diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index b55d2289c810..dbb54daf77ee 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -7,11 +7,11 @@ ase==3.22.1 ; python_version >= "3.8" and python_version < "3.12" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.12" axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.12" -babel==2.13.1 ; python_version >= "3.8" and python_version < "3.12" +babel==2.14.0 ; python_version >= "3.8" and python_version < "3.12" 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 < "3.12" -black==23.11.0 ; python_version >= "3.8" and python_version < "3.12" +black==23.12.0 ; python_version >= "3.8" and python_version < "3.12" build==1.0.3 ; python_version >= "3.8" and python_version < "3.12" cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12" @@ -25,7 +25,7 @@ click==8.1.7 ; python_version >= "3.8" and python_version < "3.12" codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.12" -coverage[toml]==7.3.2 ; python_version >= "3.8" and python_version < "3.12" +coverage[toml]==7.3.3 ; python_version >= "3.8" and python_version < "3.12" cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" cwltest==2.4.20231031143732 ; python_version >= "3.8" and python_version < "3.12" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.12" @@ -37,7 +37,7 @@ exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12" fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.12" fonttools==4.46.0 ; python_version >= "3.8" and python_version < "3.12" -frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12" +frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.12" galaxy-release-util==0.1.5 ; python_version >= "3.8" and python_version < "3.12" greenlet==3.0.1 ; python_version >= "3.8" and python_version < "3.12" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.12" @@ -49,7 +49,7 @@ importlib-metadata==7.0.0 ; python_version >= "3.8" and python_version < "3.12" importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10" iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.12" isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.12" -isort==5.12.0 ; python_version >= "3.8" and python_version < "3.12" +isort==5.13.2 ; python_version >= "3.8" and python_version < "3.12" jaraco-classes==3.3.0 ; python_version >= "3.8" and python_version < "3.12" jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "linux" jinja2==3.1.2 ; python_version >= "3.8" and python_version < "3.12" @@ -77,7 +77,7 @@ numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12" outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.12" packaging==23.2 ; python_version >= "3.8" and python_version < "3.12" -pathspec==0.11.2 ; python_version >= "3.8" and python_version < "3.12" +pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.12" pillow==10.1.0 ; python_version >= "3.8" and python_version < "3.12" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.12" pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.12" @@ -86,9 +86,9 @@ playwright==1.40.0 ; python_version >= "3.8" and python_version < "3.12" pluggy==1.3.0 ; python_version >= "3.8" and python_version < "3.12" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.12" prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.12" -prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12" +prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.12" psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.12" and sys_platform != "cygwin" -psycopg==3.1.14 ; python_version >= "3.8" and python_version < "3.12" +psycopg==3.1.15 ; python_version >= "3.8" and python_version < "3.12" pycparser==2.21 ; python_version >= "3.8" and python_version < "3.12" pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.12" pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.12" @@ -153,11 +153,11 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12" toml==0.10.2 ; python_version >= "3.8" and python_version < "3.12" 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 < "3.12" -trio==0.23.1 ; python_version >= "3.8" and python_version < "3.12" -tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12" +trio==0.23.2 ; python_version >= "3.8" and python_version < "3.12" +tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.12" twill==3.2.1 ; python_version >= "3.8" and python_version < "3.12" twine==4.0.2 ; python_version >= "3.8" and python_version < "3.12" -typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12" tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12" urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.12" urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 18619fe4d38f..dd4935ec9879 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==23.12.2 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.1.0 -ruff==0.1.7 +ruff==0.1.8 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index b262a3faf2cc..c6d9afcf6ab9 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,6 +1,6 @@ a2wsgi==1.9.0 ; python_version >= "3.8" and python_version < "3.12" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.12" -aiobotocore==2.8.0 ; python_version >= "3.8" and python_version < "3.12" +aiobotocore==2.9.0 ; python_version >= "3.8" and python_version < "3.12" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.12" aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.12" aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.12" @@ -13,16 +13,16 @@ anyio==4.1.0 ; python_version >= "3.8" and python_version < "3.12" apispec==6.3.0 ; python_version >= "3.8" and python_version < "3.12" appdirs==1.4.4 ; python_version >= "3.8" and python_version < "3.12" arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.12" -argcomplete==3.1.6 ; python_version >= "3.8" and python_version < "3.12" +argcomplete==3.2.1 ; python_version >= "3.8" and python_version < "3.12" 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 < "3.12" attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.12" -babel==2.13.1 ; python_version >= "3.8" and python_version < "3.12" +babel==2.14.0 ; python_version >= "3.8" and python_version < "3.12" 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" bagit-profile==1.3.1 ; python_version >= "3.8" and python_version < "3.12" bagit==1.8.1 ; python_version >= "3.8" and python_version < "3.12" -bcrypt==4.1.1 ; python_version >= "3.8" and python_version < "3.12" +bcrypt==4.1.2 ; python_version >= "3.8" and python_version < "3.12" bdbag==1.7.1 ; python_version >= "3.8" and python_version < "3.12" beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.12" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.12" @@ -30,7 +30,7 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.12" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.12" boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.12" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.12" -botocore==1.33.1 ; python_version >= "3.8" and python_version < "3.12" +botocore==1.33.13 ; python_version >= "3.8" and python_version < "3.12" bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.12" cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.12" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.12" @@ -49,7 +49,7 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and platfo coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.12" conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.12" cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" -cwl-upgrader==1.2.10 ; python_version >= "3.8" and python_version < "3.12" +cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.12" cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.12" cwltool==3.1.20231207110929 ; python_version >= "3.8" and python_version < "3.12" decorator==5.1.1 ; python_version >= "3.8" and python_version < "3.12" @@ -67,9 +67,9 @@ exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" fastapi-utils==0.2.1 ; python_version >= "3.8" and python_version < "3.12" fastapi==0.98.0 ; python_version >= "3.8" and python_version < "3.12" filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.12" -frozenlist==1.4.0 ; python_version >= "3.8" and python_version < "3.12" +frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.12" fs==2.4.16 ; python_version >= "3.8" and python_version < "3.12" -fsspec==2023.12.1 ; python_version >= "3.8" and python_version < "3.12" +fsspec==2023.12.2 ; python_version >= "3.8" and python_version < "3.12" future==0.18.3 ; python_version >= "3.8" and python_version < "3.12" galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.12" galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.12" @@ -125,7 +125,7 @@ pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.12" pebble==5.0.5 ; python_version >= "3.8" and python_version < "3.12" pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9" promise==2.3 ; python_version >= "3.8" and python_version < "3.12" -prompt-toolkit==3.0.41 ; python_version >= "3.8" and python_version < "3.12" +prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.12" prov==1.5.1 ; python_version >= "3.8" and python_version < "3.12" psutil==5.9.6 ; python_version >= "3.8" and python_version < "3.12" pulsar-galaxy-lib==0.15.5 ; python_version >= "3.8" and python_version < "3.12" @@ -171,7 +171,7 @@ rpds-py==0.13.2 ; python_version >= "3.8" and python_version < "3.12" rsa==4.9 ; python_version >= "3.8" and python_version < "3.12" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8" ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12" -s3fs==2023.12.1 ; python_version >= "3.8" and python_version < "3.12" +s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.12" schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.12" setuptools==69.0.2 ; python_version >= "3.8" and python_version < "3.12" @@ -180,7 +180,7 @@ six==1.16.0 ; python_version >= "3.8" and python_version < "3.12" sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.12" social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.12" sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12" -spython==0.3.11 ; python_version >= "3.8" and python_version < "3.12" +spython==0.3.13 ; python_version >= "3.8" and python_version < "3.12" sqlalchemy==1.4.50 ; python_version >= "3.8" and python_version < "3.12" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.12" sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.12" @@ -195,9 +195,9 @@ tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.12" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" tornado==6.4 ; python_version >= "3.8" and python_version < "3.12" tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.12" -tuspy==1.0.2 ; python_version >= "3.8" and python_version < "3.12" +tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.12" tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.12" -typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12" tzdata==2023.3 ; python_version >= "3.8" and python_version < "3.12" tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.12" ubiquerg==0.6.3 ; python_version >= "3.8" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 83876770d945..dc6b6e08fbcc 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -18,4 +18,4 @@ types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.12" types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.12" types-six==1.16.21.9 ; python_version >= "3.8" and python_version < "3.12" types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.12" -typing-extensions==4.8.0 ; python_version >= "3.8" and python_version < "3.12" +typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12"