diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index dd82b1fff80e..9c747f2734a7 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -8,7 +8,7 @@ async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.12" axe-selenium-python==2.1.6 ; python_version >= "3.7" and python_version < "3.12" -babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12" +babel==2.13.0 ; python_version >= "3.7" and python_version < "3.12" billiard==3.6.4.0 ; python_version >= "3.7" and python_version < "3.12" black==23.3.0 ; python_version >= "3.7" and python_version < "3.12" bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12" @@ -18,7 +18,7 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12" certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.12" cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12" +charset-normalizer==3.3.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" click-plugins==1.1.1 ; python_version >= "3.7" and python_version < "3.12" click-repl==0.3.0 ; python_version >= "3.7" and python_version < "3.12" @@ -40,6 +40,7 @@ fonttools==4.38.0 ; python_version >= "3.7" and python_version < "3.12" frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12" future==0.18.3 ; python_version >= "3.7" and python_version < "3.12" galaxy-release-util==0.1.5 ; python_version >= "3.7" and python_version < "3.12" +greenlet==2.0.2 ; python_version >= "3.7" and python_version < "3.12" h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" httpcore==0.17.3 ; python_version >= "3.7" and python_version < "3.12" httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.12" @@ -77,12 +78,13 @@ numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12" outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12" -packaging==23.1 ; python_version >= "3.7" and python_version < "3.12" +packaging==23.2 ; python_version >= "3.7" and python_version < "3.12" pathspec==0.11.2 ; python_version >= "3.7" and python_version < "3.12" pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12" pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12" pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12" -platformdirs==3.10.0 ; python_version >= "3.7" and python_version < "3.12" +platformdirs==3.11.0 ; python_version >= "3.7" and python_version < "3.12" +playwright==1.35.0 ; python_version >= "3.7" and python_version < "3.12" pluggy==1.2.0 ; python_version >= "3.7" and python_version < "3.12" port-for==0.7.1 ; python_version >= "3.7" and python_version < "3.12" prettytable==3.7.0 ; python_version >= "3.7" and python_version < "3.12" @@ -90,6 +92,7 @@ prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12" psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" and sys_platform != "cygwin" py==1.11.0 ; python_version >= "3.7" and python_version < "3.12" pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" +pyee==9.0.4 ; python_version >= "3.7" and python_version < "3.12" pygithub==2.1.1 ; python_version >= "3.7" and python_version < "3.12" pygments==2.16.1 ; python_version >= "3.7" and python_version < "3.12" pyjwt[crypto]==2.8.0 ; python_version >= "3.7" and python_version < "3.12" @@ -98,6 +101,7 @@ pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" pyproject-hooks==1.0.0 ; python_version >= "3.7" and python_version < "3.12" pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12" pytest-asyncio==0.21.1 ; python_version >= "3.7" and python_version < "3.12" +pytest-base-url==2.0.0 ; python_version >= "3.7" and python_version < "3.12" pytest-celery==0.0.0 ; python_version >= "3.7" and python_version < "3.12" pytest-cov==4.1.0 ; python_version >= "3.7" and python_version < "3.12" pytest-html==3.2.0 ; python_version >= "3.7" and python_version < "3.12" @@ -105,12 +109,13 @@ pytest-httpserver==1.0.6 ; python_version >= "3.7" and python_version < "3.12" pytest-json-report==1.5.0 ; python_version >= "3.7" and python_version < "3.12" pytest-metadata==3.0.0 ; python_version >= "3.7" and python_version < "3.12" pytest-mock==3.11.1 ; python_version >= "3.7" and python_version < "3.12" -pytest-playwright==0.3.0 ; python_version >= "3.7" and python_version < "3.12" +pytest-playwright==0.3.3 ; python_version >= "3.7" and python_version < "3.12" pytest-postgresql==4.1.1 ; python_version >= "3.7" and python_version < "3.12" pytest-shard==0.1.2 ; python_version >= "3.7" and python_version < "3.12" pytest==7.4.2 ; python_version >= "3.7" and python_version < "3.12" python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12" +python-slugify==8.0.1 ; python_version >= "3.7" and python_version < "3.12" pytz==2023.3.post1 ; python_version >= "3.7" and python_version < "3.12" pywin32-ctypes==0.2.2 ; python_version >= "3.7" and python_version < "3.12" and sys_platform == "win32" pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12" @@ -120,8 +125,8 @@ requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12" requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12" responses==0.23.3 ; python_version >= "3.7" and python_version < "3.12" rfc3986==2.0.0 ; python_version >= "3.7" and python_version < "3.12" -rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12" -ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" +rich==13.6.0 ; python_version >= "3.7" and python_version < "3.12" +ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12" schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12" scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.8" @@ -146,6 +151,7 @@ sphinxcontrib-qthelp==1.0.3 ; python_version >= "3.7" and python_version < "3.12 sphinxcontrib-serializinghtml==1.1.5 ; python_version >= "3.7" and python_version < "3.12" statsd==4.0.1 ; python_version >= "3.7" and python_version < "3.12" testfixtures==7.2.0 ; python_version >= "3.7" and python_version < "3.12" +text-unidecode==1.3 ; python_version >= "3.7" and python_version < "3.12" tinydb==4.8.0 ; python_version >= "3.7" and python_version < "3.12" toml==0.10.2 ; python_version >= "3.7" and python_version < "3.12" tomli==2.0.1 ; python_version >= "3.7" and python_full_version <= "3.11.0a6" @@ -157,11 +163,11 @@ twine==4.0.2 ; python_version >= "3.7" and python_version < "3.12" typed-ast==1.5.5 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7" types-pyyaml==6.0.12.12 ; python_version >= "3.7" and python_version < "3.12" typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12" -urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12" -urllib3[socks]==1.26.16 ; python_version >= "3.7" and python_version < "3.12" +urllib3==1.26.17 ; python_version >= "3.7" and python_version < "3.12" +urllib3[socks]==1.26.17 ; python_version >= "3.7" and python_version < "3.12" vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12" watchdog==3.0.0 ; python_version >= "3.7" and python_version < "3.12" -wcwidth==0.2.7 ; python_version >= "3.7" and python_version < "3.12" +wcwidth==0.2.8 ; python_version >= "3.7" and python_version < "3.12" webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12" werkzeug==2.2.3 ; python_version >= "3.7" and python_version < "3.12" wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index f63b2768119c..08d44e583e9b 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -5,6 +5,6 @@ importlib-metadata==4.2.0 mccabe==0.7.0 pycodestyle==2.9.1 pyflakes==2.5.0 -ruff==0.0.291 +ruff==0.0.292 typing_extensions==4.7.1 zipp==3.15.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 5707ebb1c20f..9767bc285e1e 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -1,12 +1,14 @@ a2wsgi==1.7.0 ; python_version >= "3.7" and python_version < "3.12" adal==1.2.7 ; python_version >= "3.7" and python_version < "3.12" aiobotocore==2.4.2 ; python_version >= "3.7" and python_version < "3.12" +aiodataloader==0.4.0 ; python_version >= "3.7" and python_version < "3.12" aiofiles==23.2.1 ; python_version >= "3.7" and python_version < "3.12" aiohttp==3.8.5 ; python_version >= "3.7" and python_version < "3.12" aioitertools==0.11.0 ; python_version >= "3.7" and python_version < "3.12" aiosignal==1.3.1 ; python_version >= "3.7" and python_version < "3.12" alembic==1.12.0 ; python_version >= "3.7" and python_version < "3.12" amqp==5.1.1 ; python_version >= "3.7" and python_version < "3.12" +aniso8601==9.0.1 ; python_version >= "3.7" and python_version < "3.12" anyio==3.7.1 ; python_version >= "3.7" and python_version < "3.12" apispec==6.3.0 ; python_version >= "3.7" and python_version < "3.12" appdirs==1.4.4 ; python_version >= "3.7" and python_version < "3.12" @@ -16,7 +18,7 @@ async-timeout==4.0.3 ; python_version >= "3.7" and python_version < "3.12" asynctest==0.13.0 ; python_version >= "3.7" and python_version < "3.8" attmap==0.13.2 ; python_version >= "3.7" and python_version < "3.12" attrs==23.1.0 ; python_version >= "3.7" and python_version < "3.12" -babel==2.12.1 ; python_version >= "3.7" and python_version < "3.12" +babel==2.13.0 ; python_version >= "3.7" and python_version < "3.12" backports-zoneinfo==0.2.1 ; python_version >= "3.7" and python_version < "3.9" bagit-profile==1.3.1 ; python_version >= "3.7" and python_version < "3.12" bagit==1.8.1 ; python_version >= "3.7" and python_version < "3.12" @@ -35,7 +37,7 @@ cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8" celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12" certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.12" cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12" -charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12" +charset-normalizer==3.3.0 ; python_version >= "3.7" and python_version < "3.12" cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12" circus==0.18.0 ; python_version >= "3.7" and python_version < "3.12" click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12" @@ -51,7 +53,6 @@ cryptography==41.0.4 ; python_version >= "3.7" and python_version < "3.12" cwl-upgrader==1.2.8 ; python_version >= "3.7" and python_version < "3.12" cwl-utils==0.28 ; python_version >= "3.7" and python_version < "3.12" cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12" -cython==3.0.2 ; python_version >= "3.7" and python_version < "3.12" decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.12" defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.12" deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.12" @@ -74,6 +75,9 @@ future==0.18.3 ; python_version >= "3.7" and python_version < "3.12" galaxy-sequence-utils==1.1.5 ; python_version >= "3.7" and python_version < "3.12" galaxy2cwl==0.1.4 ; python_version >= "3.7" and python_version < "3.12" graphene-sqlalchemy==3.0.0b3 ; python_version >= "3.7" and python_version < "3.12" +graphene==3.3 ; python_version >= "3.7" and python_version < "3.12" +graphql-core==3.2.3 ; python_version >= "3.7" and python_version < "3.12" +graphql-relay==3.2.0 ; python_version >= "3.7" and python_version < "3.12" gravity==1.0.3 ; python_version >= "3.7" and python_version < "3.12" greenlet==2.0.2 ; python_version >= "3.7" 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 < "3.12" gunicorn==21.2.0 ; python_version >= "3.7" and python_version < "3.12" @@ -114,13 +118,14 @@ numpy==1.26.0 ; python_version >= "3.9" and python_version < "3.12" oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12" orjson==3.9.7 ; python_version >= "3.7" and python_version < "3.12" oyaml==1.0 ; python_version >= "3.7" and python_version < "3.12" -packaging==23.1 ; python_version >= "3.7" and python_version < "3.12" +packaging==23.2 ; python_version >= "3.7" and python_version < "3.12" paramiko==3.3.1 ; python_version >= "3.7" and python_version < "3.12" parsley==1.3 ; python_version >= "3.7" and python_version < "3.12" -paste==3.5.3 ; python_version >= "3.7" and python_version < "3.12" +paste==3.6.0 ; python_version >= "3.7" and python_version < "3.12" pastedeploy==3.0.1 ; python_version >= "3.7" and python_version < "3.12" pebble==5.0.3 ; python_version >= "3.7" and python_version < "3.12" pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9" +promise==2.3 ; python_version >= "3.7" and python_version < "3.12" prompt-toolkit==3.0.39 ; python_version >= "3.7" and python_version < "3.12" prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12" psutil==5.9.5 ; python_version >= "3.7" and python_version < "3.12" @@ -144,7 +149,7 @@ pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and python_version < "3.12" pyreadline==2.1 ; sys_platform == "win32" and python_version < "3.8" and python_version >= "3.7" pyrsistent==0.19.3 ; python_version >= "3.7" and python_version < "3.12" -pysam==0.21.0 ; python_version >= "3.7" and python_version < "3.12" +pysam==0.22.0 ; python_version >= "3.7" and python_version < "3.12" python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.12" python-jose==3.3.0 ; python_version >= "3.7" and python_version < "3.12" python-magic==0.4.27 ; python_version >= "3.7" and python_version < "3.12" @@ -155,17 +160,17 @@ pyyaml==6.0.1 ; python_version >= "3.7" and python_version < "3.12" pyzmq==25.1.1 ; python_version >= "3.7" and python_version < "3.12" rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.12" -regex==2023.8.8 ; python_version >= "3.7" and python_version < "3.12" +regex==2023.10.3 ; python_version >= "3.7" and python_version < "3.12" repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.12" requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.12" requests-toolbelt==1.0.0 ; python_version >= "3.7" and python_version < "3.12" requests-unixsocket==0.3.0 ; python_version >= "3.7" and python_version < "3.12" requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12" -rich==13.5.3 ; python_version >= "3.7" and python_version < "3.12" +rich==13.6.0 ; python_version >= "3.7" and python_version < "3.12" rocrate==0.8.0 ; python_version >= "3.7" and python_version < "3.12" routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12" rsa==4.9 ; python_version >= "3.7" and python_version < "3.12" -ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" +ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7" ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.12" s3fs==2023.1.0 ; python_version >= "3.7" and python_version < "3.12" schema-salad==8.4.20230808163024 ; python_version >= "3.7" and python_version < "3.12" @@ -180,7 +185,7 @@ sqlalchemy==1.4.49 ; python_version >= "3.7" and python_version < "3.12" sqlitedict==2.1.0 ; python_version >= "3.7" and python_version < "3.12" sqlparse==0.4.4 ; python_version >= "3.7" and python_version < "3.12" starlette-context==0.3.5 ; python_version >= "3.7" and python_version < "3.12" -starlette_graphene3==0.6.0 ; python_version >= "3.7" and python_version < "3.12" +starlette-graphene3==0.6.0 ; python_version >= "3.7" and python_version < "3.12" starlette==0.27.0 ; python_version >= "3.7" and python_version < "3.12" supervisor==4.2.5 ; python_version >= "3.7" and python_version < "3.12" svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12" @@ -194,18 +199,18 @@ tuspy==1.0.1 ; python_version >= "3.7" and python_version < "3.12" tuswsgi==0.5.5 ; python_version >= "3.7" and python_version < "3.12" typing-extensions==4.7.1 ; python_version >= "3.7" and python_version < "3.12" tzdata==2023.3 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" -tzlocal==5.0.1 ; python_version >= "3.7" and python_version < "3.12" +tzlocal==5.1 ; python_version >= "3.7" and python_version < "3.12" ubiquerg==0.6.3 ; python_version >= "3.7" and python_version < "3.12" -urllib3==1.26.16 ; python_version >= "3.7" and python_version < "3.12" +urllib3==1.26.17 ; python_version >= "3.7" and python_version < "3.12" uvicorn==0.22.0 ; python_version >= "3.7" and python_version < "3.12" uvloop==0.17.0 ; python_version >= "3.7" and python_version < "3.12" vine==5.0.0 ; python_version >= "3.7" and python_version < "3.12" -wcwidth==0.2.7 ; python_version >= "3.7" and python_version < "3.12" +wcwidth==0.2.8 ; python_version >= "3.7" and python_version < "3.12" webencodings==0.5.1 ; python_version >= "3.7" and python_version < "3.12" webob==1.8.7 ; python_version >= "3.7" and python_version < "3.12" whoosh==2.7.4 ; python_version >= "3.7" and python_version < "3.12" wrapt==1.15.0 ; python_version >= "3.7" and python_version < "3.12" -yacman==0.9.1 ; python_version >= "3.7" and python_version < "3.12" +yacman==0.9.2 ; python_version >= "3.7" and python_version < "3.12" yarl==1.9.2 ; python_version >= "3.7" and python_version < "3.12" zipp==3.15.0 ; python_version >= "3.7" and python_version < "3.12" zipstream-new==1.1.8 ; python_version >= "3.7" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index bd28fe6209bf..acd6fff7f0ad 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -6,12 +6,12 @@ pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" pydantic==1.10.13 ; python_version >= "3.7" and python_version < "3.12" tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" typed-ast==1.5.5 ; python_version >= "3.7" and python_version < "3.8" -types-bleach==6.0.0.4 ; python_version >= "3.7" and python_version < "3.12" +types-bleach==6.1.0.0 ; python_version >= "3.7" and python_version < "3.12" types-boto==2.49.18.9 ; python_version >= "3.7" and python_version < "3.12" types-contextvars==2.4.7.3 ; python_version >= "3.7" and python_version < "3.12" types-dataclasses==0.6.6 ; python_version >= "3.7" and python_version < "3.12" types-docutils==0.20.0.3 ; python_version >= "3.7" and python_version < "3.12" -types-markdown==3.4.2.10 ; python_version >= "3.7" and python_version < "3.12" +types-markdown==3.5.0.0 ; python_version >= "3.7" and python_version < "3.12" types-paramiko==3.3.0.0 ; python_version >= "3.7" and python_version < "3.12" types-pkg-resources==0.1.3 ; python_version >= "3.7" and python_version < "3.12" types-python-dateutil==2.8.19.14 ; python_version >= "3.7" and python_version < "3.12"