From fe5efbea64d4b3a167ad61965471f469cf0b9714 Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 1 Jun 2024 03:23:14 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 38 ++++++++++--------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 31 +++++++-------- .../pinned-typecheck-requirements.txt | 12 +++--- 4 files changed, 42 insertions(+), 41 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 231a88f234f8..44eecc55e673 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,27 +1,29 @@ +--extra-index-url https://wheels.galaxyproject.org/simple + aiohttp==3.9.5 ; 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==4.3.0 ; python_version >= "3.8" and python_version < "3.13" -ase==3.22.1 ; 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" 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" -backports-tarfile==1.1.1 ; python_version >= "3.8" and python_version < "3.12" +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==1.34.106 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.34.106 ; python_version >= "3.8" and python_version < "3.13" +boto3==1.34.117 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.117 ; python_version >= "3.8" and python_version < "3.13" build==1.2.1 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" certifi==2024.2.2 ; 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==8.1.7 ; python_version >= "3.8" and python_version < "3.13" -codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13" +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 < "3.13" -coverage[toml]==7.5.1 ; python_version >= "3.8" and python_version < "3.13" +coverage[toml]==7.5.3 ; python_version >= "3.8" and python_version < "3.13" cryptography==42.0.7 ; python_version >= "3.8" and python_version < "3.13" cwltest==2.5.20240425111257 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" @@ -35,9 +37,9 @@ dogpile-cache==1.2.2 ; python_version >= "3.9" and python_version < "3.13" exceptiongroup==1.2.1 ; python_version >= "3.8" and python_version < "3.11" filelock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13" -fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13" +fonttools==4.53.0 ; python_version >= "3.8" and python_version < "3.13" frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13" -galaxy-release-util==0.1.9 ; python_version >= "3.8" and python_version < "3.13" +galaxy-release-util==0.1.11 ; python_version >= "3.8" and python_version < "3.13" 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" @@ -86,7 +88,7 @@ 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" pillow==10.3.0 ; 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" +pkginfo==1.11.0 ; python_version >= "3.8" and python_version < "3.13" platformdirs==4.2.2 ; python_version >= "3.8" and python_version < "3.13" playwright==1.44.0 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.5.0 ; python_version >= "3.8" and python_version < "3.13" @@ -114,7 +116,7 @@ pytest-mock==3.14.0 ; python_version >= "3.8" and python_version < "3.13" pytest-playwright==0.5.0 ; python_version >= "3.8" and python_version < "3.13" pytest-postgresql==6.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13" -pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13" +pytest==8.2.1 ; python_version >= "3.8" and python_version < "3.13" python-dateutil==2.9.0.post0 ; python_version >= "3.8" and python_version < "3.13" python-irodsclient==2.0.1 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13" @@ -125,22 +127,22 @@ 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" requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" -requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13" +requests==2.32.3 ; python_version >= "3.8" and python_version < "3.13" responses==0.25.0 ; 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==0.18.1 ; 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==34.3.0 ; python_version >= "3.9" and python_version < "3.13" +rucio-clients==34.4.1 ; python_version >= "3.9" and python_version < "3.13" s3transfer==0.10.1 ; python_version >= "3.8" and python_version < "3.13" schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" -scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13" +scipy==1.13.1 ; python_version >= "3.9" and python_version < "3.13" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux" selenium==4.21.0 ; python_version >= "3.8" and python_version < "3.13" seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.0.0 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -167,14 +169,14 @@ trio==0.25.1 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" twill==3.2.4 ; python_version >= "3.8" and python_version < "3.13" twine==5.1.0 ; python_version >= "3.8" and python_version < "3.13" -typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13" +typing-extensions==4.12.0 ; 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==1.26.18 ; python_version >= "3.8" and python_version < "3.13" urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13" -watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13" +watchdog==4.0.1 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" werkzeug==3.0.3 ; 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==3.18.2 ; python_version >= "3.8" and python_version < "3.13" +zipp==3.19.1 ; 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 805eda6a8a58..e2ced78d7f6d 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -4,4 +4,4 @@ flake8-bugbear==24.4.26 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.4.4 +ruff==0.4.7 