diff --git a/.github/workflows/dependencies.yaml b/.github/workflows/dependencies.yaml index 31405cc13498..12f2a0919a89 100644 --- a/.github/workflows/dependencies.yaml +++ b/.github/workflows/dependencies.yaml @@ -2,6 +2,7 @@ name: Update dependencies on: schedule: - cron: '0 3 * * 6' # Run every saturday at 3 am. + workflow_dispatch: jobs: update_dependencies: name: Update dependencies diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 3c1bb12a5eb7..a6a92842ef80 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -1,4 +1,4 @@ -aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alabaster==0.7.13 ; python_version >= "3.8" and python_version < "3.13" amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -11,11 +11,11 @@ babel==2.14.0 ; 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" billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13" -black==24.1.1 ; python_version >= "3.8" and python_version < "3.13" +black==24.2.0 ; python_version >= "3.8" and python_version < "3.13" build==1.0.3 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" -certifi==2023.11.17 ; python_version >= "3.8" and python_version < "3.13" +certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" click-didyoumean==0.3.0 ; python_version >= "3.8" and python_version < "3.13" @@ -26,8 +26,8 @@ codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt") contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13" coverage[toml]==7.4.1 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13" -cwltest==2.4.20231222081524 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13" +cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13" darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13" @@ -36,7 +36,7 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13" fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.13" -fonttools==4.47.2 ; python_version >= "3.8" and python_version < "3.13" +fonttools==4.48.1 ; 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==0.1.5 ; python_version >= "3.8" and python_version < "3.13" greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13" @@ -50,7 +50,7 @@ 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 < "3.13" 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==3.3.0 ; python_version >= "3.8" and python_version < "3.13" +jaraco-classes==3.3.1 ; 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==3.1.3 ; python_version >= "3.8" and python_version < "3.13" junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13" @@ -60,7 +60,7 @@ kombu==5.3.5 ; python_version >= "3.8" and python_version < "3.13" lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13" -markupsafe==2.1.4 ; python_version >= "3.8" and python_version < "3.13" +markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" matplotlib==3.7.4 ; python_version >= "3.8" and python_version < "3.9" matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13" mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -69,70 +69,70 @@ mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13" mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13" more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13" -multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.13" +multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.13" nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.13" +numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13" outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13" packaging==23.2 ; python_version >= "3.8" and python_version < "3.13" pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13" pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13" pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.13" -platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.13" -playwright==1.41.1 ; python_version >= "3.8" and python_version < "3.13" +platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13" +playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13" pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13" port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13" prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.13" prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13" psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin" -psycopg==3.1.17 ; python_version >= "3.8" and python_version < "3.13" +psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13" pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13" pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.13" -pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.13" +pygithub==2.2.0 ; python_version >= "3.8" and python_version < "3.13" pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13" pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13" pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13" pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13" pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13" -pytest-asyncio==0.23.3 ; python_version >= "3.8" and python_version < "3.13" -pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.13" +pytest-asyncio==0.23.5 ; python_version >= "3.8" and python_version < "3.13" +pytest-base-url==2.1.0 ; python_version >= "3.8" and python_version < "3.13" pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.13" pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.13" pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13" -pytest-httpserver==1.0.8 ; python_version >= "3.8" and python_version < "3.13" +pytest-httpserver==1.0.9 ; python_version >= "3.8" and python_version < "3.13" pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -pytest-metadata==3.0.0 ; python_version >= "3.8" and python_version < "3.13" +pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13" pytest-mock==3.12.0 ; python_version >= "3.8" and python_version < "3.13" -pytest-playwright==0.4.3 ; python_version >= "3.8" and python_version < "3.13" -pytest-postgresql==5.0.0 ; python_version >= "3.8" and python_version < "3.13" +pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13" +pytest-postgresql==5.1.0 ; python_version >= "3.8" and python_version < "3.13" pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.13" pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.13" python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.13" -python-irodsclient==1.1.9 ; python_version >= "3.8" and python_version < "3.13" -python-slugify==8.0.2 ; python_version >= "3.8" and python_version < "3.13" -pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.9" +python-irodsclient==2.0.0 ; 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" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" readme-renderer==42.0 ; python_version >= "3.8" and python_version < "3.13" requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13" requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13" -responses==0.24.1 ; 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==13.7.0 ; 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==0.18.5 ; python_version >= "3.8" and python_version < "3.13" +ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.12.0 ; 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==4.17.2 ; python_version >= "3.8" and python_version < "3.13" seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.0.3 ; python_version >= "3.8" and python_version < "3.13" +setuptools==69.1.0 ; python_version >= "3.8" and python_version < "3.13" six==1.16.0 ; python_version >= "3.8" and python_version < "3.13" sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.13" snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -155,14 +155,14 @@ tomli==2.0.1 ; python_version >= "3.8" and python_full_version <= "3.11.0a6" trio-websocket==0.11.1 ; python_version >= "3.8" and python_version < "3.13" trio==0.24.0 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" -twill==3.2.1 ; python_version >= "3.8" and python_version < "3.13" -twine==4.0.2 ; python_version >= "3.8" and python_version < "3.13" +twill==3.2.2 ; python_version >= "3.8" and python_version < "3.13" +twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13" typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13" -tzdata==2023.4 ; python_version >= "3.8" and python_version < "3.13" +tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13" 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" vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13" -watchdog==3.0.0 ; python_version >= "3.8" and python_version < "3.13" +watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.13" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 021b153d7ad0..6133df8e071f 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,7 +1,7 @@ attrs==23.2.0 flake8==7.0.0 -flake8-bugbear==24.1.17 +flake8-bugbear==24.2.6 mccabe==0.7.0 pycodestyle==2.11.1 pyflakes==3.2.0 -ruff==0.1.14 +ruff==0.2.1 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 6e91ef9b5338..a2f72da952c3 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,9 +1,9 @@ a2wsgi==1.10.0 ; python_version >= "3.8" and python_version < "3.13" adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13" -aiobotocore==2.11.1 ; python_version >= "3.8" and python_version < "3.13" +aiobotocore==2.11.2 ; python_version >= "3.8" and python_version < "3.13" aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13" aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13" -aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13" +aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13" aioitertools==0.11.0 ; python_version >= "3.8" and python_version < "3.13" aiosignal==1.3.1 ; python_version >= "3.8" and python_version < "3.13" alembic==1.13.1 ; python_version >= "3.8" and python_version < "3.13" @@ -31,11 +31,11 @@ bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13" bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13" boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.13" boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13" -botocore==1.34.27 ; python_version >= "3.8" and python_version < "3.13" -bx-python==0.10.0 ; python_version >= "3.8" and python_version < "3.13" +botocore==1.34.34 ; python_version >= "3.8" and python_version < "3.13" +bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13" cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13" celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13" -certifi==2023.11.17 ; python_version >= "3.8" and python_version < "3.13" +certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13" cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13" cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13" @@ -49,7 +49,7 @@ cloudbridge==3.2.0 ; python_version >= "3.8" and python_version < "3.13" colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and platform_system == "Windows" coloredlogs==15.0.1 ; python_version >= "3.8" and python_version < "3.13" conda-package-streaming==0.9.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13" +cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13" cwl-upgrader==1.2.11 ; python_version >= "3.8" and python_version < "3.13" cwl-utils==0.32 ; python_version >= "3.8" and python_version < "3.13" cwltool==3.1.20240112164112 ; python_version >= "3.8" and python_version < "3.13" @@ -65,7 +65,7 @@ ecdsa==0.18.0 ; 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==2.1.0.post1 ; python_version >= "3.8" and python_version < "3.13" exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11" -fastapi==0.109.0 ; python_version >= "3.8" and python_version < "3.13" +fastapi==0.109.2 ; python_version >= "3.8" and python_version < "3.13" filelock==3.13.1 ; 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" @@ -77,12 +77,12 @@ graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3. 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-relay==3.2.0 ; python_version >= "3.8" and python_version < "3.13" -gravity==1.0.5 ; 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 >= "3.8" 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 < "3.13" gunicorn==21.2.0 ; python_version >= "3.8" and python_version < "3.13" gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13" h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13" -h5grove==1.3.0 ; python_version >= "3.8" and python_version < "3.13" +h5grove==2.0.0 ; python_version >= "3.8" and python_version < "3.13" h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13" humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13" idna==3.6 ; python_version >= "3.8" and python_version < "3.13" @@ -99,24 +99,24 @@ jsonschema==4.21.1 ; python_version >= "3.8" and python_version < "3.13" kombu==5.3.5 ; python_version >= "3.8" and python_version < "3.13" lagom==2.6.0 ; python_version >= "3.8" and python_version < "3.13" lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13" -mako==1.3.0 ; python_version >= "3.8" and python_version < "3.13" +mako==1.3.2 ; python_version >= "3.8" and python_version < "3.13" markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13" markdown==3.5.2 ; python_version >= "3.8" and python_version < "3.13" -markupsafe==2.1.4 ; python_version >= "3.8" and python_version < "3.13" +markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13" mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13" -mercurial==6.6.2 ; python_version >= "3.8" and python_version < "3.13" +mercurial==6.6.3 ; python_version >= "3.8" and python_version < "3.13" mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13" mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13" msal==1.26.0 ; python_version >= "3.8" and python_version < "3.13" msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13" -multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.13" +multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" networkx==2.5 ; python_version >= "3.8" and python_version < "3.13" nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.13" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.13" +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" -orjson==3.9.12 ; python_version >= "3.8" and python_version < "3.13" +orjson==3.9.13 ; python_version >= "3.8" and python_version < "3.13" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13" packaging==23.2 ; python_version >= "3.8" and python_version < "3.13" paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13" @@ -152,13 +152,13 @@ pysam==0.22.0 ; python_version >= "3.8" and python_version < "3.13" python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.13" python-jose==3.3.0 ; python_version >= "3.8" and python_version < "3.13" python-magic==0.4.27 ; python_version >= "3.8" and python_version < "3.13" -python-multipart==0.0.7 ; 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==2023.3.post1 ; python_version >= "3.8" and python_version < "3.13" +pytz==2024.1 ; python_version >= "3.8" and