diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 37cfc753bfd8..7d9fb313856b 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,3 +1,5 @@ +--extra-index-url https://wheels.galaxyproject.org/simple + aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13" @@ -10,8 +12,8 @@ babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13" backports-tarfile==1.2.0 ; python_version >= "3.8" and python_version < "3.12" backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" black==24.4.2 ; python_version >= "3.8" and python_version < "3.13" -boto3==1.34.106 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13" +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" @@ -20,8 +22,9 @@ 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" 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 < "3.13" -coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13" +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" 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" @@ -33,7 +36,7 @@ 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" -filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" +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" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" @@ -45,7 +48,7 @@ httpcore==1.0.5 ; python_version >= "3.8" and python_version < "3.13" httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.7 ; python_version >= "3.8" and python_version < "3.13" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13" -importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13" +importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.10" iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" @@ -61,7 +64,7 @@ jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13" junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13" keyring==25.2.1 ; python_version >= "3.8" and python_version < "3.13" kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13" -lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" +lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13" 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" @@ -71,28 +74,28 @@ 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" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" -more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13" +more-itertools==10.3.0 ; 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" 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" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" +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" outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13" -packaging==24.0 ; python_version >= "3.8" and python_version < "3.13" +packaging==24.1 ; python_version >= "3.8" and python_version < "3.13" pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13" pbr==6.0.0 ; python_version >= "3.9" and python_version < "3.13" pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13" -pkginfo==1.11.1 ; python_version >= "3.8" and python_version < "3.13" +pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13" platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13" playwright==1.44.0 ; 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" -psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" +psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" psycopg==3.1.19 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13" @@ -126,21 +129,22 @@ readme-renderer==43.0 ; python_version >= "3.8" and python_version < "3.13" referencing==0.35.1 ; python_version >= "3.9" and python_version < "3.13" requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13" -responses==0.25.2 ; 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" 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==34.4.2 ; python_version >= "3.9" and python_version < "3.13" -s3transfer==0.10.1 ; 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" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" -scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.13" +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==4.21.0 ; python_version >= "3.8" and python_version < "3.13" +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==70.0.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.1.1 ; 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" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -165,14 +169,15 @@ 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" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" -twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13" -twine==5.1.0 ; 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" tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" -urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" -urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13" +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" watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" +websocket-client==1.8.0 ; python_version >= "3.8" and python_version < "3.13" werkzeug==3.0.3 ; python_version >= "3.8" and python_version < "3.13" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" wsproto==1.2.0 ; 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 9cd22f68931b..3df072eefc30 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,7 +1,7 @@ attrs==23.2.0 -flake8==7.0.0 +flake8==7.1.0 flake8-bugbear==24.4.26 mccabe==0.7.0 -pycodestyle==2.11.1 +pycodestyle==2.12.0 pyflakes==3.2.0 -ruff==0.4.8 +ruff==0.5.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index afe0a5f04880..30155db23840 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,14 +1,14 @@ --extra-index-url https://wheels.galaxyproject.org/simple -a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13" +a2wsgi==1.10.6 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.13.0 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.13.1 ; python_version >= "3.8" and python_version < "3.13" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13" -aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13" +aiofiles==24.1.0 ; python_version >= "3.8" and python_version < "3.13" aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13" aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" -alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13" +alembic==1.13.2 ; python_version >= "3.8" and python_version < "3.13" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13" annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" @@ -16,7 +16,7 @@ anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13" apispec==6.6.1 ; python_version >= "3.8" and python_version < "3.13" appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.13" arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.13" -argcomplete==3.3.0 ; python_version >= "3.8" and python_version < "3.13" +argcomplete==3.4.0 