Merge pull request #17420 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

.github/workflows/dependencies.yaml

@@ -2,6 +2,7 @@ name: Update dependencies
 on:
   schedule:
     - cron: '0 3 * * 6'  # Run every saturday at 3 am.
+  workflow_dispatch:
 jobs:
   update_dependencies:
     name: Update dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -1,4 +1,4 @@
-aiohttp==3.9.1 ; python_version >= "3.8" and python_version < "3.13"
+aiohttp==3.9.3 ; 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"
 amqp==5.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -11,11 +11,11 @@ babel==2.14.0 ; python_version >= "3.8" and python_version < "3.13"
 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"
 billiard==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
-black==24.1.1 ; python_version >= "3.8" and python_version < "3.13"
+black==24.2.0 ; python_version >= "3.8" and python_version < "3.13"
 build==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.8" and python_version < "3.13"
 celery==5.3.6 ; python_version >= "3.8" and python_version < "3.13"
-certifi==2023.11.17 ; python_version >= "3.8" and python_version < "3.13"
+certifi==2024.2.2 ; python_version >= "3.8" and python_version < "3.13"
 cffi==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 charset-normalizer==3.3.2 ; python_version >= "3.8" and python_version < "3.13"
 click-didyoumean==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -26,8 +26,8 @@ codespell==2.2.6 ; python_version >= "3.8" and python_version < "3.13"
 colorama==0.4.6 ; python_version >= "3.8" and python_version < "3.13" and (sys_platform == "win32" or platform_system == "Windows" or os_name == "nt")
 contourpy==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 coverage[toml]==7.4.1 ; python_version >= "3.8" and python_version < "3.13"
-cryptography==42.0.1 ; python_version >= "3.8" and python_version < "3.13"
-cwltest==2.4.20231222081524 ; python_version >= "3.8" and python_version < "3.13"
+cryptography==42.0.2 ; python_version >= "3.8" and python_version < "3.13"
+cwltest==2.4.20240129145612 ; python_version >= "3.8" and python_version < "3.13"
 cycler==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
 darker==1.7.2 ; python_version >= "3.8" and python_version < "3.13"
 defusedxml==0.7.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -36,7 +36,7 @@ docutils==0.18.1 ; python_version >= "3.8" and python_version < "3.13"
 exceptiongroup==1.2.0 ; python_version >= "3.8" and python_version < "3.11"
 filelock==3.13.1 ; python_version >= "3.8" and python_version < "3.13"
 fluent-logger==0.10.0 ; python_version >= "3.8" and python_version < "3.13"
-fonttools==4.47.2 ; python_version >= "3.8" and python_version < "3.13"
+fonttools==4.48.1 ; 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==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
 greenlet==3.0.3 ; python_version >= "3.8" and python_version < "3.13"
@@ -50,7 +50,7 @@ importlib-resources==6.1.1 ; python_version >= "3.8" and python_version < "3.10"
 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==3.3.0 ; python_version >= "3.8" and python_version < "3.13"
+jaraco-classes==3.3.1 ; 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"
@@ -60,7 +60,7 @@ kombu==5.3.5 ; 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==2.1.4 ; python_version >= "3.8" and python_version < "3.13"
+markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 matplotlib==3.7.4 ; python_version >= "3.8" and python_version < "3.9"
 matplotlib==3.8.2 ; python_version >= "3.9" and python_version < "3.13"
 mdit-py-plugins==0.4.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -69,70 +69,70 @@ mirakuru==2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 mistune==2.0.5 ; python_version >= "3.8" and python_version < "3.13"
 more-itertools==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.7 ; python_version >= "3.8" and python_version < "3.13"
-multidict==6.0.4 ; python_version >= "3.8" and python_version < "3.13"
+multidict==6.0.5 ; python_version >= "3.8" and python_version < "3.13"
 mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 myst-parser==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.15 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
-numpy==1.26.3 ; python_version >= "3.9" and python_version < "3.13"
+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==23.2 ; 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"
 pkce==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
 pkginfo==1.9.6 ; python_version >= "3.8" and python_version < "3.13"
-platformdirs==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
-playwright==1.41.1 ; python_version >= "3.8" and python_version < "3.13"
+platformdirs==4.2.0 ; python_version >= "3.8" and python_version < "3.13"
+playwright==1.41.2 ; python_version >= "3.8" and python_version < "3.13"
 pluggy==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
 port-for==0.7.2 ; python_version >= "3.8" and python_version < "3.13"
