diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 8a80cf94c58..020f8958750 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -23,7 +23,7 @@ click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.12" click==8.1.3 ; python_version >= "3.7" and python_version < "3.12" codespell==2.2.4 ; python_version >= "3.7" and python_version < "3.12" colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows") -coverage[toml]==7.2.5 ; python_version >= "3.7" and python_version < "3.12" +coverage[toml]==7.2.6 ; python_version >= "3.7" and python_version < "3.12" cryptography==40.0.2 ; python_version >= "3.7" and python_version < "3.12" cwltest==2.3.20230108193615 ; python_version >= "3.7" and python_version < "3.12" cycler==0.11.0 ; python_version >= "3.7" and python_version < "3.12" @@ -37,7 +37,7 @@ 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" h11==0.14.0 ; python_version >= "3.7" and python_version < "3.12" -httpcore==0.17.1 ; python_version >= "3.7" and python_version < "3.12" +httpcore==0.17.2 ; python_version >= "3.7" and python_version < "3.12" httpx==0.24.1 ; python_version >= "3.7" and python_version < "3.12" idna==3.4 ; python_version >= "3.7" and python_version < "3.12" imagesize==1.4.1 ; python_version >= "3.7" and python_version < "3.12" @@ -87,7 +87,7 @@ pyparsing==3.0.9 ; python_version >= "3.7" and python_version < "3.12" pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12" pytest-asyncio==0.21.0 ; 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==4.0.0 ; 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" 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" @@ -101,7 +101,7 @@ python-irodsclient==1.1.8 ; python_version >= "3.7" and python_version < "3.12" pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12" pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.12" rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.12" -requests==2.30.0 ; python_version >= "3.7" and python_version < "3.12" +requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12" responses==0.23.1 ; 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==0.17.21 ; python_version >= "3.7" and python_version < "3.12" @@ -115,7 +115,7 @@ six==1.16.0 ; python_version >= "3.7" and python_version < "3.12" sniffio==1.3.0 ; python_version >= "3.7" and python_version < "3.12" snowballstemmer==2.2.0 ; python_version >= "3.7" and python_version < "3.12" sortedcontainers==2.4.0 ; python_version >= "3.7" and python_version < "3.12" -sphinx-rtd-theme==1.2.0 ; python_version >= "3.7" and python_version < "3.12" +sphinx-rtd-theme==1.2.1 ; python_version >= "3.7" and python_version < "3.12" sphinx==5.3.0 ; python_version >= "3.7" and python_version < "3.12" sphinxcontrib-applehelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.7" and python_version < "3.12" @@ -134,10 +134,10 @@ trio==0.22.0 ; python_version >= "3.7" and python_version < "3.12" tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12" twill==3.1 ; python_version >= "3.7" and python_version < "3.12" typed-ast==1.5.4 ; python_version < "3.8" and implementation_name == "cpython" and python_version >= "3.7" -types-pyyaml==6.0.12.9 ; python_version >= "3.7" and python_version < "3.12" -typing-extensions==4.5.0 ; python_version >= "3.7" and python_version < "3.12" -urllib3==1.26.15 ; python_version >= "3.7" and python_version < "3.12" -urllib3[socks]==1.26.15 ; python_version >= "3.7" and python_version < "3.12" +types-pyyaml==6.0.12.10 ; python_version >= "3.7" and python_version < "3.12" +typing-extensions==4.6.2 ; 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" 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==0.2.6 ; 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 c7c6d3f7b45..7d142fc5d7f 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==0.0.269 -typing_extensions==4.5.0 +ruff==0.0.270 +typing_extensions==4.6.2 zipp==3.15.0 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 7b8ef6e0691..7f5fa44e718 