diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 23bbb7c25683..903a976722c6 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -11,9 +11,9 @@ babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13" backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < "3.9" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" -black==24.1.1 ; python_version >= "3.8" and python_version < "3.13" +black==24.3.0 ; python_version >= "3.8" and python_version < "3.13" build==1.1.1 ; python_version >= "3.8" and python_version < "3.13" -cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13" +cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" @@ -25,20 +25,22 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.13" codespell==2.2.6 ; 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]==7.4.3 ; python_version >= "3.8" and python_version < "3.13" +coverage[toml]==7.4.4 ; python_version >= "3.8" and python_version < "3.13" cryptography==42.0.5 ; python_version >= "3.8" and python_version < "3.13" cwltest==2.5.20240304113812 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" -darker==1.7.3 ; python_version >= "3.8" and python_version < "3.13" +darker==2.0.0 ; python_version >= "3.8" and python_version < "3.13" +darkgraylib==1.0.0 ; python_version >= "3.8" and python_version < "3.13" 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==0.18.1 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13" -fonttools==4.49.0 ; python_version >= "3.8" and python_version < "3.13" +fonttools==4.50.0 ; 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==0.1.7 ; python_version >= "3.8" and python_version < "3.13" +graylint==1.0.0 ; python_version >= "3.8" and python_version < "3.13" greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" httpcore==1.0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -46,7 +48,7 @@ httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.6 ; python_version >= "3.8" and python_version < "3.13" imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13" -importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.10" +importlib-resources==6.3.0 ; 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" isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13" @@ -66,7 +68,7 @@ matplotlib==3.8.3 ; python_version >= "3.9" and python_version < "3.13" mdit-py-plugins==0.4.0 ; 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==2.0.5 ; 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" 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" @@ -108,9 +110,9 @@ 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==3.12.0 ; python_version >= "3.8" and python_version < "3.13" pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13" -pytest-postgresql==5.1.1 ; 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==8.1.1 ; 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==2.0.0 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -126,13 +128,13 @@ 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" 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" -schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.12.0 ; python_version >= "3.9" and python_version < "3.13" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" selenium==4.18.1 ; python_version >= "3.8" and python_version < "3.13" seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13" +setuptools==69.2.0 ; 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" @@ -168,4 +170,4 @@ werkzeug==3.0.1 ; 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" yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13" -zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.13" +zipp==3.18.1 ; 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 5535c679d0b5..284a3352dfbc 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.2.6 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.3.2 +ruff==0.3.3 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 003b60c29a0b..a00ae0048ac9 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,6 +1,6 @@ ---extra-index-url https://wheels.galaxyproject.org/simple +--index-url https://wheels.galaxyproject.org/simple -a2wsgi==1.10.2 ; python_version >= "3.8" and python_version < "3.13" +a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" aiobotocore==2.12.1 ; python_version >= "3.8" and python_version < "3.13" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -13,7 +13,7 @@ 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==0.6.0 ; python_version >= "3.8" and python_version < "3.13" anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13" -apispec==6.5.0 ; python_version >= "3.8" and python_version < "3.13" +apispec==6.6.0 ; 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==3.2.3 ; python_version >= "3.8" and python_version < "3.13" @@ -26,7 +26,7 @@ backports-zoneinfo[tzdata]==0.2.1 ; python_version >= "3.8" and python_version < bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.13" bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.13" bcrypt==4.1.2 ; python_version >= "3.8" and python_version < "3.13" -bdbag==1.7.1 ; python_version >= "3.8" and python_version < "3.13" +bdbag==1.7.2 ; python_version >= "3.8" and python_version < "3.13" beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.13" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -35,7 +35,7 @@ boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.13" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13" botocore==1.34.51 ; 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]==0.13.1 ; python_version >= "3.8" and python_version < "3.13" +cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" @@ -88,9 +88,9 @@ h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13" humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.6 ; python_version >= "3.8" and python_version < "3.13" importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13" -importlib-resources==6.1.3 ; python_version >= "3.8" and python_version < "3.9" +importlib-resources==6.3.0 ; python_version >= "3.8" and python_version < "3.9" isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13" -isal==1.6.0 ; 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==3.1.3 ; python_version >= "3.8" and python_version < "3.13" jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" @@ -102,11 +102,11 @@ 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" mako==1.3.2 ; 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==3.5.2 ; 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==6.6.3 ; python_version >= "3.8" and python_version < "3.13" -mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13" +mercurial==6.7 ; 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==1.27.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.8 ; python_version >= "3.8" and python_version < "3.13" @@ -134,10 +134,10 @@ psutil==5.9.8 ; 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==2.21 ; python_version >= "3.8" and python_version < "3.13" pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.16.3 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.5.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.6.4 ; python_version >= "3.8" and python_version < "3.13" +pydantic[email]==2.6.4 ; 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" @@ -162,7 +162,7 @@ referencing==0.33.0 ; python_version >= "3.8" and python_version < "3.13" refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13" regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.13" repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13" -requests-oauthlib==1.3.1 ; python_version >= "3.8" and python_version < "3.13" +requests-oauthlib==1.4.0 ; python_version >= "3.8" and python_version < "3.13" requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13" requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13" @@ -173,9 +173,9 @@ rpds-py==0.18.0 ; 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==2023.12.2 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.1.1 ; python_version >= "3.8" and python_version < "3.13" +setuptools==69.2.0 ; 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" @@ -203,7 +203,7 @@ 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==0.7.0 ; python_version >= "3.8" and python_version < "3.13" urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" -uvicorn==0.27.1 ; python_version >= "3.8" and python_version < "3.13" +uvicorn==0.28.0 ; 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" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" @@ -213,6 +213,6 @@ whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" 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==3.17.0 ; python_version >= "3.8" and python_version < "3.13" +zipp==3.18.1 ; 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" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 877c102c0d28..88f0ebb61754 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -5,21 +5,21 @@ lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" mypy==1.9.0 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" -pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.16.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.6.4 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" -types-bleach==6.1.0.20240222 ; python_version >= "3.8" and python_version < "3.13" +types-bleach==6.1.0.20240311 ; 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==0.20.0.20240310 ; python_version >= "3.8" and python_version < "3.13" +types-docutils==0.20.0.20240316 ; 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==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13" -types-paramiko==3.4.0.20240205 ; 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==3.4.0.20240311 ; python_version >= "3.8" and python_version < "3.13" types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13" -types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13" -types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.13" +types-python-dateutil==2.9.0.20240316 ; python_version >= "3.8" and python_version < "3.13" +types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.13" types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13" -types-six==1.16.21.20240310 ; python_version >= "3.8" and python_version < "3.13" +types-six==1.16.21.20240311 ; 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==4.10.0 ; python_version >= "3.8" and python_version < "3.13"