Fix for Issue #388 which broke executable reproducibility (#389)

* Fixed #388. Bug was due to a break rather than continue in Manifest
setup. Links for other mainfests weren't created if scaninputs=True.
* Modified existing test to trigger error. Test now passes.

payu/manifest.py

@@ -359,7 +359,7 @@ def setup(self):
             if self.have_manifest[mf]:
                 # Don't make links for inputs when scaninputs is True
                 if mf == 'input' and self.scaninputs:
-                    break
+                    continue
                 print('Making {} links'.format(mf))
                 self.manifests[mf].make_links()
             else:

test/test_manifest.py

@@ -154,14 +154,21 @@ def test_exe_reproduce():
 
     # Set reproduce exe to True
     config['manifest']['reproduce']['exe'] = True
+    # Also set scaninputs to True to catch bug #388
+    config['manifest']['scaninputs'] = True
     write_config(config)
     manifests = get_manifests(ctrldir/'manifests')
 
     # Run setup with unchanged exe but reproduce exe set to True.
     # Should run without error
     payu_setup(lab_path=str(labdir))
 
+    local_exe_path = list(manifests['exe.yaml'].keys())[0]
+
     assert(manifests == get_manifests(ctrldir/'manifests'))
+    assert((ctrldir / local_exe_path).exists())
+    assert(Path(manifests['exe.yaml'][local_exe_path]['fullpath']) ==
+           (ctrldir / local_exe_path).resolve())
 
     bindir = labdir / 'bin'
     exe = config['exe']
@@ -222,6 +229,8 @@ def test_input_reproduce():
     # Set reproduce input to True
     config['manifest']['reproduce']['exe'] = False
     config['manifest']['reproduce']['input'] = True
+    # Set back to false
+    config['manifest']['scaninputs'] = False
     config['exe'] = config_orig['exe']
     write_config(config)
     manifests = get_manifests(ctrldir/'manifests')
@@ -266,8 +275,8 @@ def test_input_reproduce():
     with pytest.raises(SystemExit) as pytest_wrapped_e:
         payu_setup(lab_path=str(labdir))
 
-        assert pytest_wrapped_e.type == SystemExit
-        assert pytest_wrapped_e.value.code == 1
+    assert pytest_wrapped_e.type == SystemExit
+    assert pytest_wrapped_e.value.code == 1
 
     # Change reproduce input back to False
     config['manifest']['reproduce']['input'] = False