Update Python dependencies

by running `make update-dependencies`.
galaxyproject · Oct 19, 2024 · f4419c8 · f4419c8
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commit f4419c8
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diff --git 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
@@ -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
@@ -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"
@@ -66,16 +65,16 @@ 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"
 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"
@@ -204,16 +203,16 @@ 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"
 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
@@ -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"