diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 1b1fcdde3007..9315593bc0b2 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -16,7 +16,7 @@ boto3==1.34.131 ; python_version >= "3.8" and python_version < "3.13" botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13" build==1.2.1 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" -certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13" +certifi==2024.7.4 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" click==8.1.7 ; python_version >= "3.8" and python_version < "3.13" @@ -24,7 +24,7 @@ codespell==2.3.0 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") 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]==7.5.4 ; python_version >= "3.8" 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" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" @@ -35,10 +35,10 @@ defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13" docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13" dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13" -exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11" +exceptiongroup==1.2.2 ; python_version >= "3.8" and python_version < "3.11" filelock==3.15.4 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.11.1 ; python_version >= "3.8" and python_version < "3.13" -fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13" +fonttools==4.53.1 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13" graylint==1.1.1 ; python_version >= "3.8" and python_version < "3.13" @@ -69,7 +69,7 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13" markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9" -matplotlib==3.9.0 ; python_version >= "3.9" and python_version < "3.13" +matplotlib==3.9.1 ; python_version >= "3.9" and python_version < "3.13" mdit-py-plugins==0.4.1 ; python_version >= "3.8" and python_version < "3.13" mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13" @@ -79,7 +79,7 @@ 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" myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13" -nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13" +nh3==0.2.18 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13" onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13" @@ -94,7 +94,7 @@ platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13" playwright==1.45.0 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13" -prettytable==3.10.0 ; python_version >= "3.8" and python_version < "3.13" +prettytable==3.10.2 ; python_version >= "3.8" and python_version < "3.13" psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" psycopg==3.2.1 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" @@ -132,19 +132,19 @@ requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13" responses==0.25.3 ; python_version >= "3.8" and python_version < "3.13" rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13" rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" -rpds-py==0.18.1 ; python_version >= "3.9" 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" s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.6.20240710082410 ; 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" seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.3.0 ; 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" @@ -167,7 +167,7 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13" toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6" trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13" -trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13" +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" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 3df072eefc30..cf41e323498d 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==0.5.0 +ruff==0.5.1 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index a0b6b7e68228..6cd2ea17eb8a 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -37,7 +37,7 @@ botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13" bx-python==0.12.0 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13" -certifi==2024.6.2 ; python_version >= "3.8" and python_version < "3.13" +certifi==2024.7.4 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13" @@ -54,7 +54,7 @@ conda-package-streaming==0.10.0 ; python_version >= "3.8" and python_version < " cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13" cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13" cwl-utils==0.33 ; python_version >= "3.8" and python_version < "3.13" -cwltool==3.1.20240508115724 ; python_version >= "3.8" and python_version < "3.13" +cwltool==3.1.20240708091337 ; python_version >= "3.8" and python_version < "3.13" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13" dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -64,7 +64,7 @@ docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13" 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==1.2.1 ; python_version >= "3.8" and python_version < "3.11" +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" 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" @@ -104,9 +104,9 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown==3.6 ; python_version >= "3.8" and python_version < "3.13" 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==6.7.4 ; 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==1.5.0 ; 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" 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" @@ -132,10 +132,10 @@ psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13" +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==2.8.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.8.0 ; 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" 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" @@ -167,13 +167,13 @@ requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13" rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" rocrate==0.10.0 ; python_version >= "3.8" and python_version < "3.13" routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13" -rpds-py==0.18.1 ; python_version >= "3.8" and python_version < "3.13" +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==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.2.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.3.0 ; 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" @@ -188,7 +188,7 @@ 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" supervisor==4.2.5 ; python_version >= "3.8" and python_version < "3.13" svgwrite==1.4.3 ; python_version >= "3.8" and python_version < "3.13" -tenacity==8.4.2 ; python_version >= "3.8" and python_version < "3.13" +tenacity==8.5.0 ; python_version >= "3.8" and python_version < "3.13" tifffile==2023.7.10 ; python_version >= "3.8" and python_version < "3.13" tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index f37b1b56f55d..0aab0f8b71ce 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,8 +1,8 @@ --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]==1.34.138 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.34.138 ; 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" 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" @@ -10,15 +10,15 @@ 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" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" -pydantic-core==2.20.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.8.0 ; python_version >= "3.8" and python_version < "3.13" +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==0.20.12 ; python_version >= "3.8" and python_version < "3.13" +types-awscrt==0.21.0 ; 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" types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13" -types-docutils==0.21.0.20240423 ; python_version >= "3.8" and python_version < "3.13" +types-docutils==0.21.0.20240711 ; python_version >= "3.8" and python_version < "3.13" types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13" types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13" types-paramiko==3.4.0.20240423 ; python_version >= "3.8" and python_version < "3.13"