Merge branch 'release_24.1' into dev

lib/galaxy/dependencies/__init__.py

@@ -294,6 +294,10 @@ class ConditionalDependencies:
         # See notes in ./conditional-requirements.txt for more information.
         return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"
 
+    def check_pydyf(self):
+        # See notes in ./conditional-requirements.txt for more information.
+        return os.environ.get("GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT") == "1"
+
     def check_custos_sdk(self):
         return "custos" == self.vault_type
 

lib/galaxy/dependencies/conditional-requirements.txt

@@ -60,7 +60,12 @@ tensorflow==2.9.3
 # xref https://github.com/galaxyproject/galaxy/pull/9651
 # Run run.sh or common_startup script with GALAXY_DEPENDENCIES_INSTALL_WEASYPRINT=1
 # to install weasyprint as part of Galaxy's conditonal dependency instalation process.
-weasyprint
+weasyprint>=61.2
+# We pin the transitive weasyprint dependency pydyf here because newer versions are
+# not compatible with the last weasyprint version that still supports python 3.8.
+# This dependency is ignored on python >= 3.9 and should be removed when deprecating
+# support for python 3.8.
+pydyf<0.11; python_version<"3.9"
 
 # AWS Batch runner
 boto3

lib/galaxy/tools/__init__.py

@@ -383,7 +383,7 @@ class PersistentToolTagManager(AbstractToolTagManager):
 
     def reset_tags(self):
         log.info(
-            f"removing all tool tag associations ({str(self.sa_session.scalar(select(func.count(self.app.model.ToolTagAssociation))))})"
+            f"removing all tool tag associations ({str(self.sa_session.scalar(select(func.count(self.app.model.ToolTagAssociation.id))))})"
         )
         self.sa_session.execute(delete(self.app.model.ToolTagAssociation))
         with transaction(self.sa_session):