Merge pull request #17923 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -33,11 +33,11 @@ darker==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 darkgraylib==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
 deprecated==1.2.14 ; python_version >= "3.8" and python_version < "3.13"
-docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
+docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.13.3 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.50.0 ; python_version >= "3.8" and python_version < "3.13"
+fonttools==4.51.0 ; python_version >= "3.8" and python_version < "3.13"
 frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 galaxy-release-util==0.1.7 ; python_version >= "3.8" and python_version < "3.13"
 graylint==1.0.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -53,20 +53,20 @@ iniconfig==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isort==5.13.2 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-classes==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
-jaraco-context==4.3.0 ; python_version >= "3.8" and python_version < "3.13"
+jaraco-context==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
 jaraco-functools==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
 jeepney==0.8.0 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 jinja2==3.1.3 ; python_version >= "3.8" and python_version < "3.13"
 junit-xml==1.9 ; python_version >= "3.8" and python_version < "3.13"
-keyring==25.0.0 ; python_version >= "3.8" and python_version < "3.13"
+keyring==25.1.0 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
 kombu==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown-it-reporter==0.0.2 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 matplotlib==3.7.5 ; python_version >= "3.8" and python_version < "3.9"
-matplotlib==3.8.3 ; python_version >= "3.9" and python_version < "3.13"
+matplotlib==3.8.4 ; python_version >= "3.9" and python_version < "3.13"
 mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
 mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -82,7 +82,7 @@ numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
-pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
+pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -132,7 +132,7 @@ ruamel-yaml-clib==0.2.8 ; platform_python_implementation == "CPython" and python
 ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240311110950 ; python_version >= "3.8" and python_version < "3.13"
 scipy==1.10.1 ; python_version >= "3.8" and python_version < "3.9"
-scipy==1.12.0 ; python_version >= "3.9" and python_version < "3.13"
+scipy==1.13.0 ; python_version >= "3.9" and python_version < "3.13"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 selenium==4.19.0 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -141,7 +141,7 @@ 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"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
-sphinx-rtd-theme==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
+sphinx-rtd-theme==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 sphinx==7.1.2 ; python_version >= "3.8" and python_version < "3.13"
 sphinxcontrib-applehelp==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
 sphinxcontrib-devhelp==1.0.2 ; python_version >= "3.8" and python_version < "3.13"
@@ -161,14 +161,14 @@ trio==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 twill==3.2.3 ; python_version >= "3.8" and python_version < "3.13"
 twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
 urllib3[socks]==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
 vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
 watchdog==4.0.0 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"
-werkzeug==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
+werkzeug==3.0.2 ; 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==1.9.4 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -4,4 +4,4 @@ flake8-bugbear==24.2.6
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.3.4
+ruff==0.3.5