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -14,6 +14,7 @@ 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" arcp==0.2.1 ; python_version >= "3.7" and python_version < "3.12" argcomplete==3.0.8 ; python_version >= "3.7" and python_version < "3.12" +async-generator==1.10 ; python_version >= "3.7" and python_version < "3.12" async-timeout==4.0.2 ; 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" @@ -47,14 +48,14 @@ click-repl==0.2.0 ; python_version >= "3.7" and python_version < "3.12" click==8.1.3 ; python_version >= "3.7" and python_version < "3.12" cloudauthz==0.6.0 ; python_version >= "3.7" and python_version < "3.12" cloudbridge==3.1.0 ; python_version >= "3.7" and python_version < "3.12" -colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and platform_system == "Windows" +colorama==0.4.6 ; python_version >= "3.7" and python_version < "3.12" and (sys_platform == "win32" or platform_system == "Windows") coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.12" conda-package-streaming==0.8.0 ; python_version >= "3.7" and python_version < "3.12" cryptography==40.0.2 ; python_version >= "3.7" and python_version < "3.12" cwl-upgrader==1.2.7 ; python_version >= "3.7" and python_version < "3.12" cwl-utils==0.27 ; python_version >= "3.7" and python_version < "3.12" cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.12" -cython==0.29.34 ; python_version >= "3.7" and python_version < "3.12" +cython==0.29.35 ; 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" @@ -65,6 +66,7 @@ docutils==0.18.1 ; python_version >= "3.7" and python_version < "3.12" ecdsa==0.18.0 ; python_version >= "3.7" and python_version < "3.12" edam-ontology==1.25.2 ; python_version >= "3.7" and python_version < "3.12" email-validator==2.0.0.post2 ; python_version >= "3.7" and python_version < "3.12" +exceptiongroup==1.1.1 ; python_version >= "3.7" and python_version < "3.12" fastapi-utils==0.2.1 ; python_version >= "3.7" and python_version < "3.12" fastapi==0.95.2 ; python_version >= "3.7" and python_version < "3.12" frozenlist==1.3.3 ; python_version >= "3.7" and python_version < "3.12" @@ -84,6 +86,7 @@ humanfriendly==10.0 ; python_version >= "3.7" and python_version < "3.12" idna==3.4 ; python_version >= "3.7" and python_version < "3.12" importlib-metadata==4.13.0 ; python_version >= "3.7" and python_version < "3.12" importlib-resources==5.12.0 ; python_version >= "3.7" and python_version < "3.12" +iniconfig==2.0.0 ; python_version >= "3.7" and python_version < "3.12" isa-rwval==0.10.10 ; python_version >= "3.7" and python_version < "3.12" isodate==0.6.1 ; python_version >= "3.7" and python_version < "3.12" jinja2==3.1.2 ; python_version >= "3.7" and python_version < "3.12" @@ -110,15 +113,17 @@ nodeenv==1.8.0 ; python_version >= "3.7" and python_version < "3.12" numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.8" numpy==1.24.3 ; python_version >= "3.8" and python_version < "3.12" oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12" -orjson==3.8.12 ; python_version >= "3.7" and python_version < "3.12" +orjson==3.8.14 ; python_version >= "3.7" and python_version < "3.12" +outcome==1.2.0 ; 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" -paramiko==3.1.0 ; python_version >= "3.7" and python_version < "3.12" +paramiko==3.2.0 ; 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" 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" +pluggy==1.0.0 ; python_version >= "3.7" and python_version < "3.12" prompt-toolkit==3.0.38 ; 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" @@ -127,8 +132,8 @@ pyasn1==0.5.0 ; python_version >= "3.7" and python_version < "3.12" pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12" pycryptodome==3.18.0 ; python_version >= "3.7" and python_version < "3.12" pydantic-tes==0.1.5 ; python_version >= "3.7" and python_version < "3.12" -pydantic==1.10.7 ; python_version >= "3.7" and python_version < "3.12" -pydantic[email]==1.10.7 ; python_version >= "3.7" and python_version < "3.12" +pydantic==1.10.8 ; python_version >= "3.7" and python_version < "3.12" +pydantic[email]==1.10.8 ; python_version >= "3.7" and python_version < "3.12" pydot==1.4.2 ; python_version >= "3.7" and python_version < "3.12" pyeventsystem==0.1.0 ; python_version >= "3.7" and python_version < "3.12" pyfaidx==0.7.2.1 ; python_version >= "3.7" and python_version < "3.12" @@ -142,6 +147,8 @@ pyreadline3==3.4.1 ; sys_platform == "win32" and python_version >= "3.8" and pyt 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" +pysocks==1.7.1 ; python_version >= "3.7" and python_version < "3.12" +pytest==7.3.1 ; 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" @@ -149,14 +156,14 @@ python-multipart==0.0.6 ; python_version >= "3.7" and python_version < "3.12" python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.12" pytz==2023.3 ; python_version >= "3.7" and python_version < "3.12" pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.12" -pyzmq==25.0.2 ; python_version >= "3.7" and python_version < "3.12" +pyzmq==25.1.0 ; 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" 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==2.30.0 ; python_version >= "3.7" and python_version < "3.12" +requests==2.31.0 ; python_version >= "3.7" and python_version < "3.12" rich==13.3.5 ; python_version >= "3.7" and python_version < "3.12" rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.12" routes==2.5.1 ; python_version >= "3.7" and python_version < "3.12" @@ -165,6 +172,7 @@ ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python 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==8.4.20230511084951 ; python_version >= "3.7" and python_version < "3.12" +selenium==4.9.1 ; python_version >= "3.7" and python_version < "3.12" setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.12" setuptools==67.8.0 ; python_version >= "3.7" and python_version < "3.12" shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.12" @@ -182,14 +190,18 @@ svgwrite==1.4.3 ; python_version >= "3.7" and python_version < "3.12" tenacity==8.2.2 ; python_version >= "3.7" and python_version < "3.12" tifffile==2021.11.2 ; python_version >= "3.7" and python_version < "3.12" tinydb==4.7.1 ; python_version >= "3.7" and python_version < "3.12" +tomli==2.0.1 ; python_version >= "3.7" and python_version < "3.11" tornado==6.2 ; python_version >= "3.7" and python_version < "3.12" tqdm==4.65.0 ; python_version >= "3.7" and python_version < "3.12" +trio-websocket==0.10.2 ; python_version >= "3.7" and python_version < "3.12" +trio==0.22.0 ; python_version >= "3.7" and python_version < "3.12" tuspy==1.0.0 ; python_version >= "3.7" and python_version < "3.12" tuswsgi==0.5.5 ; python_version >= "3.7" and python_version < "3.12" -typing-extensions==4.5.0 ; python_version >= "3.7" and python_version < "3.12" +typing-extensions==4.6.2 ; python_version >= "3.7" and python_version < "3.12" tzlocal==2.1 ; python_version >= "3.7" and python_version < "3.12" ubiquerg==0.6.2 ; python_version >= "3.7" and python_version < "3.12" -urllib3==1.26.15 ; 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" 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" @@ -198,6 +210,7 @@ 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" +wsproto==1.2.0 ; python_version >= "3.7" and python_version < "3.12" yacman==0.9.0 ; 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" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 857a490fc2b..efe4ac06589 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -3,7 +3,7 @@ cryptography==40.0.2 mypy==1.3.0 mypy-extensions==1.0.0 pycparser==2.21 -pydantic==1.10.7 +pydantic==1.10.8 tomli==2.0.1 typed-ast==1.5.4 types-bleach==6.0.0.3 @@ -15,8 +15,8 @@ types-Markdown==3.4.2.9 types-paramiko==3.0.0.10 types-pkg-resources==0.1.3 types-python-dateutil==2.8.19.13 -types-PyYAML==6.0.12.9 -types-requests==2.30.0.0 +types-PyYAML==6.0.12.10 +types-requests==2.31.0.0 types-six==1.16.21.8 types-urllib3==1.26.25.13 -typing_extensions==4.5.0 +typing_extensions==4.6.2