From 2e1195968e084efce27b6cca1e9f24b2a139e7b6 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 15 Nov 2024 01:16:02 +0000
Subject: [PATCH 1/2] Always upgrade packages

otherwise `uv lock` will have no effect if the `uv.lock` file is
present and there are no changes to the project's dependencies in
`pyproject.toml` .
---
 lib/galaxy/dependencies/update.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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.

From d24ae975ec5e9badce84ca40c2c02e8095d59e24 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 15 Nov 2024 01:20:02 +0000
Subject: [PATCH 2/2] Move scipy pinning to ``contraint-dependencies``

because it's a transitive dependency (from ase).
---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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"