Merge branch 'release_24.1' into dev

lib/galaxy/dependencies/pinned-requirements.txt

@@ -135,8 +135,8 @@ pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13"
 pycryptodome==3.20.0 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
 pydantic-tes==0.1.5 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
-pydantic[email]==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
+pydantic[email]==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
 pydot==2.0.0 ; python_version >= "3.8" and python_version < "3.13"
 pyeventsystem==0.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pyfaidx==0.8.1.1 ; python_version >= "3.8" and python_version < "3.13"

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

@@ -9,7 +9,7 @@ mypy-extensions==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
 mypy==1.10.0 ; python_version >= "3.8" and python_version < "3.13"
 pycparser==2.22 ; python_version >= "3.8" and python_version < "3.13" and platform_python_implementation != "PyPy"
 pydantic-core==2.18.4 ; python_version >= "3.8" and python_version < "3.13"
-pydantic==2.7.3 ; python_version >= "3.8" and python_version < "3.13"
+pydantic==2.7.4 ; python_version >= "3.8" and python_version < "3.13"
 tomli==2.0.1 ; python_version >= "3.8" and python_version < "3.11"
 types-awscrt==0.20.11 ; python_version >= "3.8" and python_version < "3.13"
 types-bleach==6.1.0.20240331 ; python_version >= "3.8" and python_version < "3.13"

packages/app/setup.cfg

@@ -61,7 +61,7 @@ install_requires =
     paramiko!=2.9.0,!=2.9.1
     pebble
     pulsar-galaxy-lib>=0.15.0.dev0
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     pysam>=0.21
     PyJWT
     PyYAML

packages/data/setup.cfg

@@ -53,7 +53,7 @@ install_requires =
     numpy
     parsley
     pycryptodome
-    pydantic[email]>=2,!=2.6.0,!=2.6.1
+    pydantic[email]>=2.7.4
     pylibmagic
     python-magic
     pysam>=0.21

packages/schema/setup.cfg

@@ -33,7 +33,7 @@ version = 23.2.dev0
 include_package_data = True
 install_requires =
     galaxy-util
-    pydantic[email]>=2,!=2.6.0,!=2.6.1
+    pydantic[email]>=2.7.4
 packages = find:
 python_requires = >=3.8
 

packages/tool_shed/setup.cfg

@@ -50,7 +50,7 @@ install_requires =
     MarkupSafe
     mercurial
     Paste
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     Routes
     SQLAlchemy>=2.0,<2.1
     starlette

packages/tours/setup.cfg

@@ -33,7 +33,7 @@ version = 23.2.dev0
 include_package_data = True
 install_requires =
     galaxy-navigation
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     PyYAML
 packages = find:
 python_requires = >=3.8

packages/web_apps/setup.cfg

@@ -50,7 +50,7 @@ install_requires =
     Mako
     MarkupSafe
     Paste
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     PyJWT
     python-dateutil
     python-multipart  # required to support form parsing in FastAPI/Starlette

packages/web_framework/setup.cfg

@@ -37,7 +37,7 @@ install_requires =
     babel
     MarkupSafe
     paste
-    pydantic>=2,!=2.6.0,!=2.6.1
+    pydantic>=2.7.4
     requests
     Routes
     SQLAlchemy>=2.0,<2.1

pyproject.toml

@@ -92,7 +92,7 @@ pillow = "*"
 psutil = "*"
 pulsar-galaxy-lib = ">=0.15.0.dev0"
 pycryptodome = "*"
-pydantic = {version = ">=2.7.0", extras = ["email"]}  # https://github.com/pydantic/pydantic/issues/8760
+pydantic = {version = ">=2.7.4", extras = ["email"]}  # https://github.com/pydantic/pydantic/pull/9639
 PyJWT = "*"
 pykwalify = "*"
 pylibmagic = "*"
@@ -175,7 +175,7 @@ Werkzeug = "*"
 mypy = "*"
 boto3-stubs = {version = "*", extras = ["s3"]}
 lxml-stubs = "*"
-pydantic = ">=2, !=2.6.0, !=2.6.1"  # for pydantic.mypy plugin
+pydantic = ">=2.7.4"  # for pydantic.mypy plugin
 types-bleach = "*"
 types-boto = "*"
 types-contextvars = "*"