diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 3c1bb12a5eb7..42c4972769fb 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,4 +1,4 @@ -aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.9.3 ; 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" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -15,7 +15,7 @@ black==24.1.1 ; python_version >= "3.8" and python_version < "3.13" build==1.0.3 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" -certifi==2023.11.17 ; 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" charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" click-didyoumean==0.3.0 ; python_version >= "3.8" and python_version < "3.13" @@ -26,8 +26,8 @@ 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]==7.4.1 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13" -cwltest==2.4.20231222081524 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13" +cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" @@ -60,7 +60,7 @@ kombu==5.3.5 ; python_version >= "3.8" and python_version < "3.13" lxml==4.9.4 ; 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==2.1.4 ; python_version >= "3.8" and python_version < "3.13" +markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" matplotlib==3.7.4 ; python_version >= "3.8" and python_version < "3.9" matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13" mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -69,7 +69,7 @@ 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" more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13" -multidict==6.0.4 ; 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==2.0.0 ; python_version >= "3.8" and python_version < "3.13" nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.13" @@ -81,7 +81,7 @@ pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13" pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13" pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.13" -platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.13" +platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13" playwright==1.41.1 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13" @@ -91,7 +91,7 @@ psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_plat psycopg==3.1.17 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.13" -pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.13" +pygithub==2.2.0 ; python_version >= "3.8" and python_version < "3.13" pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13" pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" @@ -99,22 +99,22 @@ pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13" pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13" pytest-asyncio==0.23.3 ; python_version >= "3.8" and python_version < "3.13" -pytest-base-url==2.0.0 ; 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-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-cov==4.1.0 ; 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==1.0.8 ; 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==3.0.0 ; python_version >= "3.8" and python_version < "3.13" +pytest-metadata==3.1.0 ; 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==0.4.3 ; python_version >= "3.8" and python_version < "3.13" -pytest-postgresql==5.0.0 ; 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==5.1.0 ; 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==8.0.0 ; python_version >= "3.8" and python_version < "3.13" python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.13" python-irodsclient==1.1.9 ; python_version >= "3.8" and python_version < "3.13" -python-slugify==8.0.2 ; python_version >= "3.8" and python_version < "3.13" -pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.9" +python-slugify==8.0.3 ; python_version >= "3.8" and python_version < "3.13" +pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9" pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" @@ -155,7 +155,7 @@ 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==0.24.0 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" -twill==3.2.1 ; python_version >= "3.8" and python_version < "3.13" +twill==3.2.2 ; python_version >= "3.8" and python_version < "3.13" twine==4.0.2 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13" tzdata==2023.4 ; 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 021b153d7ad0..4dac7901b84e 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.1.17 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.1.14 +ruff==0.2.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index c8cc90525a98..712d923e46e0 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,9 +1,9 @@ a2wsgi==1.10.0 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.11.1 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.11.2 ; 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" -aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.9.3 ; 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" @@ -31,11 +31,11 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13" 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==1.34.27 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.34 ; python_version >= "3.8" and python_version < "3.13" bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" -certifi==2023.11.17 ; 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" 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" @@ -49,7 +49,7 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13" conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.2 ; 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==0.32 ; python_version >= "3.8" and python_version < "3.13" cwltool==3.1.20240112164112 ; python_version >= "3.8" and python_version < "3.13" @@ -99,17 +99,17 @@ jsonschema==4.21.1 ; python_version >= "3.8" and python_version < "3.13" kombu==5.3.5 ; 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" -mako==1.3.0 ; 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" -markupsafe==2.1.4 ; 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==6.6.2 ; python_version >= "3.8" and python_version < "3.13" mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13" mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13" msal==1.26.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13" -multidict==6.0.4 ; 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" nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13" @@ -133,10 +133,10 @@ pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" pyasn1==0.5.1 ; 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==2.16.1 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.5.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.6.0 ; python_version >= "3.8" and python_version < "3.13" +pydantic[email]==2.6.0 ; 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" @@ -154,11 +154,11 @@ python-jose==3.3.0 ; python_version >= "3.8" and python_version < "3.13" python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13" python-multipart==0.0.6 ; python_version >= "3.8" and python_version < "3.13" python3-openid==3.2.0 ; python_version >= "3.8" and python_version < "3.13" -pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.13" +pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13" pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" -referencing==0.32.1 ; python_version >= "3.8" and python_version < "3.13" +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" @@ -202,9 +202,9 @@ tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13" tzdata==2023.4 ; python_version >= "3.8" and python_version < "3.13" tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13" -ubiquerg==0.6.3 ; 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==0.27.0 ; python_version >= "3.8" and python_version < "3.13" +uvicorn==0.27.0.post1 ; 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" @@ -212,7 +212,7 @@ webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13" webob==1.8.7 ; python_version >= "3.8" and python_version < "3.13" 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==0.9.2 ; 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" zipstream-new==1.1.8 ; 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 9ae55e92df48..2649355d9e78 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,19 +1,19 @@ annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13" -cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.1 ; 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==42.0.2 ; python_version >= "3.8" and python_version < "3.13" 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==1.8.0 ; 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==2.16.1 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.6.0 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.13" types-boto==2.49.18.9 ; 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==0.20.0.20240126 ; python_version >= "3.8" and python_version < "3.13" -types-markdown==3.5.0.20240106 ; python_version >= "3.8" and python_version < "3.13" +types-docutils==0.20.0.20240201 ; 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==3.4.0.20240120 ; 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"