update test suite 00001 table and draft for 01186 table

OpenSourceBrain · Nov 4, 2024 · cce679c · cce679c
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diff --git a/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/amici_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/bionetgen_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/bionetgen_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/boolnet_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/boolnet_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/cbmpy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/cbmpy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/cobrapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/cobrapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/copasi_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/copasi_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/gillespy2_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/gillespy2_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/ginsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/ginsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/libsbmlsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/libsbmlsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/masspy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/masspy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/pysces_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/pysces_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/rbapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/rbapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_local/tellurium_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_local/tellurium_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/amici_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/amici_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/bionetgen_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/bionetgen_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/boolnet_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/boolnet_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/cbmpy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/cbmpy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/cobrapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/cobrapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/copasi_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/copasi_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/gillespy2_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/gillespy2_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/ginsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/ginsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/libsbmlsim_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/masspy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/masspy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/pysces_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/pysces_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/rbapy_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/rbapy_plot_1.pdf
diff --git a/test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf b/test_suite/test_00001/tests/d1_plots_remote/tellurium_plot_1.pdf
diff --git a/test_suite/test_00001/tests/results_compatibility_biosimulators.md b/test_suite/test_00001/tests/results_compatibility_biosimulators.md
diff --git a/test_suite/test_00001/tests/results_local.json b/test_suite/test_00001/tests/results_local.json
diff --git a/test_suite/test_00001/tests/results_remote.json b/test_suite/test_00001/tests/results_remote.json
diff --git a/test_suite/test_01186/tests/results_compatibility_biosimulators.md b/test_suite/test_01186/tests/results_compatibility_biosimulators.md
diff --git a/test_suite/test_01186/tests/results_local.json b/test_suite/test_01186/tests/results_local.json
diff --git a/test_suite/test_01186/tests/results_remote.json b/test_suite/test_01186/tests/results_remote.json
diff --git a/test_suite/test_test_suite_compatibility_biosimulators.py b/test_suite/test_test_suite_compatibility_biosimulators.py
@@ -46,8 +46,9 @@ def parse_arguments():
 
     parser.add_argument(
         "--cases",
-        action="store",
-        type=list,
+        action="extend",
+        nargs="+",
+        type=str,
         default=[],
         help="Limit to the cases listed in the file. Empty list means no limit",
     )
@@ -106,7 +107,7 @@ def process_cases(args):
     print(f"Processing {len(subfolders)} subfolders in {args.suite_path}") 
     test_folder = 'tests'
 
-    for subfolder in subfolders:
+    for subfolder in args.cases:
         # create an equivalently named folder in the starting directory
         os.chdir(args.suite_path)
         print(f"Processing {subfolder}")
@@ -139,17 +140,18 @@ def process_cases(args):
         os.chdir(new_directory)
         print(f"Changed to {new_directory}")
 
-        engines_list = list(engines.keys()) 
+        engine_list = list(engines.keys()) 
 
-        utils.run_biosimulators_remotely_and_locally(os.path.basename(sedml_file_path), 
+        utils.run_biosimulators_remotely_and_locally(engine_list,
+                                 os.path.basename(sedml_file_path), 
                                  os.path.basename(sbml_file_path),
                                  os.path.join(test_folder,'d1_plots_remote'), 
                                  os.path.join(test_folder,'d1_plots_local'),
                                  test_folder=test_folder)
 
 
 if __name__ == "__main__":
-    args = parse_arguments()
+    args = parse_arguments()    
 
     process_cases(args)
 
diff --git a/utils/__init__.py b/utils/__init__.py
@@ -21,6 +21,7 @@
 from pyneuroml import biosimulations
 import pandas as pd
 from requests.exceptions import HTTPError 
+import json
 
 ENGINES = {
     'amici': {
@@ -1233,6 +1234,15 @@ def create_combined_results_table(results_remote,
 
     suffix_remote = ' (R)'
     suffix_local = ' (L)'
+
+    # save results_remote and results_local as json files with dicts
+    path_to_results_remote = os.path.join(test_folder, 'results_remote.json')
+    path_to_results_local = os.path.join(test_folder, 'results_local.json')
+
+    with open(path_to_results_remote, 'w') as f:
+        json.dump(results_remote, f, indent=4)
+    with open(path_to_results_local, 'w') as f:
+        json.dump(results_local, f, indent=4)
 
     # Create results tables for remote and local results
     results_table_remote = create_results_table(results_remote, sbml_file_name, sedml_file_name, d1_plots_remote_dir)