Add test for the error return

openfe/protocols/openmm_rfe/equil_rfe_methods.py

@@ -1101,10 +1101,11 @@ def structural_analysis(scratch, shared) -> dict:
         analysis_out = scratch / 'structural_analysis.json'
 
         ret = subprocess.run(
-            ['openfe_analysis',  # CLI entry point
-             'RFE_analysis',  # CLI option
-             str(shared),  # Where the simulation.nc fille
-             str(analysis_out) # Where the analysis json file is written
+            [
+                'openfe_analysis',  # CLI entry point
+                'RFE_analysis',  # CLI option
+                str(shared),  # Where the simulation.nc fille
+                str(analysis_out)  # Where the analysis json file is written
             ],
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE

openfe/tests/protocols/test_openmm_equil_rfe_protocols.py

@@ -10,6 +10,7 @@
 from importlib import resources
 from unittest import mock
 import sys
+from pathlib import Path
 
 import mdtraj as mdt
 import pytest
@@ -2103,3 +2104,14 @@ def test_dry_run_complex_alchemwater_totcharge(
         assert len(htf._atom_classes['core_atoms']) == core_atoms
         assert len(htf._atom_classes['unique_new_atoms']) == new_uniq
         assert len(htf._atom_classes['unique_old_atoms']) == old_uniq
+
+
+def test_structural_analysis_error(tmpdir):
+
+    with tmpdir.as_cwd():
+        ret = openmm_rfe.RelativeHybridTopologyProtocolUnit.structural_analysis(
+            Path('.'), Path('.')
+        )
+
+    assert 'structural_analysis_error' in ret
+    assert 'structural_analysis' not in ret