From f4419c8611821ce133c114bff307e64b55b2deba Mon Sep 17 00:00:00 2001 From: galaxybot Date: Sat, 19 Oct 2024 03:20:00 +0000 Subject: [PATCH] Update Python dependencies by running `make update-dependencies`. --- lib/galaxy/dependencies/dev-requirements.txt | 26 ++++++++-------- .../dependencies/pinned-lint-requirements.txt | 2 +- .../dependencies/pinned-requirements.txt | 31 +++++++++---------- .../pinned-typecheck-requirements.txt | 16 +++++----- 4 files changed, 36 insertions(+), 39 deletions(-) diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 4d38a19dcd8a..ba3fc441e997 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -4,7 +4,7 @@ aiohappyeyeballs==2.4.3 ; 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" +anyio==4.5.2 ; 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==24.2.0 ; python_version >= "3.8" and python_version < "3.13" @@ -26,7 +26,7 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_p contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.9" 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" +cryptography==43.0.3 ; python_version >= "3.8" and python_version < "3.13" cwltest==2.5.20240906231108 ; 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" @@ -98,7 +98,7 @@ 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" +psutil==6.1.0 ; 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" pyee==12.0.0 ; python_version >= "3.8" and python_version < "3.13" @@ -109,7 +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" @@ -120,9 +120,9 @@ 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-irodsclient==2.2.0 ; python_version >= "3.8" and python_version < "3.13" python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13" pytz==2024.2 ; python_version >= "3.8" and python_version < "3.9" pywin32-ctypes==0.2.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" @@ -138,16 +138,16 @@ rich==13.9.2 ; 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==35.4.0 ; python_version >= "3.9" and python_version < "3.13" +rucio-clients==35.4.1 ; python_version >= "3.9" 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" +schema-salad==8.7.20241010092723 ; 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==1.14.1 ; 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==4.25.0 ; python_version >= "3.8" and python_version < "3.13" seletools==1.5.0 ; python_version >= "3.8" and python_version < "3.13" -setuptools==75.1.0 ; python_version >= "3.8" and python_version < "3.13" +setuptools==75.2.0 ; 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" @@ -166,13 +166,13 @@ 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" -tinydb==4.8.1 ; python_version >= "3.8" and python_version < "3.13" +tinydb==4.8.2 ; 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" -trio==0.26.2 ; python_version >= "3.8" and python_version < "3.13" +trio==0.27.0 ; python_version >= "3.8" and python_version < "3.13" tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13" -twill==3.2.5 ; python_version >= "3.8" and python_version < "3.13" +twill==3.3 ; 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==2024.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32" @@ -184,5 +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==1.15.0 ; python_version >= "3.8" and python_version < "3.13" +yarl==1.15.2 ; 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-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 37feaac86fe3..0f3613e5155a 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==0.6.9 +ruff==0.7.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index e19f442af6c6..cdbdd776d475 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -11,9 +11,8 @@ 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" 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==0.7.0 ; python_version >= "3.8" and python_version < "3.13" -anyio==4.5.0 ; python_version >= "3.8" and python_version < "3.13" +anyio==4.5.2 ; 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" @@ -52,9 +51,9 @@ 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==0.11.0 ; python_version >= "3.8" and python_version < "3.13" -cryptography==43.0.1 ; python_version >= "3.8" and python_version < "3.13" +cryptography==43.0.3 ; 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" +cwl-utils==0.35 ; 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" @@ -66,7 +65,7 @@ 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==0.115.0 ; python_version >= "3.8" and python_version < "3.13" +fastapi-slim==0.115.2 ; python_version >= "3.8" and python_version < "3.13" filelock==3.16.1 ; 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" @@ -74,8 +73,8 @@ 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" 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==3.2.4 ; python_version >= "3.8" and python_version < "3.13" +graphene==3.4 ; python_version >= "3.8" and python_version < "3.13" +graphql-core==3.2.5 ; 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" @@ -132,7 +131,7 @@ 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" +psutil==6.1.0 ; 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==3.21.0 ; python_version >= "3.8" and python_version < "3.13" @@ -175,25 +174,25 @@ 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==2024.9.0 ; python_version >= "3.8" and python_version < "3.13" -schema-salad==8.7.20240905150001 ; python_version >= "3.8" and python_version < "3.13" +schema-salad==8.7.20241010092723 ; 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" +setuptools==75.2.0 ; 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" 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==0.3.14 ; python_version >= "3.8" and python_version < "3.13" -sqlalchemy==2.0.35 ; python_version >= "3.8" and python_version < "3.13" +sqlalchemy==2.0.36 ; python_version >= "3.8" and python_version < "3.13" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13" sqlparse==0.5.1 ; 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==0.38.6 ; python_version >= "3.8" and python_version < "3.13" +starlette==0.40.0 ; 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==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==4.8.1 ; python_version >= "3.8" and python_version < "3.13" +tinydb==4.8.2 ; 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" @@ -204,8 +203,8 @@ 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==0.31.1 ; python_version >= "3.8" and python_version < "3.13" -uvloop==0.20.0 ; python_version >= "3.8" and python_version < "3.13" +uvicorn==0.32.0 ; python_version >= "3.8" and python_version < "3.13" +uvloop==0.21.0 ; 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" @@ -213,7 +212,7 @@ 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==1.15.0 ; python_version >= "3.8" and python_version < "3.13" +yarl==1.15.2 ; 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 e66208b2a104..328c76785427 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -1,14 +1,12 @@ ---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]==1.35.39 ; python_version >= "3.8" and python_version < "3.13" -botocore-stubs==1.35.39 ; python_version >= "3.8" and python_version < "3.13" +boto3-stubs[s3]==1.35.44 ; python_version >= "3.8" and python_version < "3.13" +botocore-stubs==1.35.44 ; 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" +cryptography==43.0.3 ; 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==1.35.32 ; python_version >= "3.8" and python_version < "3.13" +mypy-boto3-s3==1.35.42 ; python_version >= "3.8" and python_version < "3.13" mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13" -mypy==1.11.2 ; python_version >= "3.8" and python_version < "3.13" +mypy==1.12.0 ; 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==2.23.4 ; python_version >= "3.8" and python_version < "3.13" pydantic==2.9.2 ; python_version >= "3.8" and python_version < "3.13" @@ -19,14 +17,14 @@ types-boto==2.49.18.20240806 ; python_version >= "3.8" and python_version < "3.1 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==0.21.0.20241005 ; 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-html5lib==1.1.11.20241018 ; 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==3.5.0.20240928 ; python_version >= "3.8" and python_version < "3.13" 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==0.10.3 ; 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-setuptools==75.2.0.20241019 ; 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"