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index f25d7b6a27c7..2d530fffd137 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -2,17 +2,15 @@ a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.13.0 ; 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==3.9.5 ; 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" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" aniso8601==9.0.1 ; python_version >= "3.8" and python_version < "3.13" -annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13" -anyio==4.3.0 ; python_version >= "3.8" and python_version < "3.13" +annotated-types==0.7.0 ; python_version >= "3.8" and python_version < "3.13" +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" @@ -33,7 +31,7 @@ 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==1.34.106 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.117 ; python_version >= "3.8" and python_version < "3.13" bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.14.0 ; python_version >= "3.8" and python_version < "3.13" celery==5.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -113,7 +111,7 @@ 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==2.5 ; python_version >= "3.8" and python_version < "3.13" -nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13" +nodeenv==1.9.0 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.13" @@ -127,16 +125,16 @@ 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==10.3.0 ; python_version >= "3.8" and python_version < "3.13" promise==2.3 ; python_version >= "3.8" and python_version < "3.13" -prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13" +prompt-toolkit==3.0.45 ; python_version >= "3.8" and python_version < "3.13" prov==1.5.1 ; python_version >= "3.8" and python_version < "3.13" psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" pulsar-galaxy-lib==0.15.6 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13" -pydantic-core==2.18.2 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.18.3 ; python_version >= "3.8" and python_version < "3.13" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13" -pydantic[email]==2.7.1 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.7.2 ; python_version >= "3.8" and python_version < "3.13" +pydantic[email]==2.7.2 ; 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==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13" @@ -164,17 +162,17 @@ 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==2.31.0 ; 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" 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==0.18.1 ; python_version >= "3.8" and python_version < "3.13" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.13" and python_version >= "3.8" ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" -s3fs==2024.5.0 ; python_version >= "3.8" and python_version < "3.13" +s3fs==0.4.2 ; python_version >= "3.8" and python_version < "3.13" schema-salad==8.5.20240503091721 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.5.1 ; python_version >= "3.8" and python_version < "3.13" +setuptools==70.0.0 ; 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" @@ -197,21 +195,20 @@ tornado==6.4 ; python_version >= "3.8" and python_version < "3.13" tqdm==4.66.4 ; 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==4.11.0 ; python_version >= "3.8" and python_version < "3.13" +typing-extensions==4.12.0 ; 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==1.26.18 ; python_version >= "3.8" and python_version < "3.13" -uvicorn==0.29.0 ; python_version >= "3.8" and python_version < "3.13" +uvicorn==0.30.0 ; python_version >= "3.8" and python_version < "3.13" uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13" vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" 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==0.9.3 ; python_version >= "3.8" and python_version < "3.13" yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13" -zipp==3.18.2 ; python_version >= "3.8" and python_version < "3.13" +zipp==3.19.1 ; python_version >= "3.8" and python_version < "3.13" zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13" zstandard==0.22.0 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index a18d0745af0d..1798259555c3 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,5 +1,7 @@ -annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13" -boto3-stubs[s3]==1.34.108 ; python_version >= "3.8" and python_version < "3.13" +--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]==1.34.117 ; python_version >= "3.8" and python_version < "3.13" botocore-stubs==1.34.94 ; 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==42.0.7 ; python_version >= "3.8" and python_version < "3.13" @@ -8,8 +10,8 @@ mypy-boto3-s3==1.34.105 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" mypy==1.10.0 ; 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==2.18.2 ; python_version >= "3.8" and python_version < "3.13" -pydantic==2.7.1 ; python_version >= "3.8" and python_version < "3.13" +pydantic-core==2.18.3 ; python_version >= "3.8" and python_version < "3.13" +pydantic==2.7.2 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" types-awscrt==0.20.9 ; python_version >= "3.8" and python_version < "3.13" types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13" @@ -27,4 +29,4 @@ 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-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==4.11.0 ; python_version >= "3.8" and python_version < "3.13" +typing-extensions==4.12.0 ; python_version >= "3.8" and python_version < "3.13"