From 5bcce0ab47054776ea39db64dcc6326bb0c86d54 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 6 Dec 2025 03:25:40 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 27 ++++++++++--------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 26 ++++++++++-------- .../dependencies/pinned-test-requirements.txt | 24 +++++++++-------- .../pinned-typecheck-requirements.txt | 14 +++++----- 5 files changed, 51 insertions(+), 42 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index ac5a33bcf6b7..00cde72cb1d7 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -13,7 +13,8 @@ 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==25.11.0 +black==25.11.0 ; python_full_version < '3.10' +black==25.12.0 ; python_full_version >= '3.10' boto3==1.41.5 botocore==1.41.5 build==1.3.0 @@ -33,7 +34,7 @@ contourpy==1.3.0 ; python_full_version < '3.10' contourpy==1.3.2 ; python_full_version == '3.10.*' contourpy==1.3.3 ; python_full_version >= '3.11' coverage==7.10.7 ; python_full_version < '3.10' -coverage==7.12.0 ; python_full_version >= '3.10' +coverage==7.13.0 ; python_full_version >= '3.10' cryptography==46.0.3 cwltest==2.6.20250818005349 cycler==0.12.1 @@ -49,11 +50,12 @@ exceptiongroup==1.3.1 ; python_full_version < '3.11' 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 ; python_full_version < '3.10' +fonttools==4.60.2 ; python_full_version < '3.10' fonttools==4.61.0 ; python_full_version >= '3.10' frozenlist==1.8.0 galaxy-release-util==0.3.1 -greenlet==3.2.4 +greenlet==3.2.4 ; python_full_version < '3.10' +greenlet==3.3.0 ; python_full_version >= '3.10' h11==0.16.0 html5lib==1.1 ; python_full_version < '3.10' html5rdf==1.2.1 ; python_full_version >= '3.10' @@ -84,7 +86,7 @@ junit-xml==1.9 keyring==25.7.0 ; platform_machine != 'ppc64le' and platform_machine != 's390x' kiwisolver==1.4.7 ; python_full_version < '3.10' kiwisolver==1.4.9 ; python_full_version >= '3.10' -librt==0.6.3 +librt==0.7.3 lxml==6.0.2 markdown-it-py==3.0.0 markdown-it-reporter==0.0.2 @@ -120,8 +122,8 @@ pillow==11.3.0 ; python_full_version < '3.10' pillow==12.0.0 ; python_full_version >= '3.10' pkce==1.0.3 platformdirs==4.4.0 ; python_full_version < '3.10' -platformdirs==4.5.0 ; python_full_version >= '3.10' -playwright==1.56.0 +platformdirs==4.5.1 ; python_full_version >= '3.10' +playwright==1.57.0 pluggy==1.6.0 port-for==0.7.4 ; python_full_version < '3.10' port-for==1.0.0 ; python_full_version >= '3.10' @@ -130,7 +132,8 @@ prettytable==3.17.0 ; python_full_version >= '3.10' prompt-toolkit==3.0.52 propcache==0.4.1 psutil==7.1.3 ; sys_platform != 'cygwin' -psycopg==3.2.13 +psycopg==3.2.13 ; python_full_version < '3.10' +psycopg==3.3.2 ; python_full_version >= '3.10' pycparser==2.23 ; (implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt') or (implementation_name != 'PyPy' and platform_python_implementation != 'PyPy') pyee==13.0.0 pygithub==2.8.1 @@ -178,7 +181,7 @@ roc-validator==0.4.6 ; python_full_version >= '3.9.20' and python_full_version < roc-validator==0.7.3 ; python_full_version >= '3.10' roman-numerals-py==3.1.0 ; python_full_version >= '3.11' rpds-py==0.27.1 ; python_full_version < '3.10' -rpds-py==0.29.0 ; python_full_version >= '3.10' +rpds-py==0.30.0 ; python_full_version >= '3.10' ruamel-yaml==0.18.16 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.14' and platform_python_implementation == 'CPython' rucio-clients==38.5.1 @@ -190,7 +193,7 @@ scipy==1.16.3 ; python_full_version >= '3.11' secretstorage==3.3.3 ; python_full_version < '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux' secretstorage==3.5.0 ; python_full_version >= '3.10' and platform_machine != 'ppc64le' and platform_machine != 's390x' and sys_platform == 'linux' selenium==4.32.0 ; python_full_version < '3.10' -selenium==4.38.0 ; python_full_version >= '3.10' +selenium==4.39.0 ; python_full_version >= '3.10' seletools==1.5.0 six==1.17.0 sniffio==1.3.1 @@ -217,7 +220,7 @@ text-unidecode==1.3 tinydb==4.8.2 toml==0.10.2 tomli==2.3.0 ; python_full_version <= '3.11' -total-perspective-vortex==3.1.2 +total-perspective-vortex==3.1.3 trio==0.31.0 ; python_full_version < '3.10' trio==0.32.0 ; python_full_version >= '3.10' trio-websocket==0.12.2 @@ -232,7 +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==2.6.0 ; python_full_version >= '3.10' +urllib3==2.6.1 ; 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 a4009acb2b2f..5d07414b13d9 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==0.14.7 +ruff==0.14.8 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index e5a3ff3a1558..161e31f92abe 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -14,7 +14,8 @@ amqp==5.3.1 annotated-doc==0.0.4 annotated-types==0.7.0 anyio==4.12.0 -apispec==6.8.4 +apispec==6.8.4 ; python_full_version < '3.10' +apispec==6.9.0 ; python_full_version >= '3.10' appdirs==1.4.4 arcp==0.2.1 argcomplete==3.6.3 @@ -77,14 +78,16 @@ filelock==3.20.0 ; python_full_version >= '3.10' fissix==24.4.24 frozenlist==1.8.0 fs==2.4.16 -fsspec==2025.10.0 +fsspec==2025.10.0 ; python_full_version < '3.10' +fsspec==2025.12.0 ; python_full_version >= '3.10' future==1.0.0 google-api-core==2.28.1 google-auth==2.43.0 -google-cloud-batch==0.18.0 +google-cloud-batch==0.19.0 googleapis-common-protos==1.72.0 gravity==1.1.1 -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' +greenlet==3.2.4 ; (python_full_version < '3.10' and platform_machine == 'AMD64') or (python_full_version < '3.10' and platform_machine == 'WIN32') or (python_full_version < '3.10' and platform_machine == 'aarch64') or (python_full_version < '3.10' and platform_machine == 'amd64') or (python_full_version < '3.10' and platform_machine == 'ppc64le') or (python_full_version < '3.10' and platform_machine == 'win32') or (python_full_version < '3.10' and platform_machine == 'x86_64') +greenlet==3.3.0 ; (python_full_version >= '3.10' and platform_machine == 'AMD64') or (python_full_version >= '3.10' and platform_machine == 'WIN32') or (python_full_version >= '3.10' and platform_machine == 'aarch64') or (python_full_version >= '3.10' and platform_machine == 'amd64') or (python_full_version >= '3.10' and platform_machine == 'ppc64le') or (python_full_version >= '3.10' and platform_machine == 'win32') or (python_full_version >= '3.10' and platform_machine == 'x86_64') grpcio==1.76.0 grpcio-status==1.76.0 gunicorn==23.0.0 @@ -131,7 +134,7 @@ 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.*' -networkx==3.6 ; python_full_version >= '3.11' +networkx==3.6.1 ; python_full_version >= '3.11' nodejs-wheel==22.20.0 nodejs-wheel-binaries==22.20.0 numpy==2.0.2 ; python_full_version < '3.10' @@ -139,7 +142,7 @@ numpy==2.2.6 ; python_full_version == '3.10.*' numpy==2.3.5 ; python_full_version >= '3.11' oauthlib==3.3.1 openpyxl==3.1.5 -orjson==3.11.4 +orjson==3.11.5 oyaml==1.0 packaging==24.2 ; python_full_version < '3.10' packaging==25.0 ; python_full_version >= '3.10' @@ -153,7 +156,7 @@ pillow==12.0.0 ; python_full_version >= '3.10' prompt-toolkit==3.0.52 propcache==0.4.1 proto-plus==1.26.1 -protobuf==6.33.1 +protobuf==6.33.2 prov==1.5.1 psutil==7.1.3 pulsar-galaxy-lib==0.15.12 @@ -199,11 +202,12 @@ rich-argparse==1.7.2 rocrate==0.14.2 routes==2.5.1 rpds-py==0.27.1 ; python_full_version < '3.10' -rpds-py==0.29.0 ; python_full_version >= '3.10' +rpds-py==0.30.0 ; python_full_version >= '3.10' rsa==4.9.1 ruamel-yaml==0.18.16 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.14' and platform_python_implementation == 'CPython' -s3fs==2025.10.0 +s3fs==2025.10.0 ; python_full_version < '3.10' +s3fs==2025.12.0 ; python_full_version >= '3.10' schema-salad==8.9.20251102115403 setuptools==80.9.0 six==1.17.0 @@ -234,9 +238,9 @@ typing-extensions==4.15.0 typing-inspection==0.4.2 tzdata==2025.2 tzlocal==5.3.1 -ubiquerg==0.8.1 +ubiquerg==0.8.2 urllib3==1.26.20 ; python_full_version < '3.10' -urllib3==2.6.0 ; python_full_version >= '3.10' +urllib3==2.6.1 ; 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 ea0197be9095..f269cd902215 100644 --- a/lib/galaxy/dependencies/pinned-test-requirements.txt +++ b/lib/galaxy/dependencies/pinned-test-requirements.txt @@ -26,7 +26,7 @@ contourpy==1.3.0 ; python_full_version < '3.10' contourpy==1.3.2 ; python_full_version == '3.10.