 prettytable==3.9.0 ; python_version >= "3.8" and python_version < "3.13"
 prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"
 psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_platform != "cygwin"
-psycopg==3.1.17 ; python_version >= "3.8" and python_version < "3.13"
+psycopg==3.1.18 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.21 ; python_version >= "3.8" and python_version < "3.13"
 pyee==11.0.1 ; python_version >= "3.8" and python_version < "3.13"
-pygithub==2.1.1 ; python_version >= "3.8" and python_version < "3.13"
+pygithub==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pygments==2.17.2 ; python_version >= "3.8" and python_version < "3.13"
 pyjwt[crypto]==2.8.0 ; python_version >= "3.8" and python_version < "3.13"
 pynacl==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
 pyparsing==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
 pyproject-hooks==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pysocks==1.7.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-asyncio==0.23.3 ; python_version >= "3.8" and python_version < "3.13"
-pytest-base-url==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-asyncio==0.23.5 ; 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-celery==0.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-cov==4.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-html==4.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-httpserver==1.0.8 ; python_version >= "3.8" and python_version < "3.13"
+pytest-httpserver==1.0.9 ; python_version >= "3.8" and python_version < "3.13"
 pytest-json-report==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-metadata==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-metadata==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
 pytest-mock==3.12.0 ; python_version >= "3.8" and python_version < "3.13"
-pytest-playwright==0.4.3 ; python_version >= "3.8" and python_version < "3.13"
-pytest-postgresql==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-playwright==0.4.4 ; python_version >= "3.8" and python_version < "3.13"
+pytest-postgresql==5.1.0 ; 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"
 python-dateutil==2.8.2 ; python_version >= "3.8" and python_version < "3.13"
-python-irodsclient==1.1.9 ; python_version >= "3.8" and python_version < "3.13"
-python-slugify==8.0.2 ; python_version >= "3.8" and python_version < "3.13"
-pytz==2023.3.post1 ; python_version >= "3.8" and python_version < "3.9"
+python-irodsclient==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
+python-slugify==8.0.4 ; python_version >= "3.8" and python_version < "3.13"
+pytz==2024.1 ; python_version >= "3.8" and python_version < "3.9"
 pywin32-ctypes==0.2.2 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "win32"
 pyyaml==6.0.1 ; python_version >= "3.8" and python_version < "3.13"
 rdflib==6.3.2 ; python_version >= "3.8" and python_version < "3.13"
 readme-renderer==42.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
-responses==0.24.1 ; python_version >= "3.8" and python_version < "3.13"
+responses==0.25.0 ; python_version >= "3.8" and python_version < "3.13"
 rfc3986==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 rich==13.7.0 ; 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==0.18.5 ; python_version >= "3.8" and python_version < "3.13"
+ruamel-yaml==0.18.6 ; python_version >= "3.8" and python_version < "3.13"
 schema-salad==8.5.20240102191335 ; 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"
 secretstorage==3.3.3 ; python_version >= "3.8" and python_version < "3.13" and sys_platform == "linux"
 selenium==4.17.2 ; python_version >= "3.8" and python_version < "3.13"
 seletools==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
-setuptools==69.0.3 ; python_version >= "3.8" and python_version < "3.13"
+setuptools==69.1.0 ; python_version >= "3.8" and python_version < "3.13"
 six==1.16.0 ; python_version >= "3.8" and python_version < "3.13"
 sniffio==1.3.0 ; python_version >= "3.8" and python_version < "3.13"
 snowballstemmer==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -155,14 +155,14 @@ tomli==2.0.1 ; 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==0.24.0 ; python_version >= "3.8" and python_version < "3.13"
 tuspy==1.0.3 ; python_version >= "3.8" and python_version < "3.13"
-twill==3.2.1 ; python_version >= "3.8" and python_version < "3.13"
-twine==4.0.2 ; python_version >= "3.8" and python_version < "3.13"
+twill==3.2.2 ; python_version >= "3.8" and python_version < "3.13"
+twine==5.0.0 ; python_version >= "3.8" and python_version < "3.13"
 typing-extensions==4.9.0 ; python_version >= "3.8" and python_version < "3.13"
-tzdata==2023.4 ; 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==3.0.0 ; 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"
 wrapt==1.16.0 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -1,7 +1,7 @@
 attrs==23.2.0
 flake8==7.0.0
-flake8-bugbear==24.1.17
+flake8-bugbear==24.2.6
 mccabe==0.7.0
 pycodestyle==2.11.1
 pyflakes==3.2.0
-ruff==0.1.14
+ruff==0.2.1