diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 9315593bc0b2..9220e79583bd 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -26,7 +26,7 @@ contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9" contourpy==1.2.1 ; python_version >= "3.9" and python_version < "3.13" coverage[toml]==7.6.0 ; python_version >= "3.8" and python_version < "3.13" cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13" -cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13" +cwltest==2.5.20240714110256 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13" darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13" @@ -106,18 +106,18 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13" pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13" -pytest-asyncio==0.23.7 ; python_version >= "3.8" and python_version < "3.13" +pytest-asyncio==0.23.8 ; python_version >= "3.8" and python_version < "3.13" pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13" pytest-cov==5.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13" -pytest-httpserver==1.0.10 ; python_version >= "3.8" and python_version < "3.13" +pytest-httpserver==1.0.11 ; python_version >= "3.8" and python_version < "3.13" pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13" pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13" pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" pytest-playwright==0.5.1 ; python_version >= "3.8" and python_version < "3.13" pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13" -pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13" +pytest==8.2.2 ; python_version >= "3.8" and python_version < "3.13" python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13" python-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -135,16 +135,16 @@ rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" rpds-py==0.19.0 ; python_version >= "3.9" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" -rucio-clients==34.5.0 ; python_version >= "3.9" and python_version < "3.13" +rucio-clients==34.6.0 ; python_version >= "3.9" and python_version < "3.13" s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.7.20240718183047 ; python_version >= "3.8" and python_version < "3.13" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.10" scipy==1.14.0 ; python_version >= "3.10" and python_version < "3.13" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" -selenium==4.22.0 ; python_version >= "3.8" and python_version < "3.13" +selenium==4.23.0 ; python_version >= "3.8" and python_version < "3.13" seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==71.0.4 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -171,7 +171,7 @@ trio==0.26.0 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13" twine==5.1.1 ; python_version >= "3.8" and python_version < "3.13" -typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13" tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13" urllib3[socks]==1.26.19 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index cf41e323498d..97b76f1d54b8 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.4.26 mccabe==0.7.0 pycodestyle==2.12.0 pyflakes==3.2.0 -ruff==0.5.1 +ruff==0.5.3 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 6cd2ea17eb8a..b9d725b4780a 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -65,7 +65,7 @@ dparse==0.6.3 ; python_version >= "3.8" and python_version < "3.13" edam-ontology==1.25.2 ; python_version >= "3.8" and python_version < "3.13" email-validator==2.2.0 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11" -fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13" +fastapi-slim==0.111.1 ; python_version >= "3.8" and python_version < "3.13" filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13" @@ -106,8 +106,8 @@ markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" mercurial==6.8 ; python_version >= "3.8" and python_version < "3.13" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" -mrcfile==1.5.1 ; python_version >= "3.8" and python_version < "3.13" -msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13" +mrcfile==1.5.2 ; python_version >= "3.8" and python_version < "3.13" +msal==1.30.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13" multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" @@ -136,7 +136,7 @@ pydantic-core==2.20.1 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" pydantic==2.8.2 ; python_version >= "3.8" and python_version < "3.13" pydantic[email]==2.8.2 ; python_version >= "3.8" and python_version < "3.13" -pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13" +pydot==3.0.1 ; python_version >= "3.8" and python_version < "3.13" pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13" pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13" pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13" @@ -171,9 +171,9 @@ rpds-py==0.19.0 ; python_version >= "3.8" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" s3fs==2024.6.1 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.7.20240718183047 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==71.0.4 ; python_version >= "3.8" and python_version < "3.13" shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" @@ -182,7 +182,7 @@ sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13" spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13" sqlalchemy==2.0.31 ; python_version >= "3.8" and python_version < "3.13" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" -sqlparse==0.5.0 ; python_version >= "3.8" and python_version < "3.13" +sqlparse==0.5.1 ; python_version >= "3.8" and python_version < "3.13" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" starlette-graphene3==0.6.0 ; python_version >= "3.8" and python_version < "3.13" starlette==0.37.2 ; python_version >= "3.8" and python_version < "3.13" @@ -196,7 +196,7 @@ tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13" tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13" -typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13" tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13" ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13" @@ -213,4 +213,4 @@ yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13" yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13" zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13" zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13" -zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13" +zstandard==0.23.0 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 0aab0f8b71ce..c95977cea853 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,19 +1,19 @@ --extra-index-url https://wheels.galaxyproject.org/simple annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" -boto3-stubs[s3]==1.34.144 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.34.144 ; python_version >= "3.8" and python_version < "3.13" +boto3-stubs[s3]==1.34.145 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.34.145 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13" lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13" mypy-boto3-s3==1.34.138 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" -mypy==1.10.1 ; python_version >= "3.8" and python_version < "3.13" +mypy==1.11.0 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" pydantic-core==2.20.1 ; python_version >= "3.8" and python_version < "3.13" pydantic==2.8.2 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" -types-awscrt==0.21.0 ; python_version >= "3.8" and python_version < "3.13" +types-awscrt==0.21.2 ; python_version >= "3.8" and python_version < "3.13" types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13" types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13" types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13" @@ -29,4 +29,4 @@ types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13" types-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13" types-six==1.16.21.20240513 ; python_version >= "3.8" and python_version < "3.13" types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.13" -typing-extensions==4.12.2 ; python_version >= "3.8" and python_version < "3.13" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"