Fix tests, naming scheme.

Since the sbml ids can have two forms, the index might be off.  Also, fix the name of the test file.

biosimulators_masspy/core.py

@@ -314,7 +314,11 @@ def preprocess_sed_task(task, variables, config=None):
     invalid_changes = []
     for target, sbml_id in model_change_target_sbml_id_map.items():
         if sbml_id in met_ids:
-            model_change_target_mass_map[target] = (mass_model.metabolites[met_ids.index(sbml_id)], 'ic')
+            try:
+                model_change_target_mass_map[target] = (mass_model.metabolites[met_ids.index(sbml_id)], 'ic')
+            except:
+                #If the id has a "M_" in front of it:
+                model_change_target_mass_map[target] = (mass_model.metabolites[met_ids.index(sbml_id) - len(mass_model.metabolites)], 'ic')
 
         elif sbml_id in sbml_id_mass_parameter_map:
             model_change_target_mass_map[target] = sbml_id_mass_parameter_map[sbml_id]

tests/test_core_main.py

@@ -648,10 +648,11 @@ def test_exec_sedml_docs_in_combine_archive_with_docker_image(self):
 
     def test_exec_sedml_docs_in_combine_archive(self):
             # with reports
-            archive_filename = 'fixtures/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex'
+            archive_filename = 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex'
+            archive_filename = os.path.join(os.path.dirname(__file__), 'fixtures', archive_filename)
 
             dirname = os.path.join(self.dirname, 'reports')
-            _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, dirname)
+            _, log = core.exec_sedml_docs_in_combine_archive(str(archive_filename), dirname)
             if log.exception:
                 raise log.exception