' diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index ebbc519d10b..00033f82fe5 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==1.42.5 -botocore-stubs==1.42.5 +boto3-stubs==1.42.9 +botocore-stubs==1.42.9 cffi==2.0.0 ; platform_python_implementation != 'PyPy' cryptography==46.0.3 librt==0.7.3 @@ -15,7 +15,7 @@ pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementati pydantic==2.12.5 pydantic-core==2.41.5 tomli==2.3.0 ; python_full_version < '3.11' -types-awscrt==0.29.2 +types-awscrt==0.30.0 types-bleach==6.3.0.20251115 types-boto==2.49.18.20241019 types-contextvars==2.4.7.3 @@ -36,4 +36,4 @@ types-urllib3==1.26.25.14 ; python_full_version < '3.10' types-webencodings==0.5.0.20251108 typing-extensions==4.15.0 typing-inspection==0.4.2 -urllib3==2.6.1 ; python_full_version >= '3.10' +urllib3==2.6.2 ; python_full_version >= '3.10'