python_version < "3.13" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13" pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.13" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13" -referencing==0.32.1 ; python_version >= "3.8" and python_version < "3.13" +referencing==0.33.0 ; python_version >= "3.8" and python_version < "3.13" refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13" regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.13" repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13" @@ -172,11 +172,11 @@ routes==2.5.1 ; python_version >= "3.8" and python_version < "3.13" rpds-py==0.17.1 ; python_version >= "3.8" and python_version < "3.13" rsa==4.9 ; 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==0.18.5 ; python_version >= "3.8" and python_version < "3.13" +ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13" s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.13" schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.13" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.13" -setuptools==69.0.3 ; python_version >= "3.8" and python_version < "3.13" +setuptools==69.1.0 ; 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==1.3.0 ; python_version >= "3.8" and python_version < "3.13" @@ -188,7 +188,7 @@ sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" sqlparse==0.4.4 ; 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==0.35.1 ; python_version >= "3.8" and python_version < "3.13" +starlette==0.36.3 ; 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==8.2.3 ; python_version >= "3.8" and python_version < "3.13" @@ -196,15 +196,15 @@ 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 ; python_version >= "3.8" and python_version < "3.13" -tqdm==4.66.1 ; python_version >= "3.8" and python_version < "3.13" +tqdm==4.66.2 ; 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==4.9.0 ; python_version >= "3.8" and python_version < "3.13" -tzdata==2023.4 ; 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==0.6.3 ; python_version >= "3.8" and python_version < "3.13" +ubiquerg==0.7.0 ; python_version >= "3.8" and python_version < "3.13" urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13" -uvicorn==0.27.0 ; python_version >= "3.8" and python_version < "3.13" +uvicorn==0.27.1 ; python_version >= "3.8" and python_version < "3.13" uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13" vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13" wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13" @@ -212,7 +212,7 @@ webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.13" webob==1.8.7 ; python_version >= "3.8" and python_version < "3.13" whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.13" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13" -yacman==0.9.2 ; python_version >= "3.8" and python_version < "3.13" +yacman==0.9.3 ; python_version >= "3.8" and python_version < "3.13" yarl==1.9.4 ; python_version >= "3.8" and python_version < "3.13" zipp==3.17.0 ; python_version >= "3.8" and python_version < "3.13" zipstream-new==1.1.8 ; python_version >= "3.8" and python_version < "3.13" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 9ae55e92df48..27e7dfdccf1a 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,6 +1,6 @@ annotated-types==0.6.0 ; python_version >= "3.8" and python_version < "3.13" -cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13" +cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy" +cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13" lxml-stubs==0.5.1 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" mypy==1.8.0 ; python_version >= "3.8" and python_version < "3.13" @@ -9,12 +9,12 @@ pydantic-core==2.14.6 ; python_version >= "3.8" and python_version < "3.13" pydantic==2.5.3 ; python_version >= "3.8" and python_version < "3.13" tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11" types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.13" -types-boto==2.49.18.9 ; python_version >= "3.8" and python_version < "3.13" +types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13" types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.13" types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.13" -types-docutils==0.20.0.20240126 ; python_version >= "3.8" and python_version < "3.13" -types-markdown==3.5.0.20240106 ; python_version >= "3.8" and python_version < "3.13" -types-paramiko==3.4.0.20240120 ; python_version >= "3.8" and python_version < "3.13" +types-docutils==0.20.0.20240201 ; python_version >= "3.8" and python_version < "3.13" +types-markdown==3.5.0.20240129 ; python_version >= "3.8" and python_version < "3.13" +types-paramiko==3.4.0.20240205 ; python_version >= "3.8" and python_version < "3.13" types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.13" types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.13" types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.13" diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index d5e9717649ef..4360d7181811 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -61,7 +61,7 @@ install_requires = paramiko!