From 138b61526a3862d78c3de2c4187fcbed588a9f60 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 6 Feb 2026 18:38:29 +0000
Subject: [PATCH] Update dependencies of pydantic-ai

---
 lib/galaxy/dependencies/dev-requirements.txt         |  2 +-
 lib/galaxy/dependencies/pinned-requirements.txt      | 11 ++++++-----
 lib/galaxy/dependencies/pinned-test-requirements.txt |  2 +-
 lib/galaxy/tool_util/version.py                      |  2 +-
 pyproject.toml                                       |  2 +-
 5 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 5163000cb7a..fd68d635905 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -112,7 +112,7 @@ oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==7.1.4
-packaging==26.0
+packaging==25.0
 pathspec==1.0.4
 pfzy==0.3.4
 pillow==12.1.0
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 8b84cb20cce..4a6d8c1a375 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -13,7 +13,7 @@ alembic==1.18.3
 amqp==5.3.1
 annotated-doc==0.0.4
 annotated-types==0.7.0
-anthropic==0.77.0
+anthropic==0.78.0
 anyio==4.12.1
 apispec==6.9.0
 appdirs==1.4.4
@@ -181,7 +181,7 @@ opentelemetry-semantic-conventions==0.60b1
 opentelemetry-util-http==0.60b1
 orjson==3.11.6
 oyaml==1.0
-packaging==26.0
+packaging==25.0
 paramiko==4.0.0
 parsley==1.3
 paste==3.10.1
@@ -207,10 +207,10 @@ pycparser==3.0 ; (implementation_name != 'PyPy' and platform_python_implementati
 pycryptodome==3.23.0
 pydantic==2.12.5
 pydantic-ai==1.56.0
-pydantic-ai-slim==1.44.0
+pydantic-ai-slim==1.56.0
 pydantic-core==2.41.5
-pydantic-evals==1.44.0
-pydantic-graph==1.44.0
+pydantic-evals==1.56.0
+pydantic-graph==1.56.0
 pydantic-settings==2.12.0
 pydantic-tes==0.2.0
 pydicom==3.0.1
@@ -309,6 +309,7 @@ webob==1.8.9
 websockets==15.0.1
 whoosh==2.7.4
 wrapt==1.17.3
+xai-sdk==1.6.1
 yacman==0.9.4
 yarl==1.22.0
 zipp==3.23.0
diff --git a/lib/galaxy/dependencies/pinned-test-requirements.txt b/lib/galaxy/dependencies/pinned-test-requirements.txt
index cd2c9e345bb..3007468bb4c 100644
--- a/lib/galaxy/dependencies/pinned-test-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-test-requirements.txt
@@ -87,7 +87,7 @@ oauthlib==3.3.1
 onedatafilerestclient==21.2.5.2
 outcome==1.3.0.post0
 owlrl==7.1.4
-packaging==26.0
+packaging==25.0
 pathspec==1.0.4
 pfzy==0.3.4
 pillow==12.1.0
diff --git a/lib/galaxy/tool_util/version.py b/lib/galaxy/tool_util/version.py
index 83ca6f1c1b5..4f17224417a 100644
--- a/lib/galaxy/tool_util/version.py
+++ b/lib/galaxy/tool_util/version.py
@@ -59,7 +59,7 @@ class LegacyVersion(_BaseVersion):
         self._version = str(version)
 
     @property
-    def _key(self) -> LegacyCmpKey:
+    def _key(self) -> LegacyCmpKey:  # type: ignore[override,unused-ignore]
         return _legacy_cmpkey(self._version)
 
     def __str__(self) -> str:
diff --git a/pyproject.toml b/pyproject.toml
index 3bf2df10d18..4dbe9983c38 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -76,7 +76,7 @@ dependencies = [
     "pulsar-galaxy-lib>=0.15.10",
     "pycryptodome",
     "pydantic[email]>=2.7.4",  # https://github.com/pydantic/pydantic/pull/9639
-    "pydantic-ai>=0.1.16",  # AI agent framework
+    "pydantic-ai>=1.56.0",  # https://github.com/pydantic/pydantic-ai/security/advisories/GHSA-2jrp-274c-jhv3
     "pydicom; python_version >= '3.10'",
     "PyJWT",
     "pykwalify",