From a398c0a0c2542ba89fcafe1f18a01e3c2ca179b4 Mon Sep 17 00:00:00 2001
From: bernadette <b.j.mohr@uva.nl>
Date: Mon, 4 Nov 2024 10:37:09 +0100
Subject: [PATCH 1/2] Fix shape mismatch of bond_list in model_system (#145)

Co-authored-by: Bernadette Mohr <bernadette.mohr@physik.hu-berlin.de>
---
 src/nomad_simulations/schema_packages/model_system.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/nomad_simulations/schema_packages/model_system.py b/src/nomad_simulations/schema_packages/model_system.py
index d47bf673..66364d5e 100644
--- a/src/nomad_simulations/schema_packages/model_system.py
+++ b/src/nomad_simulations/schema_packages/model_system.py
@@ -1082,6 +1082,7 @@ class ModelSystem(System):
     # TODO improve description and add an example using the case in atom_indices
     bond_list = Quantity(
         type=np.int32,
+        shape=['*', 2],
         description="""
         List of pairs of atom indices corresponding to bonds (e.g., as defined by a force field)
         within this atoms_group.

From 50154d5c92163104f0e2761fd91408a0c3029f8e Mon Sep 17 00:00:00 2001
From: ndaelman-hu <107392603+ndaelman-hu@users.noreply.github.com>
Date: Mon, 18 Nov 2024 11:06:50 +0100
Subject: [PATCH 2/2] Bump dependencies (#147)

Co-authored-by: ndaelman <ndaelman@physik.hu-berlin.de>
---
 pyproject.toml | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index da497aba..79cdc04d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,12 +40,13 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    "mypy==1.0.1",
-    "ruff",
-    "pytest",
-    "pytest-timeout",
-    "pytest-cov",
-    "structlog",
+    'mypy==1.0.1',
+    'pytest>= 5.3.0, <8',
+    'pytest-timeout>=1.4.2',
+    'pytest-cov>=2.7.1',
+    'ruff>=0.6',
+    'structlog>=1.0',
+    'typing-extensions>=4.12',
 ]
 
 [tool.uv]