diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 3cd3ac96a376..cee7b0cc4f00 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -5,7 +5,7 @@ amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.12" anyio==4.2.0 ; python_version >= "3.8" and python_version < "3.12" ase==3.22.1 ; python_version >= "3.8" and python_version < "3.12" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" -attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.12" +attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.12" axe-selenium-python==2.1.6 ; python_version >= "3.8" and python_version < "3.12" babel==2.14.0 ; python_version >= "3.8" and python_version < "3.12" backports-zoneinfo==0.2.1 ; python_version >= "3.8" and python_version < "3.9" @@ -27,7 +27,7 @@ colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.12" and (sys_p contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.12" coverage[toml]==7.4.0 ; python_version >= "3.8" and python_version < "3.12" cryptography==41.0.7 ; python_version >= "3.8" and python_version < "3.12" -cwltest==2.4.20231031143732 ; python_version >= "3.8" and python_version < "3.12" +cwltest==2.4.20231222081524 ; python_version >= "3.8" and python_version < "3.12" cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.12" darker==1.7.2 ; python_version >= "3.8" and python_version < "3.12" defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.12" @@ -74,11 +74,11 @@ mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12" myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.12" nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.12" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12" +numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.12" outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.12" packaging==23.2 ; python_version >= "3.8" and python_version < "3.12" pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.12" -pillow==10.1.0 ; python_version >= "3.8" and python_version < "3.12" +pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.12" pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.12" pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.12" platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.12" @@ -98,7 +98,7 @@ pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.12" pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.12" pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.12" pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.12" -pytest-asyncio==0.23.2 ; python_version >= "3.8" and python_version < "3.12" +pytest-asyncio==0.23.3 ; python_version >= "3.8" and python_version < "3.12" pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.12" pytest-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.12" pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.12" @@ -110,7 +110,7 @@ pytest-mock==3.12.0 ; python_version >= "3.8" and python_version < "3.12" pytest-playwright==0.4.3 ; python_version >= "3.8" and python_version < "3.12" pytest-postgresql==5.0.0 ; python_version >= "3.8" and python_version < "3.12" pytest-shard==0.1.2 ; python_version >= "3.8" and python_version < "3.12" -pytest==7.4.3 ; python_version >= "3.8" and python_version < "3.12" +pytest==7.4.4 ; python_version >= "3.8" and python_version < "3.12" python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.12" python-irodsclient==1.1.9 ; python_version >= "3.8" and python_version < "3.12" python-slugify==8.0.1 ; python_version >= "3.8" and python_version < "3.12" @@ -126,7 +126,7 @@ rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.12" rich==13.7.0 ; python_version >= "3.8" and python_version < "3.12" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8" ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12" -schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12" +schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.12" scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9" scipy==1.11.4 ; python_version >= "3.9" and python_version < "3.12" secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.12" and sys_platform == "linux" @@ -163,7 +163,7 @@ urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.12" urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.12" vine==5.1.0 ; python_version >= "3.8" and python_version < "3.12" watchdog==3.0.0 ; python_version >= "3.8" and python_version < "3.12" -wcwidth==0.2.12 ; python_version >= "3.8" and python_version < "3.12" +wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.12" werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.12" wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.12" wsproto==1.2.0 ; python_version >= "3.8" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt index 1acd282d8150..d8ff88cf0f62 100644 --- a/lib/galaxy/dependencies/pinned-lint-requirements.txt +++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt @@ -1,7 +1,7 @@ -attrs==23.1.0 -flake8==6.1.0 +attrs==23.2.0 +flake8==7.0.0 flake8-bugbear==23.12.2 mccabe==0.7.0 pycodestyle==2.11.1 -pyflakes==3.1.0 -ruff==0.1.9 +pyflakes==3.2.0 +ruff==0.1.11 diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 1ba8403cdfd2..667b4a7eda42 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -16,7 +16,7 @@ arcp==0.2.1 ; python_version >= "3.8" and python_version < "3.12" argcomplete==3.2.1 ; python_version >= "3.8" and python_version < "3.12" async-timeout==4.0.3 ; python_version >= "3.8" and python_version < "3.11" attmap==0.13.2 ; python_version >= "3.8" and python_version < "3.12" -attrs==23.1.0 ; python_version >= "3.8" and python_version < "3.12" +attrs==23.2.0 ; python_version >= "3.8" and python_version < "3.12" babel==2.14.0 ; python_version >= "3.8" and python_version < "3.12" 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" @@ -112,7 +112,7 @@ mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.12" networkx==2.5 ; python_version >= "3.8" and python_version < "3.12" nodeenv==1.8.0 ; python_version >= "3.8" and python_version < "3.12" numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9" -numpy==1.26.2 ; python_version >= "3.9" and python_version < "3.12" +numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.12" oauthlib==3.2.2 ; python_version >= "3.8" and python_version < "3.12" orjson==3.9.10 ; python_version >= "3.8" and python_version < "3.12" oyaml==1.0 ; python_version >= "3.8" and python_version < "3.12" @@ -134,7 +134,7 @@ pycryptodome==3.19.1 ; python_version >= "3.8" and python_version < "3.12" pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.12" pydantic==1.10.13 ; python_version >= "3.8" and python_version < "3.12" pydantic[email]==1.10.13 ; python_version >= "3.8" and python_version < "3.12" -pydot==1.4.2 ; python_version >= "3.8" and python_version < "3.12" +pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.12" pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.12" pyfaidx==0.7.2.2 ; python_version >= "3.8" and python_version < "3.12" pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.12" @@ -155,7 +155,7 @@ pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.12" pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.12" pyzmq==25.1.2 ; python_version >= "3.8" and python_version < "3.12" rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.12" -referencing==0.32.0 ; python_version >= "3.8" and python_version < "3.12" +referencing==0.32.1 ; python_version >= "3.8" and python_version < "3.12" refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.12" regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.12" repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.12" @@ -171,7 +171,7 @@ rsa==4.9 ; python_version >= "3.8" and python_version < "3.12" ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python_version < "3.12" and python_version >= "3.8" ruamel-yaml==0.18.5 ; python_version >= "3.8" and python_version < "3.12" s3fs==2023.12.2 ; python_version >= "3.8" and python_version < "3.12" -schema-salad==8.5.20231201181309 ; python_version >= "3.8" and python_version < "3.12" +schema-salad==8.5.20240102191335 ; python_version >= "3.8" and python_version < "3.12" setuptools-scm==5.0.2 ; python_version >= "3.8" and python_version < "3.12" setuptools==69.0.3 ; python_version >= "3.8" and python_version < "3.12" shellescape==3.8.1 ; python_version >= "3.8" and python_version < "3.12" @@ -180,7 +180,7 @@ sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.12" social-auth-core[openidconnect]==4.0.3 ; python_version >= "3.8" and python_version < "3.12" sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.12" spython==0.3.13 ; python_version >= "3.8" and python_version < "3.12" -sqlalchemy==1.4.50 ; python_version >= "3.8" and python_version < "3.12" +sqlalchemy==1.4.51 ; python_version >= "3.8" and python_version < "3.12" sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.12" sqlparse==0.4.4 ; python_version >= "3.8" and python_version < "3.12" starlette-context==0.3.6 ; python_version >= "3.8" and python_version < "3.12" @@ -204,7 +204,7 @@ urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.12" uvicorn==0.25.0 ; python_version >= "3.8" and python_version < "3.12" uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.12" vine==5.1.0 ; python_version >= "3.8" and python_version < "3.12" -wcwidth==0.2.12 ; python_version >= "3.8" and python_version < "3.12" +wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.12" webencodings==0.5.1 ; python_version >= "3.8" and python_version < "3.12" webob==1.8.7 ; python_version >= "3.8" and python_version < "3.12" whoosh==2.7.4 ; python_version >= "3.8" and python_version < "3.12" diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt index 57a3f369a2cc..163367008ef7 100644 --- a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt +++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt @@ -9,13 +9,13 @@ types-bleach==6.1.0.1 ; python_version >= "3.8" and python_version < "3.12" types-boto==2.49.18.9 ; python_version >= "3.8" and python_version < "3.12" types-contextvars==2.4.7.3 ; python_version >= "3.8" and python_version < "3.12" types-dataclasses==0.6.6 ; python_version >= "3.8" and python_version < "3.12" -types-docutils==0.20.0.3 ; python_version >= "3.8" and python_version < "3.12" -types-markdown==3.5.0.3 ; python_version >= "3.8" and python_version < "3.12" -types-paramiko==3.3.0.2 ; python_version >= "3.8" and python_version < "3.12" +types-docutils==0.20.0.20240106 ; python_version >= "3.8" and python_version < "3.12" +types-markdown==3.5.0.20240106 ; python_version >= "3.8" and python_version < "3.12" +types-paramiko==3.4.0.20240106 ; python_version >= "3.8" and python_version < "3.12" types-pkg-resources==0.1.3 ; python_version >= "3.8" and python_version < "3.12" -types-python-dateutil==2.8.19.14 ; python_version >= "3.8" and python_version < "3.12" +types-python-dateutil==2.8.19.20240106 ; python_version >= "3.8" and python_version < "3.12" types-pyyaml==6.0.12.12 ; python_version >= "3.8" and python_version < "3.12" types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.12" -types-six==1.16.21.9 ; python_version >= "3.8" and python_version < "3.12" +types-six==1.16.21.20240106 ; python_version >= "3.8" and python_version < "3.12" types-urllib3==1.26.25.14 ; python_version >= "3.8" and python_version < "3.12" typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.12"