Merge pull request galaxyproject#17819 from galaxybot/dev_auto_update…

…_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -18,7 +18,7 @@ celery==5.3.6 ; 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"
+click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13"
 click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 click-repl==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
@@ -47,16 +47,18 @@ httpcore==1.0.4 ; python_version >= "3.8" and python_version < "3.13"
 httpx==0.27.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
 imagesize==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.3.1 ; python_version >= "3.8" and python_version < "3.10"
+importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
+importlib-resources==6.4.0 ; 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==3.3.1 ; python_version >= "3.8" and python_version < "3.13"
+jaraco-context==4.3.0 ; 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==24.3.1 ; python_version >= "3.8" and python_version < "3.13"
+keyring==25.0.0 ; python_version >= "3.8" and python_version < "3.13"
 kiwisolver==1.4.5 ; python_version >= "3.8" and python_version < "3.13"
 kombu==5.3.5 ; python_version >= "3.8" and python_version < "3.13"
 lxml==4.9.4 ; python_version >= "3.8" and python_version < "3.13"
@@ -93,22 +95,22 @@ psutil==5.9.8 ; python_version >= "3.8" and python_version < "3.13" and sys_plat
 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==2.2.0 ; python_version >= "3.8" and python_version < "3.13"
+pygithub==2.3.0 ; 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==3.1.2 ; 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==0.23.5.post1 ; python_version >= "3.8" and python_version < "3.13"
+pytest-asyncio==0.23.6 ; 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-cov==5.0.0 ; 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==1.0.10 ; 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==3.1.1 ; python_version >= "3.8" and python_version < "3.13"
-pytest-mock==3.12.0 ; python_version >= "3.8" and python_version < "3.13"
+pytest-mock==3.14.0 ; 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==6.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pytest-shard==0.1.2 ; 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==0.3.3
+ruff==0.3.4

lib/galaxy/dependencies/pinned-requirements.txt

@@ -42,7 +42,7 @@ 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"
 cheetah3==3.2.6.post1 ; python_version >= "3.8" and python_version < "3.13"
 circus==0.18.0 ; python_version >= "3.8" and python_version < "3.13"
-click-didyoumean==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
+click-didyoumean==0.3.1 ; python_version >= "3.8" and python_version < "3.13"
 click-plugins==1.1.1 ; python_version >= "3.8" and python_version < "3.13"
 click-repl==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
 click==8.1.7 ; python_version >= "3.8" and python_version < "3.13"
@@ -83,12 +83,12 @@ greenlet==3.0.3 ; python_version >= "3.8" and (platform_machine == "aarch64" or
 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"
-h5grove==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
+h5grove==2.1.0 ; python_version >= "3.8" and python_version < "3.13"
 h5py==3.10.0 ; python_version >= "3.8" and python_version < "3.13"
 humanfriendly==10.0 ; python_version >= "3.8" and python_version < "3.13"
 idna==3.6 ; python_version >= "3.8" and python_version < "3.13"
-importlib-metadata==7.0.2 ; python_version >= "3.8" and python_version < "3.13"
-importlib-resources==6.3.1 ; python_version >= "3.8" and python_version < "3.9"
+importlib-metadata==7.1.0 ; python_version >= "3.8" and python_version < "3.13"
+importlib-resources==6.4.0 ; python_version >= "3.8" and python_version < "3.9"
 isa-rwval==0.10.10 ; python_version >= "3.8" and python_version < "3.13"
 isal==1.6.1 ; python_version >= "3.8" and python_version < "3.13"
 isodate==0.6.1 ; python_version >= "3.8" and python_version < "3.13"
@@ -105,10 +105,10 @@ markdown-it-py==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 markdown==3.6 ; python_version >= "3.8" and python_version < "3.13"
 markupsafe==2.1.5 ; python_version >= "3.8" and python_version < "3.13"
 mdurl==0.1.2 ; python_version >= "3.8" and python_version < "3.13"
-mercurial==6.7 ; python_version >= "3.8" and python_version < "3.13"
+mercurial==6.7.1 ; python_version >= "3.8" and python_version < "3.13"
 mistune==3.0.2 ; python_version >= "3.8" and python_version < "3.13"
 mrcfile==1.5.0 ; python_version >= "3.8" and python_version < "3.13"
-msal==1.27.0 ; python_version >= "3.8" and python_version < "3.13"
+msal==1.28.0 ; python_version >= "3.8" and python_version < "3.13"
 msgpack==1.0.8 ; 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"
@@ -124,7 +124,7 @@ 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"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
-pebble==5.0.6 ; 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"
 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"
@@ -162,7 +162,7 @@ referencing==0.34.0 ; python_version >= "3.8" and python_version < "3.13"
 refgenconf==0.12.2 ; python_version >= "3.8" and python_version < "3.13"
 regex==2023.12.25 ; python_version >= "3.8" and python_version < "3.13"
 repoze-lru==0.7 ; python_version >= "3.8" and python_version < "3.13"
-requests-oauthlib==1.4.0 ; python_version >= "3.8" and python_version < "3.13"
+requests-oauthlib==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-toolbelt==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 requests-unixsocket==0.3.0 ; python_version >= "3.8" and python_version < "3.13"
 requests==2.31.0 ; python_version >= "3.8" and python_version < "3.13"
@@ -203,7 +203,7 @@ 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"
 urllib3==1.26.18 ; python_version >= "3.8" and python_version < "3.13"
-uvicorn==0.27.1 ; 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"
 vine==5.1.0 ; python_version >= "3.8" and python_version < "3.13"
 wcwidth==0.2.13 ; python_version >= "3.8" and python_version < "3.13"