force `subprocess.run` to check return code is 0

In general, this should help to capture unintentional errors.

Where the change has created failures, they have been fixed. (Mostly because the git repository that was looked for was missing.)

tests.py

@@ -118,6 +118,7 @@ def test_setup_log_cmd(tmp_path):
         initial_bytes = 0
 
     # run the prepare_env functionality
+    create_mock_git_repository(target_directory=script_dir, create_directory=True)
     mod.prepare_environment(mpsd_release=mpsd_release_to_test, script_dir=(script_dir))
 
     # check that logs/install-software-environment.log is updated
@@ -163,6 +164,7 @@ def test_install_environment(tmp_path):
     toolchain_to_test = "global_generic"
     mpsd_microarch = os.getenv("MPSD_MICROARCH", "UNKNOWN_MICROARCH")
     release_base_dir = script_dir / mpsd_release_to_test
+    create_mock_git_repository(target_directory=script_dir, create_directory=False)
     mod.prepare_environment(mpsd_release=mpsd_release_to_test, script_dir=(script_dir))
     # Patch the spack environments to create a fake global_generic
     # create a test toolchain