Allow export of parameters.

MassPy seems to have a love-hate relationship with compartments, so those can't be exported, but parameters can.  No idea what actually triggers an element to be stuck in the 'boundary_conditions' list, since putting in a boundary species just puts it on the normal species concentrations list.  But if they put something there at some point, we'll be ready?  I guess?  At any rate, the new test checks for exporting a parameter and a boundary species.

biosimulators_masspy/_version.py

@@ -1 +1 @@
-__version__ = '0.1.1'
+__version__ = '0.1.2'

biosimulators_masspy/core.py

@@ -210,6 +210,11 @@ def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None
                 variable_results[variable.id] = rxn_fluxes[sbml_id][-(sim.number_of_points + 1):]
             elif sbml_id[2:] in rxn_fluxes:
                 variable_results[variable.id] = rxn_fluxes[sbml_id[2:]][-(sim.number_of_points + 1):]
+            elif sbml_id in mass_model.custom_parameters:
+                variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), mass_model.custom_parameters[sbml_id])
+            elif sbml_id in mass_model.boundary_conditions:
+                variable_results[variable.id] = numpy.full((sim.number_of_points + 1,), mass_model.boundary_conditions[sbml_id])
+
             else:
                 raise_errors_warnings(validation.validate_task(task),
                                       error_summary='Unable to find variable `{}` in output.'.format(sbml_id))
@@ -311,6 +316,9 @@ def preprocess_sed_task(task, variables, config=None):
     for sbml_id in mass_model.boundary_conditions.keys():
         sbml_id_mass_parameter_map[sbml_id] = (mass_model.boundary_conditions, sbml_id)
 
+    for sbml_id in mass_model.compartments.keys():
+        sbml_id_mass_parameter_map[sbml_id] = (mass_model.compartments, sbml_id)
+
     invalid_changes = []
     for target, sbml_id in model_change_target_sbml_id_map.items():
         if sbml_id in met_ids:
@@ -349,7 +357,7 @@ def preprocess_sed_task(task, variables, config=None):
         else:
             sbml_id = variable_target_sbml_id_map.get(variable.target, None)
 
-            if not sbml_id or not (sbml_id in met_ids or sbml_id in rxn_ids):
+            if not sbml_id or not (sbml_id in met_ids or sbml_id in rxn_ids or sbml_id in sbml_id_mass_parameter_map):
                 invalid_targets.append(variable.target)
 
     if invalid_symbols:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biosimulators-masspy"
-version = "0.1.1"
+version = "0.1.2"
 description = "BioSimulators-compliant command-line interface to the MassPY simulation program <https://masspy.readthedocs.io/>."
 authors = ["Center for Reproducible Biomedical Modeling <[email protected]>"]
 license = "MIT"

tests/test_core_main.py

@@ -656,5 +656,15 @@ def test_exec_sedml_docs_in_combine_archive(self):
             if log.exception:
                 raise log.exception
 
+    def test_exec_sedml_docs_in_combine_archive_b(self):
+            # with reports
+            archive_filename = 'Cilbarto_with_param_and_boundary.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(str(archive_filename), dirname)
+            if log.exception:
+                raise log.exception
+
 if __name__ == "__main__":
     unittest.main()