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.13" attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -33,7 +33,7 @@ bioblend==1.3.0 ; python_version >= "3.8" and python_version < "3.13" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13" boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.131 ; python_version >= "3.8" and python_version < "3.13" bx-python==0.11.0 ; 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" @@ -55,7 +55,6 @@ 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" -decorator==5.1.1 ; 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" @@ -64,13 +63,13 @@ docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13" 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==2.1.1 ; 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" fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13" -filelock==3.14.0 ; 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" fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13" -fsspec==2024.6.0 ; python_version >= "3.8" and python_version < "3.13" +fsspec==2024.6.1 ; python_version >= "3.8" and python_version < "3.13" future==1.0.0 ; python_version >= "3.8" and python_version < "3.13" galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13" galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13" @@ -79,7 +78,7 @@ graphene==3.3 ; python_version >= "3.8" and python_version < "3.13" graphql-core==3.2.3 ; python_version >= "3.8" and python_version < "3.13" graphql-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13" gravity==1.0.6 ; python_version >= "3.8" and python_version < "3.13" -greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") +greenlet==3.0.3 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.8" gunicorn==22.0.0 ; python_version >= "3.8" and python_version < "3.13" gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" @@ -87,9 +86,9 @@ h5grove==2.2.0 ; python_version >= "3.8" and python_version < "3.13" h5py==3.11.0 ; python_version >= "3.8" and python_version < "3.13" humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.7 ; python_version >= "3.8" and python_version < "3.13" -importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13" +importlib-metadata==8.0.0 ; python_version >= "3.8" and python_version < "3.13" importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9" -isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13" +isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@3d989181058d2765a93cb0e7ca85d6955e0eb6ef ; python_version >= "3.8" and python_version < "3.13" isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13" jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13" @@ -99,7 +98,7 @@ jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_versio jsonschema==4.20.0 ; python_version >= "3.8" and python_version < "3.13" kombu==5.3.7 ; python_version >= "3.8" and python_version < "3.13" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" -lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" +lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13" mako==1.3.5 ; python_version >= "3.8" and python_version < "3.13" 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" @@ -108,18 +107,18 @@ 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" 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" -msal==1.28.0 ; 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" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" -networkx==2.5 ; python_version >= "3.8" and python_version < "3.13" +networkx==3.1 ; python_version >= "3.8" and python_version < "3.13" nodeenv==1.9.1 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" +numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" -orjson==3.10.3 ; python_version >= "3.8" and python_version < "3.13" +orjson==3.10.5 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" -packaging==24.0 ; python_version >= "3.8" and python_version < "3.13" +packaging==24.1 ; python_version >= "3.8" and python_version < "3.13" paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13" parsley==1.3 ; python_version >= "3.8" and python_version < "3.13" paste==3.10.1 ; python_version >= "3.8" and python_version < "3.13" @@ -127,9 +126,9 @@ pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13" pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13" pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13" promise==2.3 ; python_version >= "3.8" and python_version < "3.13" -prompt-toolkit==3.0.46 ; python_version >= "3.8" and python_version < "3.13" +prompt-toolkit==3.0.47 ; python_version >= "3.8" and python_version < "3.13" prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13" -psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" +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" @@ -171,17 +170,17 @@ 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" 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==2024.6.0 ; 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" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.1.1 ; 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" social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13" 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==2.0.30 ; 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" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" @@ -189,7 +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==8.3.0 ; python_version >= "3.8" and python_version < "3.13" +tenacity==8.4.2 ; 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" @@ -201,7 +200,7 @@ typing-extensions==4.12.2 ; 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" -urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" +urllib3==1.26.19 ; python_version >= "3.8" and python_version < "3.13" uvicorn==0.30.1 ; python_version >= "3.8" and python_version < "3.13" uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13" vine==5.1.0 ; 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 4ea5a1375235..2286f6de6be0 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,17 +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]==1.34.122 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.34.122 ; python_version >= "3.8" and python_version < "3.13" +boto3-stubs[s3]==1.34.136 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.34.136 ; 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==1.34.120 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" -mypy==1.10.0 ; 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==2.18.4 ; python_version >= "3.8" and python_version < "3.13" pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" -types-awscrt==0.20.11 ; python_version >= "3.8" and python_version < "3.13" +types-awscrt==0.20.12 ; 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"