lib/galaxy/dependencies/pinned-requirements.txt

@@ -2,7 +2,7 @@
 
 a2wsgi==1.10.4 ; python_version >= "3.8" and python_version < "3.13"
 adal==1.2.7 ; python_version >= "3.8" and python_version < "3.13"
-aiobotocore==2.12.1 ; python_version >= "3.8" and python_version < "3.13"
+aiobotocore==2.12.2 ; python_version >= "3.8" and python_version < "3.13"
 aiodataloader==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
 aiofiles==23.2.1 ; python_version >= "3.8" and python_version < "3.13"
 aiohttp==3.9.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -31,7 +31,7 @@ beaker==1.12.1 ; python_version >= "3.8" and python_version < "3.13"
 billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
 bioblend==1.2.0 ; python_version >= "3.8" and python_version < "3.13"
 bleach==6.1.0 ; python_version >= "3.8" and python_version < "3.13"
-boltons==23.1.1 ; python_version >= "3.8" and python_version < "3.13"
+boltons==24.0.0 ; python_version >= "3.8" and python_version < "3.13"
 boto==2.49.0 ; python_version >= "3.8" and python_version < "3.13"
 botocore==1.34.51 ; python_version >= "3.8" and python_version < "3.13"
 bx-python==0.11.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -61,12 +61,12 @@ deprecation==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 dictobj==0.4 ; python_version >= "3.8" and python_version < "3.13"
 dnspython==2.6.1 ; python_version >= "3.8" and python_version < "3.13"
 docopt==0.6.2 ; python_version >= "3.8" and python_version < "3.13"
-docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
+docutils==0.20.1 ; python_version >= "3.8" and python_version < "3.13"
 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==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
-fastapi==0.110.0 ; python_version >= "3.8" and python_version < "3.13"
+fastapi==0.110.1 ; python_version >= "3.8" and python_version < "3.13"
 filelock==3.13.3 ; 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"
@@ -79,7 +79,7 @@ graphene==3.3 ; python_version >= "3.8" and python_version < "3.13"
 graphql-core==3.2.3 ; 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 >= "3.8" 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 < "3.13"
+greenlet==3.0.3 ; python_version >= "3.8" and 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")
 gunicorn==21.2.0 ; python_version >= "3.8" and python_version < "3.13"
 gxformat2==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
 h11==0.14.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -122,10 +122,10 @@ oyaml==1.0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
 paramiko==3.4.0 ; python_version >= "3.8" and python_version < "3.13"
 parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
-paste==3.8.0 ; python_version >= "3.8" and python_version < "3.13"
+paste==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.7 ; python_version >= "3.8" and python_version < "3.13"
-pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
+pillow==10.3.0 ; python_version >= "3.8" and python_version < "3.13"
 pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
 prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
@@ -182,12 +182,12 @@ sniffio==1.3.1 ; python_version >= "3.8" and python_version < "3.13"
 social-auth-core==4.5.3 ; python_version >= "3.8" and python_version < "3.13"
 sortedcontainers==2.4.0 ; python_version >= "3.8" and python_version < "3.13"
 spython==0.3.13 ; python_version >= "3.8" and python_version < "3.13"
-sqlalchemy==2.0.25 ; python_version >= "3.8" and python_version < "3.13"
+sqlalchemy==2.0.29 ; python_version >= "3.8" and python_version < "3.13"
 sqlitedict==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 sqlparse==0.4.4 ; 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==0.36.3 ; python_version >= "3.8" and python_version < "3.13"
+starlette==0.37.2 ; 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==8.2.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -198,10 +198,10 @@ tornado==6.4 ; python_version >= "3.8" and python_version < "3.13"
 tqdm==4.66.2 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 tuswsgi==0.5.5 ; python_version >= "3.8" and python_version < "3.13"
-typing-extensions==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"
 tzdata==2024.1 ; python_version >= "3.8" and python_version < "3.13"
 tzlocal==5.2 ; python_version >= "3.8" and python_version < "3.13"
-ubiquerg==0.7.0 ; python_version >= "3.8" and python_version < "3.13"
+ubiquerg==0.8.0 ; python_version >= "3.8" and python_version < "3.13"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
 uvicorn==0.29.0 ; python_version >= "3.8" and python_version < "3.13"
 uvloop==0.19.0 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/dependencies/pinned-typecheck-requirements.txt

@@ -12,7 +12,7 @@ types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.1
 types-boto==2.49.18.20240205 ; python_version >= "3.8" and python_version < "3.13"
 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==0.20.0.20240331 ; python_version >= "3.8" and python_version < "3.13"
+types-docutils==0.20.0.20240406 ; python_version >= "3.8" and python_version < "3.13"
 types-html5lib==1.1.11.20240228 ; python_version >= "3.8" and python_version < "3.13"
 types-markdown==3.6.0.20240316 ; python_version >= "3.8" and python_version < "3.13"
 types-paramiko==3.4.0.20240311 ; python_version >= "3.8" and python_version < "3.13"
@@ -22,4 +22,4 @@ types-pyyaml==6.0.12.20240311 ; python_version >= "3.8" and python_version < "3.
 types-requests==2.31.0.6 ; python_version >= "3.8" and python_version < "3.13"
 types-six==1.16.21.20240311 ; 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==4.10.0 ; python_version >= "3.8" and python_version < "3.13"
+typing-extensions==4.11.0 ; python_version >= "3.8" and python_version < "3.13"

pyproject.toml

@@ -158,7 +158,7 @@ selenium = "*"
 urllib3 = "<2"  # Necessary for poetry for resolve deps for Python 3.8+
 seletools = "*"
 Sphinx = ">=4.0"  # support docutils 0.17
-sphinx-rtd-theme = ">=1.0.0,<2"  # https://github.com/python-poetry/poetry/issues/8194
+sphinx-rtd-theme = "*"
 statsd = "*"
 testfixtures = "*"
 tuspy = "*"