=2.9.0,!=2.9.1 pebble pulsar-galaxy-lib>=0.15.0.dev0 - pydantic>=2 + pydantic>=2,!=2.6.0,!=2.6.1 pysam>=0.21 PyJWT PyYAML diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index b7f5afea24c9..5e97372d47ec 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -51,7 +51,7 @@ install_requires = numpy parsley pycryptodome - pydantic[email]>=2 + pydantic[email]>=2,!=2.6.0,!=2.6.1 pylibmagic python-magic pysam>=0.21 diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 2257e1f6efd5..496b60c2ce75 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -34,7 +34,7 @@ version = 23.2.dev0 include_package_data = True install_requires = galaxy-util - pydantic>=2 + pydantic>=2,!=2.6.0,!=2.6.1 PyYAML packages = find: python_requires = >=3.7 diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index e374603fc2d0..dce6efc479ef 100644 --- a/packages/schema/setup.cfg +++ b/packages/schema/setup.cfg @@ -33,7 +33,7 @@ version = 23.2.dev0 include_package_data = True install_requires = galaxy-util - pydantic[email]>=2 + pydantic[email]>=2,!=2.6.0,!=2.6.1 packages = find: python_requires = >=3.8 diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index e338e4989d36..e0753f1af3f0 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -38,7 +38,7 @@ install_requires = lxml!=4.2.2 MarkupSafe packaging - pydantic>=2 + pydantic>=2,!=2.6.0,!=2.6.1 PyYAML requests sortedcontainers diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 8ec2300750ff..1e14d2215a75 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -33,7 +33,7 @@ version = 23.2.dev0 include_package_data = True install_requires = galaxy-navigation - pydantic>=2 + pydantic>=2,!=2.6.0,!=2.6.1 PyYAML packages = find: python_requires = >=3.8 diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index 79a0bddbd172..77b1bed42159 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -51,7 +51,7 @@ install_requires = MarkupSafe mercurial Paste - pydantic>=2 + pydantic>=2,!=2.6.0,!=2.6.1 PyJWT python-dateutil python-multipart # required to support form parsing in FastAPI/Starlette diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 78b9b55b5439..e04d3f101f32 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -37,7 +37,7 @@ install_requires = babel MarkupSafe paste - pydantic>=2 + pydantic>=2,!=2.6.0,!=2.6.1 requests Routes SQLAlchemy>=1.4.25,<2 diff --git a/pyproject.toml b/pyproject.toml index 6e4dafeafe8a..34faa14f63e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -88,7 +88,7 @@ pebble = "*" psutil = "*" pulsar-galaxy-lib = ">=0.15.0.dev0" pycryptodome = "*" -pydantic = {version = ">=2", extras = ["email"]} +pydantic = {version = ">=2, !=2.6.0, !=2.6.1", extras = ["email"]} # https://github.com/pydantic/pydantic/issues/8760 PyJWT = "*" pykwalify = "*" pylibmagic = "*" @@ -168,7 +168,7 @@ Werkzeug = "*" [tool.poetry.group.typecheck.dependencies] mypy = "*" lxml-stubs = "*" -pydantic = ">=2" # for pydantic.mypy plugin +pydantic = ">=2, !=2.6.0, !=2.6.1" # for pydantic.mypy plugin types-bleach = "*" types-boto = "*" types-contextvars = "*" @@ -183,10 +183,15 @@ types-requests = "*" types-six = "*" [tool.ruff] +target-version = "py38" +exclude = [ + "lib/tool_shed/test/test_data/repos" +] + +[tool.ruff.lint] # Enable: pycodestyle errors (E), Pyflakes (F), flake8-bugbear (B), # flake8-logging-format (G) and pyupgrade (UP) select = ["E", "F", "B", "G", "UP"] -target-version = "py38" # Exceptions: # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body) # B9 flake8-bugbear opinionated warnings @@ -194,17 +199,14 @@ target-version = "py38" # E501 is line length (delegated to black) # G* are TODOs ignore = ["B008", "B9", "E402", "E501", "G001", "G002", "G004"] -exclude = [ - "lib/tool_shed/test/test_data/repos" -] -[tool.ruff.isort] +[tool.ruff.lint.isort] # We are not selecting "I" rules in ruff yet because support for all the isort # options we need is not complete, but these are the one currently implemented. combine-as-imports = true relative-imports-order = "closest-to-furthest" -[tool.ruff.per-file-ignores] +[tool.ruff.lint.per-file-ignores] # Don't check pyupgrade rules on tool scripts, which may use different Python versions "test/functional/tools/*" = ["UP"] "tools/*" = ["UP"] diff --git a/test/integration/test_structured_dataset.py b/test/integration/test_structured_dataset.py index 0f9a8196dd7d..ba81c3365cef 100644 --- a/test/integration/test_structured_dataset.py +++ b/test/integration/test_structured_dataset.py @@ -39,7 +39,7 @@ def test_api_meta(self): response = self._get(f"datasets/{dataset_id}/content/meta") self._assert_status_code_is(response, 200) hvals = response.json() - self._assert_has_keys(hvals, "attributes", "name", "type") + self._assert_has_keys(hvals, "attributes", "name", "kind") def test_api_attr(self): dataset = self.dataset_populator.new_dataset(