From e29b56689b483ed1ce82d7b7b06a6880d63e7104 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 12 Oct 2024 03:18:26 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 25 +++++++++--------- .../dependencies/pinned-requirements.txt | 26 +++++++++---------- .../pinned-typecheck-requirements.txt | 8 +++--- 3 files changed, 30 insertions(+), 29 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index d2596d1322af..7733cef921c0 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,7 +1,7 @@ --extra-index-url https://wheels.galaxyproject.org/simple aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13" -aiohttp==3.10.9 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.10.10 ; 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==4.5.0 ; python_version >= "3.8" and python_version < "3.13" @@ -13,13 +13,13 @@ 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==24.8.0 ; python_version >= "3.8" and python_version < "3.13" -boto3==1.35.23 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.35.23 ; python_version >= "3.8" and python_version < "3.13" -build==1.2.2 ; python_version >= "3.8" and python_version < "3.13" +boto3==1.35.36 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.35.36 ; python_version >= "3.8" and python_version < "3.13" +build==1.2.2.post1 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" certifi==2024.8.30 ; 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" +charset-normalizer==3.4.0 ; 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") @@ -83,7 +83,7 @@ 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==2.0.2 ; python_version >= "3.9" and python_version < "3.10" -numpy==2.1.1 ; python_version >= "3.10" and python_version < "3.13" +numpy==2.1.2 ; 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" @@ -97,6 +97,7 @@ playwright==1.47.0 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.3 ; python_version >= "3.8" and python_version < "3.13" prettytable==3.11.0 ; python_version >= "3.8" and python_version < "3.13" +propcache==0.2.0 ; 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==3.2.3 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" @@ -108,7 +109,7 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" pyparsing==3.1.4 ; python_version >= "3.8" and python_version < "3.13" pyproject-hooks==1.2.0 ; python_version >= "3.8" and python_version < "3.13" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13" -pytest-asyncio==0.23.8 ; 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" @@ -119,7 +120,7 @@ pytest-mock==3.14.0 ; 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==8.3.3 ; 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==2.1.0 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -138,7 +139,7 @@ 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==35.4.0 ; python_version >= "3.9" and python_version < "3.13" -s3transfer==0.10.2 ; python_version >= "3.8" and python_version < "3.13" +s3transfer==0.10.3 ; 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" @@ -151,7 +152,7 @@ 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" sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13" -sphinx-rtd-theme==2.0.0 ; python_version >= "3.8" and python_version < "3.13" +sphinx-rtd-theme==3.0.1 ; python_version >= "3.8" and python_version < "3.13" sphinx==7.1.2 ; python_version >= "3.8" and python_version < "3.13" sphinxcontrib-applehelp==1.0.4 ; python_version >= "3.8" and python_version < "3.13" sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.8" and python_version < "3.13" @@ -165,7 +166,7 @@ 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" -tinydb==4.8.0 ; python_version >= "3.8" and python_version < "3.13" +tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13" toml==0.10.2 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.2 ; 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" @@ -183,5 +184,5 @@ websocket-client==1.8.0 ; 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==1.13.1 ; python_version >= "3.8" and python_version < "3.13" +yarl==1.15.0 ; python_version >= "3.8" and python_version < "3.13" zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 3a004d0918eb..e19f442af6c6 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -2,11 +2,11 @@ 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==2.15.1 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.15.2 ; 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" aiohappyeyeballs==2.4.3 ; python_version >= "3.8" and python_version < "3.13" -aiohttp==3.10.9 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.10.10 ; 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==1.13.3 ; python_version >= "3.8" and python_version < "3.13" @@ -17,7 +17,7 @@ anyio==4.5.0 ; 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==3.5.0 ; python_version >= "3.8" and python_version < "3.13" +argcomplete==3.5.1 ; 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==24.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -34,13 +34,13 @@ 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==1.35.23 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.35.36 ; python_version >= "3.8" and python_version < "3.13" bx-python==0.13.0 ; 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==2024.8.30 ; 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" +charset-normalizer==3.4.0 ; 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" click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13" @@ -51,11 +51,11 @@ cloudauthz==0.6.0 ; python_version >= "3.8" and python_version < "3.13" 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" +conda-package-streaming==0.11.0 ; 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==0.34 ; python_version >= "3.8" and python_version < "3.13" -cwltool==3.1.20240909164951 ; python_version >= "3.8" and python_version < "3.13" +cwltool==3.1.20241007082533 ; python_version >= "3.8" and python_version < "3.13" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13" dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -116,7 +116,7 @@ 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==2.0.2 ; python_version >= "3.9" and python_version < "3.10" -numpy==2.1.1 ; python_version >= "3.10" and python_version < "3.13" +numpy==2.1.2 ; python_version >= "3.10" and python_version < "3.13" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" orjson==3.10.7 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" @@ -130,6 +130,7 @@ 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==3.0.48 ; python_version >= "3.8" and python_version < "3.13" +propcache==0.2.0 ; python_version >= "3.8" and python_version < "3.13" prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13" psutil==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" @@ -141,7 +142,7 @@ pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13" pydantic[email]==2.9.2 ; 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==0.8.1.2 ; python_version >= "3.8" and python_version < "3.13" +pyfaidx==0.8.1.3 ; python_version >= "3.8" and python_version < "3.13" pygments==2.18.0 ; 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" @@ -177,7 +178,6 @@ 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==75.1.0 ; 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" social-auth-core==4.5.4 ; python_version >= "3.8" and python_version < "3.13" @@ -193,7 +193,7 @@ 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==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" +tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.2 ; python_version >= "3.8" and python_version < "3.11" tornado==6.4.1 ; python_version >= "3.8" and python_version < "3.13" tqdm==4.66.5 ; python_version >= "3.8" and python_version < "3.13" @@ -204,7 +204,7 @@ tzdata==2024.2 ; 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==1.26.20 ; python_version >= "3.8" and python_version < "3.13" -uvicorn==0.31.0 ; python_version >= "3.8" and python_version < "3.13" +uvicorn==0.31.1 ; 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" @@ -213,7 +213,7 @@ 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==1.13.1 ; python_version >= "3.8" and python_version < "3.13" +yarl==1.15.0 ; python_version >= "3.8" and python_version < "3.13" zipp==3.20.2 ; python_version >= "3.8" and python_version < "3.13" zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13" zstandard==0.23.0 ; 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 b83712cde9d6..e66208b2a104 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,8 +1,8 @@ --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]==1.35.34 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.35.34 ; python_version >= "3.8" and python_version < "3.13" +boto3-stubs[s3]==1.35.39 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.35.39 ; 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" @@ -25,8 +25,8 @@ types-paramiko==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3 types-python-dateutil==2.9.0.20241003 ; python_version >= "3.8" and python_version < "3.13" types-pyyaml==6.0.12.20240917 ; 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==0.10.2 ; python_version >= "3.8" and python_version < "3.13" +types-s3transfer==0.10.3 ; python_version >= "3.8" and python_version < "3.13" types-setuptools==75.1.0.20240917 ; 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-six==1.16.21.20241009 ; 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"