Merge pull request #16485 from galaxybot/dev_auto_update_dependencies

Update Python dependencies

lib/galaxy/dependencies/dev-requirements.txt

@@ -16,7 +16,7 @@ build==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.12"
 cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
 celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
-certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12"
+certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.12"
 cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
 charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 click-didyoumean==0.3.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -77,7 +77,7 @@ numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.25.1 ; python_version >= "3.9" and python_version < "3.12"
 outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.12"
 packaging==23.1 ; python_version >= "3.7" and python_version < "3.12"
-pathspec==0.11.1 ; python_version >= "3.7" and python_version < "3.12"
+pathspec==0.11.2 ; python_version >= "3.7" and python_version < "3.12"
 pillow==9.5.0 ; python_version >= "3.7" and python_version < "3.12"
 pkce==1.0.3 ; python_version >= "3.7" and python_version < "3.12"
 pkginfo==1.9.6 ; python_version >= "3.7" and python_version < "3.12"

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==0.0.279
+ruff==0.0.280
 typing_extensions==4.7.1
 zipp==3.15.0

lib/galaxy/dependencies/pinned-requirements.txt

@@ -30,11 +30,11 @@ bleach==6.0.0 ; python_version >= "3.7" and python_version < "3.12"
 boltons==23.0.0 ; python_version >= "3.7" and python_version < "3.12"
 boto==2.49.0 ; python_version >= "3.7" and python_version < "3.12"
 botocore==1.27.59 ; python_version >= "3.7" and python_version < "3.12"
-bx-python==0.9.0 ; python_version >= "3.7" and python_version < "3.12"
+bx-python==0.10.0 ; python_version >= "3.7" and python_version < "3.12"
 cachecontrol[filecache]==0.13.1 ; python_version >= "3.7" and python_version < "3.12"
 cached-property==1.5.2 ; python_version >= "3.7" and python_version < "3.8"
 celery==5.2.7 ; python_version >= "3.7" and python_version < "3.12"
-certifi==2023.5.7 ; python_version >= "3.7" and python_version < "3.12"
+certifi==2023.7.22 ; python_version >= "3.7" and python_version < "3.12"
 cffi==1.15.1 ; python_version >= "3.7" and python_version < "3.12"
 charset-normalizer==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
 cheetah3==3.2.6.post1 ; python_version >= "3.7" and python_version < "3.12"
@@ -95,13 +95,13 @@ lagom==2.4.1 ; python_version >= "3.7" and python_version < "3.12"
 lxml==4.9.3 ; python_version >= "3.7" and python_version < "3.12"
 mako==1.2.4 ; python_version >= "3.7" and python_version < "3.12"
 markdown-it-py==2.2.0 ; python_version >= "3.7" and python_version < "3.12"
-markdown==3.4.3 ; python_version >= "3.7" and python_version < "3.12"
+markdown==3.4.4 ; python_version >= "3.7" and python_version < "3.12"
 markupsafe==2.1.3 ; python_version >= "3.7" and python_version < "3.12"
 mdurl==0.1.2 ; python_version >= "3.7" and python_version < "3.12"
 mercurial==6.5 ; python_version >= "3.7" and python_version < "3.12"
 mistune==2.0.5 ; python_version >= "3.7" and python_version < "3.12"
 mrcfile==1.4.3 ; python_version >= "3.7" and python_version < "3.12"
-msal==1.22.0 ; python_version >= "3.7" and python_version < "3.12"
+msal==1.23.0 ; python_version >= "3.7" and python_version < "3.12"
 msgpack==1.0.5 ; python_version >= "3.7" and python_version < "3.12"
 multidict==6.0.4 ; python_version >= "3.7" and python_version < "3.12"
 mypy-extensions==1.0.0 ; python_version >= "3.7" and python_version < "3.12"
@@ -114,7 +114,7 @@ oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.12"
 orjson==3.9.2 ; 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==3.2.0 ; python_version >= "3.7" and python_version < "3.12"
+paramiko==3.3.1 ; 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"
@@ -128,8 +128,8 @@ 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==1.10.11 ; python_version >= "3.7" and python_version < "3.12"
-pydantic[email]==1.10.11 ; python_version >= "3.7" and python_version < "3.12"
+pydantic==1.10.12 ; python_version >= "3.7" and python_version < "3.12"
+pydantic[email]==1.10.12 ; 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"

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

@@ -3,7 +3,7 @@ cryptography==41.0.2
 mypy==1.4.1
 mypy-extensions==1.0.0
 pycparser==2.21
-pydantic==1.10.11
+pydantic==1.10.12
 tomli==2.0.1
 typed-ast==1.5.5
 types-bleach==6.0.0.4