Disallow SQLAlchemy 2.0.41

due to //github.com/sqlalchemy/sqlalchemy/issues/12600 .

Author: nsoranzo

packages/app/setup.cfg

@@ -72,7 +72,7 @@ install_requires =
     refgenconf>=0.12.0
     regex
     requests
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
     sqlitedict
     starlette
     svgwrite

packages/data/setup.cfg

@@ -58,7 +58,7 @@ install_requires =
     pysam>=0.21
     rocrate
     social-auth-core>=4.5.0
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
     tifffile
     typing-extensions
 packages = find:

packages/job_execution/setup.cfg

@@ -38,7 +38,7 @@ install_requires =
     galaxy-tool-util
     galaxy-util
     MarkupSafe
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
 packages = find:
 python_requires = >=3.9
 

packages/tool_shed/setup.cfg

@@ -49,7 +49,7 @@ install_requires =
     Paste
     pydantic>=2.7.4
     Routes
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
     slowapi
     starlette
     starlette-context

packages/web_apps/setup.cfg

@@ -57,7 +57,7 @@ install_requires =
     PyYAML
     requests
     Routes
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
     starlette
     starlette-context
     tuswsgi

packages/web_framework/setup.cfg

@@ -40,7 +40,7 @@ install_requires =
     pydantic>=2.7.4
     requests
     Routes
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
     WebOb
 
 packages = find:

packages/web_stack/setup.cfg

@@ -34,7 +34,7 @@ include_package_data = True
 install_requires =
     galaxy-data
     galaxy-util
-    SQLAlchemy>=2.0,<2.1,!=2.0.36
+    SQLAlchemy>=2.0.37,<2.1,!=2.0.41
 packages = find:
 python_requires = >=3.9
 

pyproject.toml

@@ -93,7 +93,7 @@ dependencies = [
     "slowapi",
     "social-auth-core>=4.5.0",  # to drop dependency on abandoned python-jose
     "sortedcontainers",
-    "SQLAlchemy>=2.0,<2.1,!=2.0.36",  # https://github.com/sqlalchemy/sqlalchemy/issues/12019,
+    "SQLAlchemy>=2.0.37,<2.1,!=2.0.41",  # https://github.com/sqlalchemy/sqlalchemy/issues/12019 , https://github.com/sqlalchemy/sqlalchemy/issues/12600
     "sqlitedict",
     "sqlparse",
     "starlette",