added runtime arg to test functions

vivarium-collective · Jan 15, 2024 · 2bd57a0 · 2bd57a0
1 parent 158d08a
commit 2bd57a0
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Showing 3 changed files with 13 additions and 12 deletions.
diff --git a/biosimulator_processes/tests/test_copasi.py b/biosimulator_processes/tests/test_copasi.py
@@ -1,14 +1,14 @@
 from process_bigraph import Composite, pf
 
 
-def test_process():
+def test_process(model_filepath: str = 'biosimulator_processes/tests/model_files/Caravagna2010.xml'):
     # 1. Define the sim state schema:
     initial_sim_state = {
         'copasi': {
             '_type': 'process',
             'address': 'local:copasi',
             'config': {
-                'model_file': 'biosimulator_processes/tests/model_files/Caravagna2010.xml'
+                'model_file': model_filepath
             },
             'inputs': {
                 'floating_species': ['floating_species_store'],

diff --git a/biosimulator_processes/tests/test_smoldyn.py b/biosimulator_processes/tests/test_smoldyn.py
@@ -1,8 +1,7 @@
-from process_bigraph import Composite
-# from biosimulator_processes.smoldyn_process import SmoldynProcess
+from process_bigraph import Composite, pp, pf
 
 
-def test_process():
+def test_process(model_filepath: str = 'biosimulator_processes/tests/model_files/minE_model.txt'):
     """Test the smoldyn process using the crowding model."""
 
     # this is the instance for the composite process to run
@@ -11,7 +10,7 @@ def test_process():
             '_type': 'process',
             'address': 'local:smoldyn',
             'config': {
-                'model_filepath': 'biosimulator_processes/tests/model_files/minE_model.txt',
+                'model_filepath': model_filepath,
                 'animate': False,
             },
             'inputs': {
@@ -45,17 +44,19 @@ def test_process():
         }
     }
 
+    total_time = 1
+
     # make the composite
     workflow = Composite({
         'state': instance
     })
 
     # run
-    workflow.run(1)
+    workflow.run(total_time)
 
     # gather results
     results = workflow.gather_results()
-    print(f'RESULTS: {results}')
+    pp(f'RESULTS: {pf(results)}')
 
 
 # def manually_test_process():
@@ -68,10 +69,10 @@ def test_process():
 #
 #     stop = 1
 #
-#     result = test_smoldyn_manually(stop, process, historical=True)
+#     result = run_smoldyn_manually(stop, process, historical=True)
 
 
-# def test_smoldyn_manually(stop_time: int, process: SmoldynProcess, historical: bool = False):
+# def run_smoldyn_manually(stop_time: int, process: SmoldynProcess, historical: bool = False):
 #     current_state = process.initial_state()
 #     runs = []
 #     for t, _ in enumerate(list(range(stop_time)), 1):

diff --git a/biosimulator_processes/tests/test_tellurium.py b/biosimulator_processes/tests/test_tellurium.py
@@ -1,14 +1,14 @@
 from process_bigraph import Composite, pf
 
 
-def test_process():
+def test_process(model_filepath: str = 'biosimulator_processes/tests/model_files/BIOMD0000000061_url.xml'):
     # this is the instance for the composite process to run...process instance keys may pertain to methods and not simulators directly
     instance = {
         'tellurium': {
             '_type': 'process',
             'address': 'local:tellurium',  # using a local toy process
             'config': {
-                'sbml_model_path': 'biosimulator_processes/tests/model_files/BIOMD0000000061_url.xml',
+                'sbml_model_path': model_filepath,
             },
             'inputs': {
                 'time': ['time_store'],