Trying to speed up CI a little bit

openfe/tests/protocols/conftest.py

@@ -10,17 +10,23 @@
 import pooch
 
 
+@pytest.fixture(scope='session')
+def charged_benzene(benzene_modifications):
+    benzene_offmol = benzene_modifications['benzene'].to_openff()
+    benzene_offmol.assign_partial_charges(partial_charge_method='gasteiger')
+    return openfe.SmallMoleculeComponent.from_openff(benzene_offmol)
+
 @pytest.fixture
-def benzene_vacuum_system(benzene_modifications):
+def benzene_vacuum_system(charged_benzene):
     return openfe.ChemicalSystem(
-        {'ligand': benzene_modifications['benzene']},
+        {'ligand': charged_benzene},
     )
 
 
 @pytest.fixture(scope='session')
-def benzene_system(benzene_modifications):
+def benzene_system(charged_benzene):
     return openfe.ChemicalSystem(
-        {'ligand': benzene_modifications['benzene'],
+        {'ligand': charged_benzene,
          'solvent': openfe.SolventComponent(
              positive_ion='Na', negative_ion='Cl',
              ion_concentration=0.15 * unit.molar)
@@ -29,27 +35,34 @@ def benzene_system(benzene_modifications):
 
 
 @pytest.fixture
-def benzene_complex_system(benzene_modifications, T4_protein_component):
+def benzene_complex_system(charged_benzene, T4_protein_component):
     return openfe.ChemicalSystem(
-        {'ligand': benzene_modifications['benzene'],
+        {'ligand': charged_benzene,
          'solvent': openfe.SolventComponent(
              positive_ion='Na', negative_ion='Cl',
              ion_concentration=0.15 * unit.molar),
          'protein': T4_protein_component,}
     )
 
 
+@pytest.fixture(scope='session')
+def charged_toluene(benzene_modifications):
+    offmol = benzene_modifications['toluene'].to_openff()
+    offmol.assign_partial_charges(partial_charge_method='gasteiger')
+    return openfe.SmallMoleculeComponent.from_openff(offmol)
+
+
 @pytest.fixture
-def toluene_vacuum_system(benzene_modifications):
+def toluene_vacuum_system(charged_toluene):
     return openfe.ChemicalSystem(
-        {'ligand': benzene_modifications['toluene']},
+        {'ligand': charged_toluene},
     )
 
 
 @pytest.fixture(scope='session')
-def toluene_system(benzene_modifications):
+def toluene_system(charged_toluene):
     return openfe.ChemicalSystem(
-        {'ligand': benzene_modifications['toluene'],
+        {'ligand': charged_toluene,
          'solvent': openfe.SolventComponent(
              positive_ion='Na', negative_ion='Cl',
              ion_concentration=0.15 * unit.molar),
@@ -58,9 +71,9 @@ def toluene_system(benzene_modifications):
 
 
 @pytest.fixture
-def toluene_complex_system(benzene_modifications, T4_protein_component):
+def toluene_complex_system(charged_toluene, T4_protein_component):
     return openfe.ChemicalSystem(
-        {'ligand': benzene_modifications['toluene'],
+        {'ligand': charged_toluene,
          'solvent': openfe.SolventComponent(
              positive_ion='Na', negative_ion='Cl',
              ion_concentration=0.15 * unit.molar),
@@ -69,13 +82,10 @@ def toluene_complex_system(benzene_modifications, T4_protein_component):
 
 
 @pytest.fixture(scope='session')
-def benzene_to_toluene_mapping(benzene_modifications):
+def benzene_to_toluene_mapping(charged_benzene, charged_toluene):
     mapper = openfe.setup.LomapAtomMapper(element_change=False)
 
-    molA = benzene_modifications['benzene']
-    molB = benzene_modifications['toluene']
-
-    return next(mapper.suggest_mappings(molA, molB))
+    return next(mapper.suggest_mappings(charged_benzene, charged_toluene))
 
 
 @pytest.fixture

openfe/tests/protocols/test_openmm_equil_rfe_protocols.py

@@ -995,19 +995,16 @@ def test_missing_ligand(benzene_system, benzene_to_toluene_mapping):
         )
 
 
-def test_vaccuum_PME_error(benzene_vacuum_system, benzene_modifications,
-                           benzene_to_toluene_mapping):
-    # state B doesn't have a solvent component (i.e. its vacuum)
-    stateB = openfe.ChemicalSystem({'ligand': benzene_modifications['toluene']})
-
+def test_vacuum_PME_error(benzene_vacuum_system, toluene_vacuum_system,
+                          benzene_to_toluene_mapping):
     p = openmm_rfe.RelativeHybridTopologyProtocol(
         settings=openmm_rfe.RelativeHybridTopologyProtocol.default_settings(),
     )
     errmsg = "PME cannot be used for vacuum transform"
     with pytest.raises(ValueError, match=errmsg):
         _ = p.create(
             stateA=benzene_vacuum_system,
-            stateB=stateB,
+            stateB=toluene_vacuum_system,
             mapping=benzene_to_toluene_mapping,
         )
 

openfe/tests/protocols/test_openmmutils.py

@@ -227,8 +227,9 @@ def get_settings():
 
 class TestFEAnalysis:
 
-    # Note: class scope _will_ cause this to segfault - the reporter has to close
-    @pytest.fixture(scope='function')
+    # Note: scope on this can sometimes cause segfault, may need to revert to
+    # function scope if it happens.
+    @pytest.fixture(scope='class')
     def reporter(self):
         with resources.files('openfe.tests.data.openmm_rfe') as d:
             ncfile = str(d / 'vacuum_nocoord.nc')
@@ -244,7 +245,7 @@ def reporter(self):
         finally:
             r.close()
 
-    @pytest.fixture()
+    @pytest.fixture(scope='class')
     def analyzer(self, reporter):
         return multistate_analysis.MultistateEquilFEAnalysis(
             reporter, sampling_method='repex',