diff --git a/lib/galaxy/dependencies/update.sh b/lib/galaxy/dependencies/update.sh
index 12078ddbed3d..201f510ee9b6 100755
--- a/lib/galaxy/dependencies/update.sh
+++ b/lib/galaxy/dependencies/update.sh
@@ -38,7 +38,7 @@ uv="${uv_venv}/bin/uv"
 if [ -n "$pkg" ]; then
     ${uv} lock --upgrade-package "$pkg"
 else
-    ${uv} lock
+    ${uv} lock --upgrade
 fi
 
 # Update pinned requirements files.
diff --git a/pyproject.toml b/pyproject.toml
index 104425646e30..be857e903b7f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -149,7 +149,6 @@ dev = [
     "pytest-shard",
     "responses",
     "rucio-clients>=33.6.0 ; python_version>='3.9'",  # https://github.com/galaxyproject/galaxy/pull/17156
-    "scipy>=1.14.1; python_version>='3.10'",  # ase dependency, Python 3.13 support
     "selenium",
     "seletools",
     "Sphinx>=4.0",  # support docutils 0.17
@@ -238,6 +237,9 @@ keep-runtime-typing = true
 "lib/tool_shed_client/schema/trs_service_info.py" = ["UP006", "UP007"]
 
 [tool.uv]
+constraint-dependencies = [
+    "scipy>=1.14.1; python_version>='3.10'",  # Python 3.13 support
+]
 default-groups = []
 extra-index-url = ["https://wheels.galaxyproject.org/simple"]
 index-strategy = "unsafe-best-match"