From f2d62b031cd6dea6cb6602f08bd4ac74bb91c458 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 7 Sep 2024 03:45:13 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 118 +++++++++--------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 117 ++++++++--------- .../pinned-typecheck-requirements.txt | 37 +++--- 4 files changed, 138 insertions(+), 136 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 8e9d0db4f533..ab59d963c4f5 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,32 +1,31 @@ ---extra-index-url https://wheels.galaxyproject.org/simple - -aiohttp==3.9.5 ; python_version >= "3.8" and python_version < "3.13" +aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.10.5 ; 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" anyio==4.4.0 ; python_version >= "3.8" and python_version < "3.13" ase==3.23.0 ; python_version >= "3.8" and python_version < "3.13" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" -attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.13" +attrs==24.2.0 ; python_version >= "3.8" and python_version < "3.13" axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.13" -babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13" +babel==2.16.0 ; 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==1.34.131 ; 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" +black==24.8.0 ; python_version >= "3.8" and python_version < "3.13" +boto3==1.35.7 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.35.7 ; python_version >= "3.8" and python_version < "3.13" +build==1.2.2 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" -certifi==2024.7.4 ; python_version >= "3.8" and python_version < "3.13" -cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" +certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13" +cffi==1.17.1 ; 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" 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]==7.6.0 ; 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" +contourpy==1.3.0 ; python_version >= "3.9" and python_version < "3.13" +coverage[toml]==7.6.1 ; python_version >= "3.8" and python_version < "3.13" +cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13" +cwltest==2.5.20240714110256 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" darker==2.1.1 ; python_version >= "3.8" and python_version < "3.13" darkgraylib==1.2.1 ; python_version >= "3.8" and python_version < "3.13" @@ -34,7 +33,7 @@ decorator==5.1.1 ; python_version >= "3.9" 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==0.20.1 ; python_version >= "3.8" and python_version < "3.13" -dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13" +dogpile-cache==1.3.3 ; python_version >= "3.9" and python_version < "3.13" 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" @@ -45,85 +44,86 @@ graylint==1.1.1 ; 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==1.0.5 ; 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" +httpx==0.27.2 ; python_version >= "3.8" and python_version < "3.13" +idna==3.8 ; python_version >= "3.8" and python_version < "3.13" imagesize==1.4.1 ; 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" +importlib-metadata==8.4.0 ; python_version >= "3.8" and python_version < "3.13" +importlib-resources==6.4.4 ; 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" jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13" -jaraco-context==5.3.0 ; python_version >= "3.8" and python_version < "3.13" -jaraco-functools==4.0.1 ; python_version >= "3.8" and python_version < "3.13" +jaraco-context==6.0.1 ; python_version >= "3.8" and python_version < "3.13" +jaraco-functools==4.0.2 ; python_version >= "3.8" and python_version < "3.13" jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" jinja2==3.1.4 ; python_version >= "3.8" and python_version < "3.13" jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" jsonschema-specifications==2023.12.1 ; python_version >= "3.9" and python_version < "3.13" -jsonschema==4.20.0 ; python_version >= "3.9" and python_version < "3.13" +jsonschema==4.23.0 ; 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==5.2.2 ; python_version >= "3.8" and python_version < "3.13" +keyring==25.3.0 ; python_version >= "3.8" and python_version < "3.13" +kiwisolver==1.4.7 ; python_version >= "3.8" and python_version < "3.13" +lxml==5.3.0 ; 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" matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9" -matplotlib==3.9.1 ; python_version >= "3.9" and python_version < "3.13" +matplotlib==3.9.2 ; 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" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" -more-itertools==10.3.0 ; python_version >= "3.8" and python_version < "3.13" +more-itertools==10.5.0 ; 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==0.2.18 ; 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" +numpy==2.0.2 ; python_version >= "3.9" and python_version < "3.10" +numpy==2.1.1 ; python_version >= "3.10" and python_version < "3.13" onedatafilerestclient==21.2.5.2 ; python_version >= "3.8" and python_version < "3.13" outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13" packaging==24.1 ; 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" +pbr==6.1.0 ; python_version >= "3.9" and python_version < "3.13" pillow==10.4.0 ; python_version >= "3.8" and python_version < "3.13" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13" pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13" platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13" -playwright==1.45.0 ; python_version >= "3.8" and python_version < "3.13" +playwright==1.46.0 ; 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==3.10.2 ; python_version >= "3.8" and python_version < "3.13" +port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13" +prettytable==3.11.0 ; 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" pyee==11.1.0 ; python_version >= "3.8" and python_version < "3.13" -pygithub==2.3.0 ; python_version >= "3.8" and python_version < "3.13" +pygithub==2.4.0 ; python_version >= "3.8" and python_version < "3.13" pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13" -pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" +pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13" pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13" +pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13" pyproject-hooks==1.1.0 ; python_version >= "3.8" and python_version < "3.13" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13" -pytest-asyncio==0.23.7 ; python_version >= "3.8" and python_version < "3.13" +pytest-asyncio==0.24.0 ; 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-cov==5.0.0 ; 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==1.0.10 ; python_version >= "3.8" and python_version < "3.13" +pytest-httpserver==1.1.0 ; 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==3.1.1 ; python_version >= "3.8" and python_version < "3.13" pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" -pytest-playwright==0.5.1 ; python_version >= "3.8" and python_version < "3.13" -pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13" +pytest-playwright==0.5.2 ; python_version >= "3.8" and python_version < "3.13" +pytest-postgresql==6.1.1 ; 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==8.3.2 ; 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==2.0.1 ; python_version >= "3.8" and python_version < "3.13" +python-irodsclient==2.1.0 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; 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" +pywin32-ctypes==0.2.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" +pyyaml==6.0.2 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" 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" @@ -131,20 +131,20 @@ 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==0.25.3 ; 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==0.19.0 ; python_version >= "3.9" and python_version < "3.13" +rich==13.8.0 ; python_version >= "3.8" and python_version < "3.13" +rpds-py==0.20.0 ; 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" +rucio-clients==35.2.1 ; python_version >= "3.9" and python_version < "3.13" s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.7.20240905150001 ; 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" +scipy==1.14.1 ; 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" +selenium==4.24.0 ; python_version >= "3.8" and python_version < "3.13" seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==74.1.2 ; 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" @@ -159,7 +159,7 @@ sphinxcontrib-jsmath==1.0.1 ; python_version >= "3.8" and python_version < "3.13 sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.8" and python_version < "3.13" sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.8" and python_version < "3.13" statsd==4.0.1 ; python_version >= "3.8" and python_version < "3.13" -stevedore==5.2.0 ; python_version >= "3.9" and python_version < "3.13" +stevedore==5.3.0 ; python_version >= "3.9" and python_version < "3.13" tabulate==0.9.0 ; python_version >= "3.9" and python_version < "3.13" testfixtures==8.3.0 ; python_version >= "3.8" and python_version < "3.13" text-unidecode==1.3 ; python_version >= "3.8" and python_version < "3.13" @@ -167,19 +167,19 @@ 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==0.26.0 ; python_version >= "3.8" and python_version < "3.13" +trio==0.26.2 ; 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" 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==1.26.19 ; 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" +urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13" +urllib3[socks]==1.26.20 ; python_version >= "3.8" and python_version < "3.13" +watchdog==4.0.2 ; 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" +werkzeug==3.0.4 ; 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==3.19.2 ; python_version >= "3.8" and python_version < "3.13" +yarl==1.10.0 ; python_version >= "3.8" and python_version < "3.13" +zipp==3.20.1 ; 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 c043874bc5bc..d8b3ed8f0e2a 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.8.19 mccabe==0.7.0 pycodestyle==2.12.1 pyflakes==3.2.0 -ruff==0.6.3 +ruff==0.6.4 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 9e022cbeb8d7..a6288cba9e49 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,12 +1,13 @@ --extra-index-url https://wheels.galaxyproject.org/simple -a2wsgi==1.10.6 ; python_version >= "3.8" and python_version < "3.13" +a2wsgi==1.10.7 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.13.1 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.14.0 ; python_version >= "3.8" and python_version < "3.13" aiodataloader==0.4.0 ; 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" +aiohappyeyeballs==2.4.0 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.10.5 ; python_version >= "3.8" and python_version < "3.13" +aioitertools==0.12.0 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alembic==1.13.2 ; python_version >= "3.8" and python_version < "3.13" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -16,16 +17,16 @@ 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==3.4.0 ; python_version >= "3.8" and python_version < "3.13" +argcomplete==3.5.0 ; 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" -babel==2.15.0 ; python_version >= "3.8" and python_version < "3.13" +attrs==24.2.0 ; python_version >= "3.8" and python_version < "3.13" +babel==2.16.0 ; 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" 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==4.1.3 ; python_version >= "3.8" and python_version < "3.13" +bcrypt==4.2.0 ; python_version >= "3.8" and python_version < "3.13" bdbag==1.7.3 ; python_version >= "3.8" and python_version < "3.13" beaker==1.13.0 ; python_version >= "3.8" and python_version < "3.13" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -33,12 +34,12 @@ 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==1.34.131 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.35.7 ; 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==2024.7.4 ; python_version >= "3.8" and python_version < "3.13" -cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" +certifi==2024.8.30 ; python_version >= "3.8" and python_version < "3.13" +cffi==1.17.1 ; 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" circus==0.18.0 ; python_version >= "3.8" and python_version < "3.13" @@ -51,7 +52,7 @@ 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==0.10.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.8 ; python_version >= "3.8" and python_version < "3.13" +cryptography==43.0.1 ; 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==3.1.20240708091337 ; python_version >= "3.8" and python_version < "3.13" @@ -65,66 +66,68 @@ 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==1.2.2 ; python_version >= "3.8" and python_version < "3.11" -fastapi-slim==0.111.0 ; python_version >= "3.8" and python_version < "3.13" +fastapi-slim==0.114.0 ; 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==2024.6.1 ; python_version >= "3.8" and python_version < "3.13" +fsspec==2024.9.0 ; 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" graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13" 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-core==3.2.4 ; 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 < "3.13" 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" +gunicorn==23.0.0 ; python_version >= "3.8" and python_version < "3.13" gxformat2==0.20.0 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" 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==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" +idna==3.8 ; python_version >= "3.8" and python_version < "3.13" +importlib-metadata==8.4.0 ; python_version >= "3.8" and python_version < "3.13" +importlib-resources==6.4.4 ; python_version >= "3.8" and python_version < "3.9" 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" +isal==1.7.0 ; 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" jmespath==1.0.1 ; python_version >= "3.8" and python_version < "3.13" jsonref==1.1.0 ; python_version >= "3.8" and python_version < "3.13" jsonschema-specifications==2023.12.1 ; python_version >= "3.8" and python_version < "3.13" -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" +jsonschema==4.23.0 ; python_version >= "3.8" and python_version < "3.13" +kombu==5.4.0 ; python_version >= "3.8" and python_version < "3.13" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" -lxml==5.2.2 ; python_version >= "3.8" and python_version < "3.13" +lxml==5.3.0 ; 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" +markdown==3.7 ; 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==6.8.1 ; python_version >= "3.8" and python_version < "3.13" mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13" -mrcfile==1.5.1 ; python_version >= "3.8" and python_version < "3.13" -msal==1.29.0 ; python_version >= "3.8" and python_version < "3.13" +mrcfile==1.5.3 ; python_version >= "3.8" and python_version < "3.13" +msal==1.31.0 ; 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==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==2.0.0 ; python_version >= "3.9" and python_version < "3.13" +numpy==2.0.2 ; python_version >= "3.9" and python_version < "3.10" +numpy==2.1.1 ; python_version >= "3.10" and python_version < "3.13" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" -orjson==3.10.6 ; python_version >= "3.8" and python_version < "3.13" +orjson==3.10.7 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; 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" +paramiko==3.4.1 ; 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" 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==10.4.0 ; python_version >= "3.8" and python_version < "3.13" +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 < "3.13" 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" @@ -132,20 +135,20 @@ 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==2.20.1 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.23.2 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.8.2 ; 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" +pydantic==2.9.0 ; python_version >= "3.8" and python_version < "3.13" +pydantic[email]==2.9.0 ; python_version >= "3.8" and python_version < "3.13" +pydot==3.0.1 ; 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" +pyfaidx==0.8.1.2 ; python_version >= "3.8" and python_version < "3.13" pygments==2.18.0 ; python_version >= "3.8" and python_version < "3.13" -pyjwt==2.8.0 ; python_version >= "3.8" and python_version < "3.13" -pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" +pyjwt==2.9.0 ; python_version >= "3.8" and python_version < "3.13" +pyjwt[crypto]==2.9.0 ; python_version >= "3.8" and python_version < "3.13" pykwalify==1.8.0 ; python_version >= "3.8" and python_version < "3.13" pylibmagic==0.5.0 ; python_version >= "3.8" and python_version < "3.13" pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -pyparsing==3.1.2 ; python_version >= "3.8" and python_version < "3.13" +pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13" pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.13" pysam==0.22.1 ; python_version >= "3.8" and python_version < "3.13" python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13" @@ -153,64 +156,64 @@ python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13" python-multipart==0.0.9 ; python_version >= "3.8" and python_version < "3.13" python3-openid==3.2.0 ; 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==26.0.3 ; python_version >= "3.8" and python_version < "3.13" +pyyaml==6.0.2 ; python_version >= "3.8" and python_version < "3.13" +pyzmq==26.2.0 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" referencing==0.35.1 ; python_version >= "3.8" and python_version < "3.13" refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13" -regex==2024.5.15 ; python_version >= "3.8" and python_version < "3.13" +regex==2024.7.24 ; python_version >= "3.8" and python_version < "3.13" repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13" requests-oauthlib==2.0.0 ; 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==2.32.3 ; python_version >= "3.8" and python_version < "3.13" -rich==13.7.1 ; python_version >= "3.8" and python_version < "3.13" +rich==13.8.0 ; 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==0.19.0 ; python_version >= "3.8" and python_version < "3.13" +rpds-py==0.20.0 ; 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==8.6.20240710082410 ; python_version >= "3.8" and python_version < "3.13" +s3fs==2024.9.0 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==70.3.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==74.1.2 ; 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==2.0.31 ; python_version >= "3.8" and python_version < "3.13" +sqlalchemy==2.0.34 ; 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" +sqlparse==0.5.1 ; python_version >= "3.8" and python_version < "3.13" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.13" 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" +starlette==0.38.4 ; 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==8.5.0 ; python_version >= "3.8" and python_version < "3.13" +tenacity==9.0.0 ; 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" tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13" -tqdm==4.66.4 ; python_version >= "3.8" and python_version < "3.13" +tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" tuswsgi==0.5.5 ; 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" 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==1.26.19 ; 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" +urllib3==1.26.20 ; python_version >= "3.8" and python_version < "3.13" +uvicorn==0.30.6 ; python_version >= "3.8" and python_version < "3.13" +uvloop==0.20.0 ; 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" 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" +webob==1.8.8 ; 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==0.9.3 ; python_version >= "3.8" and python_version < "3.13" -yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13" -zipp==3.19.2 ; python_version >= "3.8" and python_version < "3.13" +yarl==1.10.0 ; python_version >= "3.8" and python_version < "3.13" +zipp==3.20.1 ; 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" +zstandard==0.23.0 ; 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 45c2ad37343e..1eed62f5e754 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,32 +1,31 @@ ---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]==1.34.144 ; 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" +boto3-stubs[s3]==1.35.14 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.35.14 ; python_version >= "3.8" and python_version < "3.13" +cffi==1.17.1 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" +cryptography==43.0.1 ; 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==1.34.138 ; python_version >= "3.8" and python_version < "3.13" +mypy-boto3-s3==1.35.2 ; 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" +mypy==1.11.2 ; 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==2.20.1 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.8.2 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.23.2 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.9.0 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" -types-awscrt==0.21.0 ; python_version >= "3.8" and python_version < "3.13" +types-awscrt==0.21.5 ; 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-boto==2.49.18.20240806 ; 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==0.21.0.20240711 ; 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-docutils==0.21.0.20240907 ; python_version >= "3.8" and python_version < "3.13" +types-html5lib==1.1.11.20240806 ; python_version >= "3.8" and python_version < "3.13" +types-markdown==3.7.0.20240822 ; python_version >= "3.8" and python_version < "3.13" types-paramiko==3.4.0.20240423 ; 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-python-dateutil==2.9.0.20240906 ; python_version >= "3.8" and python_version < "3.13" +types-pyyaml==6.0.12.20240808 ; 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-s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13" -types-setuptools==71.1.0.20240813 ; python_version >= "3.8" and python_version < "3.13" +types-s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13" +types-setuptools==74.1.0.20240907 ; python_version >= "3.8" and python_version < "3.13" types-six==1.16.21.20240513 ; 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==4.12.2 ; python_version >= "3.8" and python_version < "3.13" +tzdata==2024.1 ; python_version >= "3.9" and python_version < "3.13"