*' contourpy==1.3.3 ; python_full_version >= '3.11' coverage==7.10.7 ; python_full_version < '3.10' -coverage==7.12.0 ; python_full_version >= '3.10' +coverage==7.13.0 ; python_full_version >= '3.10' cwltest==2.6.20250818005349 cycler==0.12.1 decorator==5.2.1 @@ -38,10 +38,11 @@ exceptiongroup==1.3.1 ; python_full_version < '3.11' 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 ; python_full_version < '3.10' +fonttools==4.60.2 ; python_full_version < '3.10' fonttools==4.61.0 ; python_full_version >= '3.10' frozenlist==1.8.0 -greenlet==3.2.4 +greenlet==3.2.4 ; python_full_version < '3.10' +greenlet==3.3.0 ; python_full_version >= '3.10' h11==0.16.0 html5lib==1.1 ; python_full_version < '3.10' html5rdf==1.2.1 ; python_full_version >= '3.10' @@ -63,7 +64,7 @@ jsonschema-specifications==2025.9.1 junit-xml==1.9 kiwisolver==1.4.7 ; python_full_version < '3.10' kiwisolver==1.4.9 ; python_full_version >= '3.10' -librt==0.6.3 +librt==0.7.3 lxml==6.0.2 markdown-it-py==3.0.0 markupsafe==3.0.3 @@ -92,8 +93,8 @@ pillow==11.3.0 ; python_full_version < '3.10' pillow==12.0.0 ; python_full_version >= '3.10' pkce==1.0.3 platformdirs==4.4.0 ; python_full_version < '3.10' -platformdirs==4.5.0 ; python_full_version >= '3.10' -playwright==1.56.0 +platformdirs==4.5.1 ; python_full_version >= '3.10' +playwright==1.57.0 pluggy==1.6.0 port-for==0.7.4 ; python_full_version < '3.10' port-for==1.0.0 ; python_full_version >= '3.10' @@ -102,7 +103,8 @@ prettytable==3.17.0 ; python_full_version >= '3.10' prompt-toolkit==3.0.52 propcache==0.4.1 psutil==7.1.3 ; sys_platform != 'cygwin' -psycopg==3.2.13 +psycopg==3.2.13 ; python_full_version < '3.10' +psycopg==3.3.2 ; python_full_version >= '3.10' pycparser==2.23 ; implementation_name != 'PyPy' and implementation_name != 'pypy' and os_name == 'nt' pyee==13.0.0 pygments==2.19.2 @@ -140,7 +142,7 @@ 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' rpds-py==0.27.1 ; python_full_version < '3.10' -rpds-py==0.29.0 ; python_full_version >= '3.10' +rpds-py==0.30.0 ; python_full_version >= '3.10' ruamel-yaml==0.18.16 ruamel-yaml-clib==0.2.15 ; python_full_version < '3.14' and platform_python_implementation == 'CPython' rucio-clients==38.5.1 @@ -150,7 +152,7 @@ scipy==1.13.1 ; python_full_version < '3.10' scipy==1.15.3 ; python_full_version == '3.10.*' scipy==1.16.3 ; python_full_version >= '3.11' selenium==4.32.0 ; python_full_version < '3.10' -selenium==4.38.0 ; python_full_version >= '3.10' +selenium==4.39.0 ; python_full_version >= '3.10' seletools==1.5.0 six==1.17.0 sniffio==1.3.1 @@ -165,7 +167,7 @@ text-unidecode==1.3 tinydb==4.8.2 toml==0.10.2 tomli==2.3.0 ; python_full_version <= '3.11' -total-perspective-vortex==3.1.2 +total-perspective-vortex==3.1.3 trio==0.31.0 ; python_full_version < '3.10' trio==0.32.0 ; python_full_version >= '3.10' trio-websocket==0.12.2 @@ -179,7 +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==2.6.0 ; python_full_version >= '3.10' +urllib3==2.6.1 ; 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 35e87a4851aa..ebbc519d10b3 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,21 +1,21 @@ # 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==1.41.5 -botocore-stubs==1.41.5 +boto3-stubs==1.42.5 +botocore-stubs==1.42.5 cffi==2.0.0 ; platform_python_implementation != 'PyPy' cryptography==46.0.3 -librt==0.6.3 +librt==0.7.3 lxml-stubs==0.5.1 mypy==1.19.0 -mypy-boto3-s3==1.41.1 +mypy-boto3-s3==1.42.3 mypy-extensions==1.1.0 pathspec==0.12.1 pycparser==2.23 ; implementation_name != 'PyPy' and platform_python_implementation != 'PyPy' pydantic==2.12.5 pydantic-core==2.41.5 tomli==2.3.0 ; python_full_version < '3.11' -types-awscrt==0.29.1 +types-awscrt==0.29.2 types-bleach==6.3.0.20251115 types-boto==2.49.18.20241019 types-contextvars==2.4.7.3 @@ -29,11 +29,11 @@ types-python-slugify==8.0.2.20240310 types-pyyaml==6.0.12.20250915 types-requests==2.31.0.6 ; python_full_version < '3.10' types-requests==2.32.4.20250913 ; python_full_version >= '3.10' -types-s3transfer==0.15.0 +types-s3transfer==0.16.0 types-setuptools==80.9.0.20250822 types-six==1.17.0.20251009 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==2.6.0 ; python_full_version >= '3.10' +urllib3==2.6.1 ; python_full_version >= '3.10'